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 Users Guide

Chem & Bio Office Desktop 2006

for Windows

Chem & Bio Office is an integrated suite including

Chem & Bio Draw for chemical structure drawing,
Chem & Bio 3D for molecular modeling and analysis,
BioAssay for biological data retrieval and visualization,
Inventory for managing and searching reagents,
E-Notebook for electronic journal and information,
ChemFinder for searching and information integration, and
ChemInfo for chemical and reference databases.

Chem & Bio Office

Chem & Bio 3D, Finder and E-Notebook

License Information

ChemOffice, BioOffice ChemDraw, Chem3D, ChemINDEX, ChemFinder, and ChemInfo programs, all resources
in the ChemOffice, ChemDraw, Chem3D, ChemFinder, and ChemInfo application files, and this manual are
Copyright 1986-2006 by CambridgeSoft Corporation (CS) with all rights reserved worldwide. MOPAC 2002 is
Copyright 1993-2006 by Fujitsu Limited with all rights reserved. Information in this document is subject to
change without notice and does not represent a commitment on the part of CS. Both these materials and the right
to use them are owned exclusively by CS. Use of these materials is licensed by CS under the terms of a software license
agreement; they may be used only as provided for in said agreement.

ChemOffice, ChemDraw, Chem3D, CS MOPAC, ChemFinder, Inventory, E-Notebook, BioAssay, and ChemInfo
are not supplied with copy protection. Do not duplicate any of the copyrighted materials except for your personal
backups without written permission from CS. To do so would be in violation of federal and international law, and
may result in criminal as well as civil penalties. You may use ChemOffice, ChemDraw, Chem3D, CS MOPAC,
ChemFinder, Inventory, E-Notebook, BioAssay, and ChemInfo on any computer owned by you; however, extra
copies may not be made for that purpose. Consult the CS License Agreement for Software and Database Products for
further details.

Trademarks

ChemOffice, BioOffice, ChemDraw, Chem3D, ChemINDEX, ChemFinder, ChemInfo and ChemACX are
registered trademarks of CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.).

The Merck Index is a registered trademark of Merck & Co., Inc. 2006 All rights reserved.

MOPAC 2002 is a trademark of Fujitsu Limited.

Microsoft Windows, Windows 2000, Windows XP, and Microsoft Word are registered trademarks of Microsoft Corp.

Apple Events, Macintosh, Laserwriter, Imagewriter, QuickDraw and AppleScript are registered trademarks of Apple
Computer, Inc. Geneva, Monaco, and TrueType are trademarks of Apple Computer, Inc.

The ChemSelect Reaction Database is copyrighted by InfoChem GmbH 1997.

AspTear is copyrighted by Softwing.

InChI is a trademark of the International Union of Pure and Applied Chemistry. InChI Material in ChemDraw
is IUPAC 2005.

SCHRDINGER Jaguar

GAMESS is copyrighted by Ames Laboratory

Copyright 1986-2006 CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.) All Rights Reserved.
Printed in the United States of America.

All other trademarks are the property of their respective holders.

CambridgeSoft End-User License Agreement for Software Products

Important: This CambridgeSoft Software License Agreement (Agreement) is a legal agreement between you, the
end user (either an individual or an entity), and CambridgeSoft Corporation (CS) regarding the use of CS Software
Products, which may include computer software, the associated media, any printed materials, and any online or
electronic documentation. By installing, copying, or otherwise using any CS Software Product, you signify that you
have read the CS End User License Agreement and agree to be bound by its terms. If you do not agree to the
Agreements terms, promptly return the package and all its contents to the place of purchase for a full refund.

CambridgeSoft Software License

1. Grant of License. CambridgeSoft (CS) Software Products are licensed, not sold. CS grants and you hereby accept
a nonexclusive license to use one copy of the enclosed Software Product (Software) in accordance with the terms of
this Agreement. This licensed copy of the Software may only be used on a single computer, except as provided below.
You may physically transfer the Software from one computer to another for your own use, provided the Software is
in use (or installed) on only one computer at a time. If the Software is permanently installed on your computer (other
than a network server), you may also use the Software on a portable or home computer, provided that you use the
software on only one computer at a time. You may not (a) electronically transfer the Software from one computer to
another, (b) distribute copies of the Software to others, or (c) modify or translate the Software without the prior writ-
ten consent of CS, (d) place the software on a server so that it is accessible via a public network such as the Internet,
(e) sublicense, rent, lease or lend any portion of the Software or Documentation, (f ) modify or adapt the Software or
merge it into another program, (g) modify or circumvent the software activation, or (h) reverse engineer the software
activation so as to circumvent it. The Software may be placed on a file or disk server connected to a network, provid-
ed that a license has been purchased for every computer with access to that server. You may make only those copies
of the Software which are necessary to install and use it as permitted by this agreement, or are for purposes of back-
up and archival records; all copies shall bear CSs copyright and proprietary notices. You may not make copies of any
accompanying written materials.

With a fixed license, the software cannot be installed on more than the number of computers equivalent to the num-
ber of fixed licenses purchased. For example, a 10-user fixed license means the software can be installed on no more
than 10 different computers. A fixed license cannot be installed on a server. With a concurrent license, the software
can be installed on any number of computers at the organization, but the number of computers using the software at
any one time cannot exceed the number of concurrent licenses purchased. For example, a 10-user concurrent license
can be installed on 20 computers, but no more than 10 users can be using it at any one time. If the number of users
of the software could potentially exceed the number of licensed copies, then Licensee must have a reasonable mech-
anism or process in place to assure that the number of persons using the software does not exceed the number of
copies. CambridgeSoft reserves the right to conduct periodic audits no more than once per year to review the imple-
mentation of this agreement at the Licensees site. At CambridgeSofts request, Licensee will provide a knowledgeable
employee to assist in said audit

2. Ownership. The Software is and at all times shall remain the sole property of CS. This ownership is protected by
the copyright laws of the United States and by international treaty provisions. Upon expiration or termination of this
agreement, you shall promptly return all copies of the Software and accompanying written materials to CS. You may
not modify, decompile, reverse engineer, or disassemble the Software.

3. Assignment Restrictions. You may not rent, lease, or otherwise sublet the Software or any part thereof. You may
transfer on a permanent basis the rights granted under this license provided you transfer this Agreement and all copies
of the Software, including prior versions, and all accompanying materials. The recipient must agree to the terms of
this Agreement in full and register this transfer in writing with CS.
4. Use of Included Data. All title and copyrights in and to the Software product, including but not limited to any
images, photographs, animations, video, audio, music, text, applets, Java applets, and data files and databases (the
Included Data), are owned by CS or its suppliers.

You may not copy, distribute or otherwise make the Included Data publicly available.

Licensed users of ChemOffice Enterprise and Workgroup and the accompanying Plugin software products may
access, search, and view the Included Data and may transmit the results of any search of the Included Data to other
users of the licensed ChemOffice Enterprise and Workgroup software products within your organization only, provided
that such transmission is via an internal corporate (or university) network and is not accessible by the public.

You may not install the Included Data on non-licensed computers nor distribute or otherwise make the Included
Data publicly available.

You may use the Software to organize personal data, and you may transmit such personal data over the Internet pro-
vided that the transmission does not contain any Included Data.

All rights not specifically granted under this Agreement are reserved by CS.

5. Separation of Components. The Software is licensed as a single product. Its component parts may not be sepa-
rated for use on more than one computer, except in the case of ChemOffice Enterprise. ChemOffice Enterprise
includes licenses for ChemDraw ActiveX and licenses for Chem3D ActiveX. The ActiveX software products may be
installed on computers other than that one on which ChemOffice Enterprise is installed. However, each copy of the
ActiveX is individually subject to the provisions of Paragraphs 1 through 4 of this Agreement.

6. Educational Use Only of Student Licenses. If you are a student enrolled at an educational institution, the CS
License Agreement grants to you personally a license to use one copy of the enclosed Software in accordance with the
terms of this Agreement. In this case the CS License Agreement does not permit commercial use of the Software nor
does it permit you to allow any other person to use the Software.

7. Termination. You may terminate the license at any time by destroying all copies of the Software and documenta-
tion in your possession. Without prejudice to any other rights, CS may terminate this Agreement if you fail to com-
ply with its terms and conditions. In such event, you must destroy all copies of the Software Product and all of its
component parts.

8. Confidentiality. The Software contains trade secrets and proprietary know-how that belong to CS and are
being made available to you in strict confidence. ANY USE OR DISCLOSURE OF THE SOFTWARE, OR USE OF ITS
ALGORITHMS, PROTOCOLS OR INTERFACES, OTHER THAN IN STRICT ACCORDANCE WITH THIS LICENSE
AGREEMENT, MAY BE ACTIONABLE AS A VIOLATION OF OUR TRADE SECRET RIGHTS.

CS Limited Warranty

Limited Warranty. CSs sole warranty with respect to the Software is that it shall be free of errors in program logic
or documentation, attributable to CS, which prevent the performance of the principal computing functions of the
Software. CS warrants this for a period of thirty (30) days from the date of receipt.
CSs Liability. In no event shall CS be liable for any indirect, special, or consequential damages, such as, but not lim-
ited to, loss of anticipated profits or other economic loss in connection with or arising out of the use of the software
by you or the services provided for in this agreement, even if CS has been advised of the possibility of such damages.
CSs entire liability and your exclusive remedy shall be, at CSs discretion, either (A) return of any license fee, or (B)
correction or replacement of software that does not meet the terms of this limited warranty and that is returned to
CS with a copy of your purchase receipt.
NO OTHER WARRANTIES. CS DISCLAIMS OTHER IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, AND IMPLIED WAR-
RANTIES ARISING BY USAGE OF TRADE, COURSE OF DEALING, OR COURSE OF PERFORMANCE. NOTWITH-
STANDING THE ABOVE, WHERE APPLICABLE, IF YOU QUALIFY AS A CONSUMER UNDER THE MAGNUSON-
MOSS WARRANTY ACT, THEN YOU MAY BE ENTITLED TO ANY IMPLIED WARRANTIES ALLOWED BY LAW FOR
THE PERIOD OF THE EXPRESS WARRANTY AS SET FORTH ABOVE. SOME STATES DO NOT ALLOW LIMITATIONS
ON IMPLIED WARRANTIES, SO THE ABOVE LIMITATION MIGHT NOT APPLY TO YOU. THIS WARRANTY GIVES
YOU SPECIFIC LEGAL RIGHTS, AND YOU MAY ALSO HAVE OTHER RIGHTS WHICH VARY FROM STATE TO STATE.

No Waiver. The failure of either party to assert a right hereunder or to insist upon compliance with any term or con-
dition of this Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform
any such term or condition by the other party.

Governing Law. This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts.

Export. You agree that the Software will not be shipped, transferred, or exported into any country or used in any man-
ner prohibited by the United States Export Administration Act or any other export laws, restrictions, or regulations.

End-User License Agreement for CambridgeSoft Database Products

Important: This CambridgeSoft End-User License Agreement is a legal agreement between you (either an individual
or a single entity) and CambridgeSoft Corporation for the CambridgeSoft supplied database product(s) and may
include associated media, printed materials, and online or electronic documentation. By using the database prod-
uct(s) you agree that you have read, understood and will be bound by this license agreement.

Database Product License

1. Copyright Notice. The materials contained in CambridgeSoft Database Products, including but not limited to,
ChemACX, ChemIndex, and The Merck Index, are protected by copyright laws and international copyright treaties,
as well as other intellectual property laws and treaties. Copyright in the materials contained on the CD and internet
subscription products, including, but not limited to, the textual material, chemical structures representations,
artwork, photographs, computer software, audio and visual elements, is owned or controlled separately by
CambridgeSoft Corporation (CS).

CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has no editorial
control over such information. Database Suppliers (Supplier) individually own all right, title, and interest, includ-
ing copyright, in their databaseand retain all such rights in providing information to Customers.

The materials contained in The Merck Index are protected by copyright laws and international copyright treaties, as
well as other intellectual property laws and treaties. Copyright in the materials contained on the CD and internet sub-
scription products, including, but not limited to, the textual material, chemical structures representations, artwork,
photographs, computer software, audio and visual elements, is owned or controlled separately by the Merck & Co.,
Inc., (Merck) and CambridgeSoft Corporation (CS).

2. Limitations on Use. Except as expressly provided by copyright law, copying, redistribution, or publication,
whether for commercial or non-commercial purposes, must be with the express permission of CS and/or Merck. In
any copying, redistribution, or publication of copyrighted material, any changes to or deletion of author attribution
or copyright notice, or any other proprietary notice of CS, Merck, or other Database producer are prohibited.
3. Grant of License, CD/DVD Databases. CambridgeSoft Software Products are licensed, not sold. CambridgeSoft
grants and you hereby accept a nonexclusive license to use one copy of the enclosed Software Product (Software) in
accordance with the terms of this Agreement. This licensed copy of the Software may only be used on a single com-
puter, except as provided below. You may physically transfer the Software from one computer to another for your own
use, provided the Software is in use (or installed) on only one computer at a time. If the Software is permanently
installed on your computer (other than a network server), you may also use the Software on a portable or home com-
puter, provided that you use the software on only one computer at a time. You may not (a) electronically transfer the
Software from one computer to another, (b) distribute copies of the Software to others, or (c) modify or translate the
Software without the prior written consent of CambridgeSoft, (d) place the software on a server so that it is accessi-
ble via a public network such as the Internet, (e) sublicense, rent, lease or lend any portion of the Software or
Documentation, or (f ) modify or adapt the Software or merge it into another program. The Software may be placed
on a file or disk server connected to a network, provided that a license has been purchased for every computer with
access to that server. You may make only those copies of the Software which are necessary to install and use it as per-
mitted by this agreement, or are for purposes of backup and archival records; all copies shall bear CambridgeSofts
copyright and proprietary notices. You may not make copies of any accompanying written materials.

4. Assignment Restrictions for CD/DVD databases. You may not rent, lease, or otherwise sublet the Software or
any part thereof. You may transfer on a permanent basis the rights granted under this license provided you transfer
this Agreement and all copies of the Software, including prior versions, and all accompanying materials. The recipi-
ent must agree to the terms of this Agreement in full and register this transfer in writing with CambridgeSoft.

5. Revocation of Subscription Access. Any use which is commercial and/or non-personal is strictly prohibited, and
may subject the Subscriber making such uses to revocation of access to this Paid Subscription Service, as well as any
other applicable civil or criminal penalties. Similarly, sharing a Subscriber password with a non-Subscriber or other-
wise making this Paid Subscription Service available to third parties other than the Authorized User as defined above
is strictly prohibited, and may subject the Subscriber participating in such activities to revocation of access to the Paid
Subscription Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties under
copyright or other laws. In the case of an authorized site license, a Subscriber shall cause any employee, agent or other
third party which the Subscriber allows to use the Paid Subscription Service materials to abide by all of the terms and
conditions of this Agreement. In all other cases, only the Subscriber is permitted to access the Paid Subscription
Service materials. Should CambridgeSoft become aware of any use that might cause revocation of the license, they
shall notify the Subscriber. The Subscriber shall have 90 days from date of notice to correct such violation before any
action will be taken.

6. Trademark Notice. THE MERCK INDEX is a trademark of Merck & Company Incorporated, Whitehouse
Station, New Jersey, USA and is registered in the United States Patent and Trademark Office. CambridgeSoft and
ChemACX are trademarks of CambridgeSoft Corporation, Cambridge,Massachusetts, USA and are registered in the
United States Patent and Trademark Office, the European Union (CTM) and Japan.

Any use of the marks in connection with the sale, offering for sale, distribution or advertising of any goods and serv-
ices, including any other website, or in connection with labels, signs, prints, packages, wrappers, receptacles or adver-
tisements used for the sale, offering for sale, distribution or advertising of any goods and services, including any other
website, which is likely to cause confusion, to cause mistake or to deceive, is strictly prohibited.

7. Modification of Databases, Websites, or Subscription Services. CS reserves the right to change, modify, sus-
pend or discontinue any or all parts of any Paid Subscription Services and databases at any time.
8. Representations and Warranties. The User shall indemnify, defend and hold CS, Merck, and/or other Supplier
harmless from any damages, expenses and costs (including reasonable attorneys fees) arising out of any breach or
alleged breach of these Terms and Conditions, representations and/or warranties herein, by the User or any third party
to whom User shares her/his password or otherwise makes available this Subscription Service. The User shall cooper-
ate in the defense of any claim brought against CambridgeSoft, Merck, and/or other Database Suppliers.

In no event shall CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential damages, such
as, but not limited to, loss of anticipated profits or other economic loss in connection with or arising out of the use
of the software by you or the services provided for in this agreement, even if CS, Merck, and/or other Supplier has
been advised of the possibility of such damages. CS and/or Mercks entire liability and your exclusive remedy shall be,
at CSs discretion a return of any pro-rata portion of the subscription fee.

The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition of this
Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform any such term
or condition by the other party.

This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts, United States of
America.
 : IS IT OK TO COPY MY COLLEAGUES
Q SOFTWARE?
NO, its not okay to copy your colleagues
software. Software is protected by federal copyright law,
which says that you can't make such additional copies
without the permission of the copyright holder. By
protecting the investment of computer software
companies in software development, the copyright law
serves the cause of promoting broad public availability of
new, creative, and innovative products. These companies
devote large portions of their earnings to the creation of
new software products and they deserve a fair return on
their investment. The creative teams who develop the
softwareprogrammers, writers, graphic artists and
othersalso deserve fair compensation for their efforts.
Without the protection given by our copyright laws, they
would be unable to produce the valuable programs that
have become so important to our daily lives: educational
software that teaches us much needed skills; business
software that allows us to save time, effort and money;
and entertainment and personal productivity software
that enhances leisure time.
Q: That makes sense, but what do I get out of
purchasing my own software?
A: When you purchase authorized copies of software
programs, you receive user guides and tutorials, quick
reference cards, the opportunity to purchase
upgrades, and technical support from the software
publishers. For most software programs, you can read
about user benefits in the registration brochure or
upgrade flyer in the product box.
Q: What exactly does the law say about copying
software?
A: The law says that anyone who purchases a copy of
software has the right to load that copy onto a single
computer and to make another copy for archival
purposes only or, in limited circumstances, for
purposes only of maintenance or repair. It is illegal
to use that software on more than one computer or to
make or distribute copies of that software for any
other purpose unless specific permission has been
obtained from the copyright owner. If you pirate
software, you may face not only a civil suit for
damages and other relief, but criminal liability as well,
including fines and jail terms of up to one year
Q: So I'm never allowed to copy software for any other
reason?
A: Thats correct. Other than copying the software you
purchase onto a single computer and making another
copy for archival purposes only or purposes only of
maintenance or repair, the copyright law prohibits
you from making additional copies of the software for
any other reason unless you obtain the permission of
the software company.
Q: At my company, we pass disks around all the time.
We all assume that this must be okay since it was
the company that purchased the software in the
first place.
A: Many employees dont realize that corporations are
bound by the copyright laws, just like everyone else.
Such conduct exposes the company (and possibly the
persons involved) to liability for copyright
infringement. Consequently, more and more
corporations concerned about their liability have
written policies against such softlifting. Employees
may face disciplinary action if they make extra copies
of the companys software for use at home or on
additional computers within the office. A good rule to
remember is that there must be one authorized copy
of a software product for every computer upon which
it is run
Q: Can I take a piece of software owned by my
company and install it on my personal computer at
home if instructed by my supervisor?
A: A good rule of thumb to follow is one software
package per computer, unless the terms of the license
agreement allow for multiple use of the program. But
some software publishers licenses allow for remote
or home use of their software. If you travel or
telecommute, you may be permitted to copy your
software onto a second machine for use when you are
not at your office computer. Check the license care-
fully to see if you are allowed to do this.
Q: What should I do if become aware of a company
that is not compliant with the copyright law or its
software licenses?
A: Cases of retail, corporate and Internet piracy or non-
compliance with software licenses can be reported on
the Internet at http://www.siia.net/piracy/report.asp
or by calling the Anti-Piracy Hotline:
(800) 388-7478.
Q: Do the same rules apply to bulletin boards and user SIIA also offers a number of other materials designed to
groups? I always thought that the reason they got help you comply with the Federal Copyright Law. These
together was to share software. materials include:

A: Yes. Bulletin boards and user groups are bound by the

copyright law just as individuals and corporations.
However, to the extent they offer shareware or public
domain software, this is a perfectly acceptable
practice. Similarly, some software companies offer
bulletin boards and user groups special demonstration
versions of their products, which in some instances
may be copied. In any event, it is the responsibility of
the bulletin board operator or user group to respect
copyright law and to ensure that it is not used as a
vehicle for unauthorized copying or distribution.
Q: I'll bet most of the people who copy software don't
even know that they're breaking the law.
A: Because the software industry is relatively new, and
because copying software is so easy, many people are
either unaware of the laws governing software use or
choose to ignore them. It is the responsibility of each
and every software user to understand and adhere to
copyright law. Ignorance of the law is no excuse. If
you are part of an organization, see what you an do to
initiate a policy statement that everyone respects.
Also, suggest that your management consider
conducting a software audit. Finally, as an individual,
help spread the word that users should be software
legal.
Q: What are the penalties for copyright infringement?
"It's Just Not Worth the Risk" video.
This 12minute video, available $10, has helped over
20,000 organizations dramatize to their employees the
implications and consequences of software piracy.
Dont Copy that Floppy video
This 9 minute rap video, available for $10, is designed
to educate students on the ethical use of software.
Other education materials including, Software Use
and the Law, a brochure detailing the copyright law
and how software should be used by educational
institutions, corporations and individuals; and several
posters to help emphasize the message that unauthorized
copying of software is illegal.
To order any of these materials, please send your request to:
SIIA Anti-Piracy Materials
Software & Information Industry Association
1090 Vermont Ave, Sixth Floor,
Washington, D.C. 20005
(202) 289-7442
We urge you to make as many copies as you would like
in order to help us spread the word that unauthorized
copying of software is illegal.

A: The Copyright Act allows a copyright owner to

recover monetary damages measured either by: (1) its
actual damages plus any additional profits of the
infringer attributable to the infringement, or (2)
statutory damages, of up to $150,000 for each copy-
righted work infringed. The copyright owner also has
the right to permanently enjoin an infringer from
engaging in further infringing activities and may be
awarded costs and attorneys fees. The law also
permits destruction or other reasonable disposition of
all infringing copies and devices by which infringing
copies have been made or used in violation of the
copyright owners exclusive rights. In cases of willful
infringement, criminal penalties may also be assessed
against the infringer.
 A Guide to CambridgeSoft Manuals
Ch Ch
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Includes ls da
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o
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Chem & Bio Draw

Chem & Bio 3D
Chem & Bio Finder
Software

BioAssay Desktop
BioViz Desktop
Inventory Desktop
E-Notebook Desktop

ChemDraw/Excel
Desktop Applications

Struct <=> Name

CombiChem/Excel
ChemNMR
ChemFinder/Office
MOPAC, GAMESS, MM2
CS Gaussian, Jaguar Interface

Chem & Bio Office Enterprise

E-Notebook Enterprise, Workgroup
Enterprise Solutions

Document Enterprise
BioAssay Enterprise, Workgroup
BioSAR Enterprise
Inventory Enterprise, Workgroup
Registration Enterprise
Formulations & Mixtures
Oracle Cartridge

The Merck Index

ChemACX, ChemMSDX
Sigma Aldrich MSDS
Databases

ChemINDEX, NCI & AIDS, ChemRXN

Ashgate Drugs, Traditional Chinese Medicines
ChemSynth, ChemReact68
Medicinal Chemistry

Structure Drawing Tips

Tips

Searching Tips
Importing SD Files
Contents
Chem & BioOffice Introduction . . . . . 23
About Chem3D . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
About ChemFinder . . . . . . . . . . . . . . . . . . . . . . . . 23
ChemFinder/Office . . . . . . . . . . . . . . . . . . . . 23
About CombiChem/Excel . . . . . . . . . . . . . . . . . . 23
About E-Notebook . . . . . . . . . . . . . . . . . . . . . . . . 24
About This Users Guide . . . . . . . . . . . . . . . . . . . 24
Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Additional Information . . . . . . . . . . . . . . . . . . . . . 24
Quick Reference Card . . . . . . . . . . . . . . . . . . 25
Help System . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
CambridgeSoft Web Pages . . . . . . . . . . . . . . 25
Installation and System Requirements . . . . 25
Microsoft Windows Requirements .25
Site License Network Installation
Instructions . . . . . . . . . . . . . . . . . . . . . . . . . 26
Section I: Chem3D Introduction . . . . . 27
About Chem3D . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
COEA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
About CS MOPAC . . . . . . . . . . . . . . . . . . . . . 27
About Gaussian . . . . . . . . . . . . . . . . . . . . . . . . 27
About Jaguar . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Whats New in Chem3D 10? . . . . . . . . . . . . . . . . 28
For Users of Chem3D 9 . . . . . . . . . . . . . . . . . . . . 28
For Users of Chem3D Versions 6 to 8 . . . 31
Chapter 1: Chem3D Basics . . . . . . . . . 33
The Graphical User Interface . . . . . . . . . . . . . . . 33
Model Window . . . . . . . . . . . . . . . . . . . . . . . . 33
Rotation Bars . . . . . . . . . . . . . . . . . . . . . . . . 34
Preferences Dialog Box . . . . . . . . . . . . . . . . . 34
Menus and Toolbars . . . . . . . . . . . . . . . . . . . . 35
The File Menu . . . . . . . . . . . . . . . . . . . . . . . 35
The Edit Menu . . . . . . . . . . . . . . . . . . . . . . 35
The View Menu/Model Display
Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
The Structure Menu . . . . . . . . . . . . . . . . . . 38
Chem & BioOffice 2006 /Contents
The Standard Toolbar . . . . . . . . . . . . . . . .40
The Building Toolbar . . . . . . . . . . . . . . . . .40
The Model Display Toolbar . . . . . . . . . . .41
The Surfaces Toolbar . . . . . . . . . . . . . . . . .41
The Movie Toolbar . . . . . . . . . . . . . . . . . . .42
The Demo Toolbar . . . . . . . . . . . . . . . . . . .42
The Calculation Toolbar . . . . . . . . . . . . . .42
The ChemDraw Panel . . . . . . . . . . . . . . . . . .42
The Model Information Panel . . . . . . . . . . .43
The Output and Comments Windows . . . .44
Model Building Basics . . . . . . . . . . . . . . . . . . . . . .44
Internal and External Tables . . . . . . . . . . . . .44
The Model Setting Dialog Box . . . . . . . . . . .45
Model Display . . . . . . . . . . . . . . . . . . . . . . . . .46
Model Data Labels . . . . . . . . . . . . . . . . . . .46
Atom Types . . . . . . . . . . . . . . . . . . . . . . . . .47
Rectification . . . . . . . . . . . . . . . . . . . . . . . . .48
Bond Lengths and Bond Angles . . . . . . .48
The Model Explorer . . . . . . . . . . . . . . . . . . . .48
Model Coordinates . . . . . . . . . . . . . . . . . . . . .48
Z-matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . .48
Cartesian Coordinates . . . . . . . . . . . . . . . .49
The Measurements Table . . . . . . . . . . . . .49
Chapter 2: Chem3D Tutorials . . . . . . . 51
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .51
Tutorial 1: Working with ChemDraw . . . . . . . .51
Tutorial 2: Building Models with the
Bond Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52
Tutorial 3: Building Models with the
Text Building Tool . . . . . . . . . . . . . . . . . . . . . . . . .56
Replacing Atoms . . . . . . . . . . . . . . . . . . . . . . .56
Using Labels to Create Models . . . . . . . . . . .57
Using Substructures . . . . . . . . . . . . . . . . . . . .58
Tutorial 4: Examining Conformations. . . . . . . .59
Tutorial 5: Mapping Conformations with
the Dihedral Driver . . . . . . . . . . . . . . . . . . . . . . . .62
Rotating two dihedrals . . . . . . . . . . . . . . . .62
Customizing the Graph . . . . . . . . . . . . . . .63
 Tutorial 6: Overlaying Models . . . . . . . . . . . . . . 63
Tutorial 7: Docking Models . . . . . . . . . . . . . . . . 65
Tutorial 8: Viewing Molecular Surfaces . . . . . . 68
Tutorial 9: Mapping Properties onto Surfaces 69
Administrator
Tutorial 10: Computing Partial Charges . . . . . . 71
Chapter 3: Displaying Models. . . . . . . 75
Structure Displays . . . . . . . . . . . . . . . . . . . . . . . . . 75
Model Types . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Displaying Solid Spheres . . . . . . . . . . . . . . . . 77
Setting Solid Sphere Size . . . . . . . . . . . . . 78
Displaying Dot Surfaces . . . . . . . . . . . . . . . . 78
Coloring Displays . . . . . . . . . . . . . . . . . . . . . . 79
Coloring by Element . . . . . . . . . . . . . . . . . 79
Coloring by Group . . . . . . . . . . . . . . . . . . 79
Coloring by Partial Charge . . . . . . . . . . . . 79
Coloring by depth for Chromatek
stereo viewers . . . . . . . . . . . . . . . . . . . . . . 80
Red-blue Anaglyphs . . . . . . . . . . . . . . . . . . 80
Depth Fading3D enhancement: . . . . . . . 80
Perspective Rendering . . . . . . . . . . . . . . . . 80
Coloring the Background Window . . . . . . . 81
Coloring Individual Atoms . . . . . . . . . . . . . . 81
Displaying Atom Labels . . . . . . . . . . . . . . . . 81
Setting Default Atom Label Display
Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Displaying Labels Atom by Atom . . . . . 82
Displaying Group Labels . . . . . . . . . . . . . . . 82
Displaying Measurements . . . . . . . . . . . . . . . 82
Using Stereo Pairs. . . . . . . . . . . . . . . . . . . . . . 83
Using Hardware Stereo Graphic
Enhancement . . . . . . . . . . . . . . . . . . . . . . . . . 83
Molecular Surface Displays . . . . . . . . . . . . . . . . . 84
Extended Hckel . . . . . . . . . . . . . . . . . . . . . . 85
Displaying Molecular Surfaces . . . . . . . . . . . 85
Setting Molecular Surface Types . . . . . . . 86
Setting Molecular Surface Isovalues . . . . 87
Setting the Surface Resolution . . . . . . . . 88
Setting Molecular Surface Colors . . . . . . 88
Setting Solvent Radius . . . . . . . . . . . . . . . . 88
Setting Surface Mapping . . . . . . . . . . . . . . 89
Partial Surfaces . . . . . . . . . . . . . . . . . . . . . . 89
Solvent Accessible Surface . . . . . . . . . . . . . . 91
Connolly Molecular Surface . . . . . . . . . . . . . 91
CambridgeSoft
Total Charge Density . . . . . . . . . . . . . . . . . . . 92
Total Spin Density . . . . . . . . . . . . . . . . . . . . . 92
Molecular Electrostatic Potential . . . . . . . . 92
Molecular Orbitals . . . . . . . . . . . . . . . . . . . . . 93
Visualizing Surfaces from Other Sources . . . . 93
Chapter 4: Building and Editing
Models. . . . . . . . . . . . . . . . . . . . . . . . . . 95
Setting the Model Building Controls . . . . . . . . . 95
Building with the ChemDraw Panel . . . . . . . . . 96
Unsynchronized Mode . . . . . . . . . . . . . . . . . 96
Name=Struct . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Building with Other 2D Programs . . . . . . . 97
Building With the Bond Tools . . . . . . . . . . . . . . 97
Creating Uncoordinated Bonds . . . . . . . . . . 98
Removing Bonds and Atoms . . . . . . . . . . . . 98
Building With The Text Tool . . . . . . . . . . . . . . . 99
Using Labels . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Changing atom types . . . . . . . . . . . . . . . . 100
The Table Editor . . . . . . . . . . . . . . . . . . . 100
Specifying Order of Attachment . . . . . . 100
Using Substructures . . . . . . . . . . . . . . . . . . . 100
Building with Substructures . . . . . . . . . . . . 101
Example 1. Building Ethane with
Substructures . . . . . . . . . . . . . . . . . . . . . . 101
Example 2. Building a Model with a
Substructure and Several Other
Elements . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Example 3. Polypeptides . . . . . . . . . . . . 102
Example 4. Other Polymers . . . . . . . . . . 103
Replacing an Atom with a Substructure . 103
Building From Tables . . . . . . . . . . . . . . . . . . . . . 103
Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Changing an Atom to Another Element . . . . 104
Changing an Atom to Another Atom
Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Changing Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Creating Bonds by Bond Proximate
Addition . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Adding Fragments . . . . . . . . . . . . . . . . . . . . . . . 106
View Focus. . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Setting Measurements . . . . . . . . . . . . . . . . . . . . . 107
Setting Bond Lengths . . . . . . . . . . . . . . . . . 108
 Setting Bond Angles . . . . . . . . . . . . . . . . . . . 108
Setting Dihedral Angles . . . . . . . . . . . . . . . . 108
Setting Non-Bonded Distances . . . . . . . . . 108
Atom Movement When Setting
Measurements . . . . . . . . . . . . . . . . . . . . . . . . 108
Setting Constraints . . . . . . . . . . . . . . . . . . . . 109
Setting Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Setting Serial Numbers . . . . . . . . . . . . . . . . . . . . 109
Changing Stereochemistry . . . . . . . . . . . . . . . . . 110
Inversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Reflection . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Refining a Model . . . . . . . . . . . . . . . . . . . . . . . . . 111
Rectifying Atoms . . . . . . . . . . . . . . . . . . . . . . 112
Cleaning Up a Model . . . . . . . . . . . . . . . . . . 112
Chapter 5: Manipulating Models . . . 113
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Selecting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Selecting Single Atoms and Bonds . . . . . . 113
Selecting Multiple Atoms and Bonds . . . .114
Deselecting Atoms and Bonds . . . . . . . . . . 114
Selecting Groups of Atoms and Bonds . . 114
Using the Selection Rectangle . . . . . . . .114
Defining Groups . . . . . . . . . . . . . . . . . . . . 115
Selecting a Group or Fragment . . . . . . . 115
Selecting Atoms or Groups by Distance . 116
Showing and Hiding Atoms . . . . . . . . . . . . . . . . 116
Showing Hs and Lps . . . . . . . . . . . . . . . . . . . 117
Showing All Atoms . . . . . . . . . . . . . . . . . . . . 117
Hydrogen Bonding and Polar Hydrogen
Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Moving Atoms or Models . . . . . . . . . . . . . . . . . 118
Moving Models with the Translate Tool . 119
Rotating Models . . . . . . . . . . . . . . . . . . . . . . . . . . 119
X- Y- or Z-Axis Rotations . . . . . . . . . . . . . 120
Rotating Fragments . . . . . . . . . . . . . . . . . . . . 120
Trackball Tool . . . . . . . . . . . . . . . . . . . . . . . . 120
Internal Rotations . . . . . . . . . . . . . . . . . . . . . 120
Using the Rotation Dial . . . . . . . . . . . . . . 120
Rotating Around a Bond . . . . . . . . . . . . . 122
Rotating Around a Specific Axis . . . . . . 122
Rotating a Dihedral Angle . . . . . . . . . . . . 122
Changing Orientation . . . . . . . . . . . . . . . . . . . . . 122
Chem & BioOffice 2006 /Contents
Aligning to an Axis . . . . . . . . . . . . . . . . . . . .123
Aligning to a Plane . . . . . . . . . . . . . . . . . . . .123
Resizing Models . . . . . . . . . . . . . . . . . . . . . . . . . .124
Centering a Selection . . . . . . . . . . . . . . . . . .124
Using the Zoom Control . . . . . . . . . . . . . . .124
Scaling a Model . . . . . . . . . . . . . . . . . . . . . . .124
Changing the Z-matrix . . . . . . . . . . . . . . . . . . . .125
The First Three Atoms in a Z-matrix . . . .125
Atoms Positioned by Three Other
Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .125
Positioning Example . . . . . . . . . . . . . . . .126
Positioning by Bond Angles . . . . . . . . . .127
Positioning by Dihedral Angle . . . . . . . .127
Setting Origin Atoms . . . . . . . . . . . . . . . .127
Chapter 6: Inspecting Models . . . . . . 129
Model Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .129
Pop-up Information. . . . . . . . . . . . . . . . . . . . . . .129
Non-Bonded Distances . . . . . . . . . . . . . .130
Measurement Table . . . . . . . . . . . . . . . . . . . . . . .131
Editing Measurements . . . . . . . . . . . . . . . . .131
Optimal Measurements . . . . . . . . . . . . . . . .131
Non-Bonded Distances in Tables . . . . . . .132
Showing the Deviation from Plane . . . .132
Removing Measurements from a Table 132
Displaying the Coordinates Tables . . . . . .133
Internal Coordinates . . . . . . . . . . . . . . . . .133
Cartesian Coordinates . . . . . . . . . . . . . . .133
Comparing Models by Overlay . . . . . . . . . . . . .134
Working With the Model Explorer . . . . . . . . .136
Model Explorer Objects . . . . . . . . . . . . . . .136
Creating Groups . . . . . . . . . . . . . . . . . . . .138
Adding to Groups . . . . . . . . . . . . . . . . . . .138
Pasting Substructures . . . . . . . . . . . . . . . .138
Deleting Groups . . . . . . . . . . . . . . . . . . . .139
Using the Display Mode . . . . . . . . . . . . .139
Coloring Groups . . . . . . . . . . . . . . . . . . . .139
Resetting Defaults . . . . . . . . . . . . . . . . . . .139
Animations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .139
Creating and Playing Movies . . . . . . . . . . . .139
Spinning Models . . . . . . . . . . . . . . . . . . . . . .140
Spin About Selected Axis . . . . . . . . . . . .140
Editing a Movie . . . . . . . . . . . . . . . . . . . . . . .140
Movie Control Panel . . . . . . . . . . . . . . . . . . .140
 Chapter 7: Printing and Exporting
Models. . . . . . . . . . . . . . . . . . . . . . . . . 143
Printing Models . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Specifying Print Options . . . . . . . . . . . . . . . 143
Administrator
Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Exporting Models Using Different File
Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Publishing Formats . . . . . . . . . . . . . . . . . . . 145
Image Format Features . . . . . . . . . . . . . . 145
WMF and EMF . . . . . . . . . . . . . . . . . . . . 146
BMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
EPS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
TIF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
GIF and PNG and JPG . . . . . . . . . . . . . 147
3DM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
AVI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Formats for Chemistry Modeling
Applications . . . . . . . . . . . . . . . . . . . . . . . . . 147
Alchemy . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Cartesian Coordinates . . . . . . . . . . . . . . . 148
Connection Table . . . . . . . . . . . . . . . . . . . 148
Gaussian Input . . . . . . . . . . . . . . . . . . . . . 149
Gaussian Checkpoint . . . . . . . . . . . . . . . 149
Gaussian Cube . . . . . . . . . . . . . . . . . . . . . 149
Internal Coordinates . . . . . . . . . . . . . . . . 149
MacroModel Files . . . . . . . . . . . . . . . . . . 150
Molecular Design Limited
MolFile (.MOL) . . . . . . . . . . . . . . . . . . . 150
MSI ChemNote . . . . . . . . . . . . . . . . . . . . 150
MOPAC Files . . . . . . . . . . . . . . . . . . . . . 150
MOPAC Graph Files . . . . . . . . . . . . . . . 153
Protein Data Bank Files . . . . . . . . . . . . . 153
ROSDAL Files (RDL) . . . . . . . . . . . . . . 153
Standard Molecular Data (SMD) . . . . 153
SYBYL Files . . . . . . . . . . . . . . . . . . . . . . . 153
Job Description File Formats . . . . . . . . . . 153
JDF Files . . . . . . . . . . . . . . . . . . . . . . . . . . 153
JDT Files . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Exporting With the Clipboard . . . . . . . . . . . . 154
Copying to ChemDraw . . . . . . . . . . . . . . . . 154
Copying to Other Applications . . . . . . . . . 154
Embedding Models in Other
Applications . . . . . . . . . . . . . . . . . . . . . . . . . 155
Background Effects and Images . . . . . . 156
CambridgeSoft
Chapter 8: MM2 and MM3
Computations . . . . . . . . . . . . . . . . . . . 157
MM2 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Minimize Energy . . . . . . . . . . . . . . . . . . . . . . . . . 157
Running a Minimization . . . . . . . . . . . . . . . 159
Queuing Minimizations . . . . . . . . . . . . . . . . 159
Example: Minimizing Ethane . . . . . . . . 159
Example: Comparing Two Stable
Conformations of Cyclohexane . . . . . 161
Molecular Dynamics . . . . . . . . . . . . . . . . . . . . . . 163
Performing a Molecular Dynamics
Computation . . . . . . . . . . . . . . . . . . . . . . . . 164
Dynamics Settings . . . . . . . . . . . . . . . . . . 164
Job Type Settings . . . . . . . . . . . . . . . . . . . 165
Example: Computing the Molecular
Dynamics Trajectory for a Short
Segment of PTFE . . . . . . . . . . . . . . . . . . 166
Compute Properties . . . . . . . . . . . . . . . . . . . . . . 167
Showing Used Parameters . . . . . . . . . . . . . . . . . 169
Repeating an MM2 Computation . . . . . . . 169
Using JDF Files . . . . . . . . . . . . . . . . . . . . . . . 169
Chapter 9: MOPAC Computations. . 171
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
Minimizing Energy . . . . . . . . . . . . . . . . . . . . . . . 172
Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Optimizing Geometry . . . . . . . . . . . . . . . . . 173
TS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
BFGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
LBFGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Adding Keywords . . . . . . . . . . . . . . . . . . . . . 174
Optimize to Transition State . . . . . . . . . 174
Example: Locating the Eclipsed
Transition State of Ethane . . . . . . . . . . 175
Computing Properties . . . . . . . . . . . . . . . . . . . . 176
MOPAC Properties. . . . . . . . . . . . . . . . . . . 177
Heat of Formation, DHf . . . . . . . . . . . . 177
Gradient Norm . . . . . . . . . . . . . . . . . . . . . 177
Dipole Moment . . . . . . . . . . . . . . . . . . . . 178
Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Mulliken Charges . . . . . . . . . . . . . . . . . . . 178
Charges From an Electrostatic
Potential . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Wang-Ford Charges . . . . . . . . . . . . . . . . . 179
 Electrostatic Potential . . . . . . . . . . . . . . . 179
Molecular Surfaces . . . . . . . . . . . . . . . . . . 179
Polarizability . . . . . . . . . . . . . . . . . . . . . . . . 179
COSMO Solvation in Water . . . . . . . . . . 180
Hyperfine Coupling Constants . . . . . . . 180
Spin Density . . . . . . . . . . . . . . . . . . . . . . . . 181
Example 1: The Dipole Moment of
Formaldehyde . . . . . . . . . . . . . . . . . . . . . 182
Example 2: Comparing Cation
Stabilities in a Homologous Series
of Molecules . . . . . . . . . . . . . . . . . . . . . . . 182
Example 3: Analyzing Charge
Distribution in a Series Of Mono-
substituted Phenoxy Ions . . . . . . . . . . . 183
Example 4: Calculating the Dipole
Moment of meta-Nitrotoluene . . . . . . . 184
Example 5: Comparing the Stability
of Glycine Zwitterion in Water
and Gas Phase . . . . . . . . . . . . . . . . . . . . . 185
Example 6: Hyperfine Coupling
Constants for the Ethyl Radical . . . . . . 186
Example 7: UHF Spin Density
for the Ethyl Radical . . . . . . . . . . . . . . . . 187
Example 8: RHF Spin Density
for the Ethyl Radical . . . . . . . . . . . . . . . . 188
MOPAC Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Using the *.out file . . . . . . . . . . . . . . . . . . . . 188
Creating an Input File . . . . . . . . . . . . . . . . . . 189
Running Input Files . . . . . . . . . . . . . . . . . . . 189
Running MOPAC Jobs . . . . . . . . . . . . . . . . 190
Repeating MOPAC Jobs . . . . . . . . . . . . . . . 190
Creating Structures From ARC Files . . . .190
Chapter 10: Gaussian . . . . . . . . . . . . . 193
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
New Gaussian Interface . . . . . . . . . . . . . . . . . . . 193
Predicting Spectra . . . . . . . . . . . . . . . . . . . . . 193
Multi-step Jobs . . . . . . . . . . . . . . . . . . . . . . . . 194
Partial Optimizations . . . . . . . . . . . . . . . . . . 195
Input Template . . . . . . . . . . . . . . . . . . . . . . . 195
Advanced Mode . . . . . . . . . . . . . . . . . . . . . . . 196
Support for DFT Methods . . . . . . . . . . . . . 196
Minimizing Energy. . . . . . . . . . . . . . . . . . . . . . . . 196
Other Options . . . . . . . . . . . . . . . . . . . . . . . . 198
Chem & BioOffice 2006 /Contents
Computing Properties . . . . . . . . . . . . . . . . . . . . .199
Job Description File Formats . . . . . . . . . . . . . .199
JDT Format . . . . . . . . . . . . . . . . . . . . . . . .199
JDF Format . . . . . . . . . . . . . . . . . . . . . . . .199
Running a Gaussian Input File . . . . . . . . . .200
Running a Gaussian Job . . . . . . . . . . . . . . . .200
Repeating a Gaussian Job . . . . . . . . . . . . . .201
Chapter 11: GAMESS Computations 203
GAMESS Overview . . . . . . . . . . . . . . . . . . . . . .203
Minimize Energy . . . . . . . . . . . . . . . . . . . . . . . . .203
The Job & Theory Tab . . . . . . . . . . . . . . . . .204
The General Tab . . . . . . . . . . . . . . . . . . . . . .204
Specifying Properties to Compute . . . . . . .205
Specifying the General Settings . . . . . . . . .205
Saving Customized Job Descriptions. . . . . . . .205
Running a GAMESS Job . . . . . . . . . . . . . . . . . .206
Chapter 12: Jaguar . . . . . . . . . . . . . . . 207
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .207
Minimizing Energy . . . . . . . . . . . . . . . . . . . . . . . .207
Optimize to Transition State . . . . . . . . . . . . . . .208
Predicting Spectra . . . . . . . . . . . . . . . . . . . . . . . . .209
Computing Properties . . . . . . . . . . . . . . . . . . . . .209
Advanced Mode . . . . . . . . . . . . . . . . . . . . . . . . . .210
Appendix A: Substructures. . . . . . . . . 211
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .211
Attachment point rules . . . . . . . . . . . . . . . . .211
Angles and measurements . . . . . . . . . . . . . .211
Defining Substructures . . . . . . . . . . . . . . . . . . . .212
Appendix B: Keyboard Modifiers . . . 213
Rotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .213
Zoom and Translate . . . . . . . . . . . . . . . . . . . . . .213
Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .214
Standard Selection . . . . . . . . . . . . . . . . . . .214
Radial Selection . . . . . . . . . . . . . . . . . . . . .214
Appendix C: Atom Types . . . . . . . . . . 217
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .217
Assigning Atom Types . . . . . . . . . . . . . . . . . . . .217
 Atom Type Characteristics . . . . . . . . . . . . . 217
Defining Atom Types . . . . . . . . . . . . . . . . . . . . . 218
Appendix D: 2D to 3D Conversion . . 219
Administrator
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Stereochemical Relationships . . . . . . . . . . . 219
Example 1 . . . . . . . . . . . . . . . . . . . . . . . . . 219
Example 2 . . . . . . . . . . . . . . . . . . . . . . . . . 219
Example 3 . . . . . . . . . . . . . . . . . . . . . . . . . 220
Example 4 . . . . . . . . . . . . . . . . . . . . . . . . . 220
Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
Appendix E: File Formats . . . . . . . . . 221
Editing File Format Atom Types. . . . . . . . . . . 221
Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Description. . . . . . . . . . . . . . . . . . . . . . . . . . . 221
File Format Examples . . . . . . . . . . . . . . . . . . . . 221
Alchemy File . . . . . . . . . . . . . . . . . . . . . . . . . 221
FORTRAN Formats . . . . . . . . . . . . . . . . 222
Cartesian Coordinate Files . . . . . . . . . . . . . 223
Atom Types in Cartesian Coordinate
Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
The Cartesian Coordinate File Format 223
FORTRAN Formats . . . . . . . . . . . . . . . . 226
Cambridge Crystal Data Bank Files . . . . . 226
Internal Coordinates File . . . . . . . . . . . . . . 227
Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228
FORTRAN Formats . . . . . . . . . . . . . . . . 229
MacroModel. . . . . . . . . . . . . . . . . . . . . . . . . . 229
FORTRAN Formats . . . . . . . . . . . . . . . . 230
MDL MolFile . . . . . . . . . . . . . . . . . . . . . . . . 231
Limitations . . . . . . . . . . . . . . . . . . . . . . . . . 233
FORTRAN Formats . . . . . . . . . . . . . . . . 233
MSI MolFile . . . . . . . . . . . . . . . . . . . . . . . . . . 233
FORTRAN Formats . . . . . . . . . . . . . . . . 237
MOPAC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
FORTRAN Formats . . . . . . . . . . . . . . . . 238
Protein Data Bank Files . . . . . . . . . . . . . . . 239
FORTRAN Formats . . . . . . . . . . . . . . . . 240
ROSDAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
SMD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
SYBYL MOL File. . . . . . . . . . . . . . . . . . . . . 245
FORTRAN Formats . . . . . . . . . . . . . . . . 247
SYBYL MOL2 File . . . . . . . . . . . . . . . . . . . 247
CambridgeSoft
FORTRAN Formats . . . . . . . . . . . . . . . . 250
Appendix F: Parameter Tables . . . . . 251
Parameter Table Overview . . . . . . . . . . . . . . . . 251
Parameter Table Use . . . . . . . . . . . . . . . . . . . . . . 251
Parameter Table Fields . . . . . . . . . . . . . . . . . . . . 252
Atom Type Numbers . . . . . . . . . . . . . . . . . . 252
Quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Estimating Parameters . . . . . . . . . . . . . . . . . . . . 253
Creating Parameters . . . . . . . . . . . . . . . . . . . . . . 253
The Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Symbol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Covalent Radius . . . . . . . . . . . . . . . . . . . . . . 254
Color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Atom Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Name . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
Symbol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
van der Waals Radius . . . . . . . . . . . . . . . . . . 255
Text Number (Atom Type) . . . . . . . . . . . . 255
Charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Maximum Ring Size . . . . . . . . . . . . . . . . . . . 255
Rectification Type . . . . . . . . . . . . . . . . . . . . . 255
Geometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
Number of Double Bonds, Triple
Bonds, and Delocalized Bonds . . . . . . . . 256
Bound-to Order . . . . . . . . . . . . . . . . . . . . . . 256
Bound-to Type . . . . . . . . . . . . . . . . . . . . . . . 256
Substructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Reference Number . . . . . . . . . . . . . . . . . . . . 257
Reference Description . . . . . . . . . . . . . . . . . 257
Bond Stretching Parameters . . . . . . . . . . . . . . . 257
Bond Type . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
KS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Bond Dipole . . . . . . . . . . . . . . . . . . . . . . . . . 258
Record Order . . . . . . . . . . . . . . . . . . . . . . . . . 258
Angle Bending . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
Angle Type . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
KB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
XR2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
XRH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
 XH2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Record Order . . . . . . . . . . . . . . . . . . . . . . . . . 260
Pi Atoms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Atom Type . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Electron . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Ionization . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Repulsion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Pi Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Bond Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
dForce . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
dLength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Record Order . . . . . . . . . . . . . . . . . . . . . . . . . 261
Electronegativity Adjustments . . . . . . . . . . . . . 261
MM2 Constants . . . . . . . . . . . . . . . . . . . . . . . . . . 262
Cubic and Quartic Stretch Constants . . . . 262
Type 2 (-CHR-) Bending Force
Parameters for C-C-C Angles . . . . . . . . . . 262
Stretch-Bend Parameters . . . . . . . . . . . . . . . 263
Sextic Bending Constant . . . . . . . . . . . . . . . 263
Dielectric Constants . . . . . . . . . . . . . . . . . . . 263
Electrostatic and van der Waals
Cutoff Parameters . . . . . . . . . . . . . . . . . . . . 263
MM2 Atom Types . . . . . . . . . . . . . . . . . . . . . . . . 263
Atom type number . . . . . . . . . . . . . . . . . . . . 263
R* . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Eps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Reduct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Atomic Weight . . . . . . . . . . . . . . . . . . . . . . . . 264
Lone Pairs . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Torsional Parameters . . . . . . . . . . . . . . . . . . . . . . 264
Dihedral Type. . . . . . . . . . . . . . . . . . . . . . . . . 265
V1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
V2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
V3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
Record Order . . . . . . . . . . . . . . . . . . . . . . . . . 267
Out-of-Plane Bending . . . . . . . . . . . . . . . . . . . . . 267
Bond Type. . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
Force Constant. . . . . . . . . . . . . . . . . . . . . . . . 267
Record Order . . . . . . . . . . . . . . . . . . . . . . . . . 267
VDW Interactions . . . . . . . . . . . . . . . . . . . . . . . . 268
Record Order . . . . . . . . . . . . . . . . . . . . . . . . . 268
Chem & BioOffice 2006 /Contents
Appendix G: Computation Concepts. 269
Computational Methods Overview . . . . . . . . .269
Uses of Computational Methods . . . . . . . .270
Choosing the Best Method . . . . . . . . . . . . .270
Molecular Mechanics Methods
Applications Summary . . . . . . . . . . . . . .271
Quantum Mechanical Methods
Applications Summary . . . . . . . . . . . . . .271
Potential Energy Surfaces . . . . . . . . . . . .273
Potential Energy Surfaces (PES) . . . . . .273
Single Point Energy Calculations . . . . . .273
Geometry Optimization . . . . . . . . . . . . .274
Molecular Mechanics Theory in Brief . . . . . . .275
The Force-Field . . . . . . . . . . . . . . . . . . . . . . .276
MM2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .276
Bond Stretching Energy . . . . . . . . . . . . .277
Angle Bending Energy . . . . . . . . . . . . . . .277
Torsion Energy . . . . . . . . . . . . . . . . . . . . .278
Non-Bonded Energy . . . . . . . . . . . . . . . .278
van der Waals Energy . . . . . . . . . . . . . . . .279
Cutoff Parameters for van der Waals
Interactions . . . . . . . . . . . . . . . . . . . . . . . .279
Electrostatic Energy . . . . . . . . . . . . . . . . .279
charge/charge contribution . . . . . . . . . .280
dipole/dipole contribution . . . . . . . . . . .280
dipole/charge contribution . . . . . . . . . . .280
Cutoff Parameters for Electrostatic
Interactions . . . . . . . . . . . . . . . . . . . . . . . .280
OOP Bending . . . . . . . . . . . . . . . . . . . . . .281
Pi Bonds and Atoms with Pi Bonds . . .281
Stretch-Bend Cross Terms . . . . . . . . . . .281
User-Imposed Constraints . . . . . . . . . . .282
Molecular Dynamics Simulation . . . . . . . .282
Molecular Dynamics Formulas . . . . . . .282
Methods Available in CS MOPAC . . . . . .283
RHF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .283
UHF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .283
Configuration Interaction . . . . . . . . . . . .283
Approximate Hamiltonians in MOPAC . . . . .284
Choosing a Hamiltonian . . . . . . . . . . . . . . .284
MINDO/3 Applicability and
Limitations . . . . . . . . . . . . . . . . . . . . . . . .284
MNDO Applicability and Limitations .285
AM1 Applicability and Limitations . . . .285
 PM3 Applicability and Limitations . . . . 286
MNDO-d Applicability and
Limitations . . . . . . . . . . . . . . . . . . . . . . . . 287
Administrator
Appendix H: MM2 . . . . . . . . . . . . . . . 289
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
MM2 Parameters. . . . . . . . . . . . . . . . . . . . . . 289
Other Parameters . . . . . . . . . . . . . . . . . . . . . 289
Viewing Parameters . . . . . . . . . . . . . . . . . . . . . . 289
Editing Parameters . . . . . . . . . . . . . . . . . . . . . . . 290
The MM2 Force Field in Chem3D . . . . . . . . . 290
Chem3D Changes to Allingers Force Field . 290
Charge-Dipole Interaction Term . . . . . . . 290
Quartic Stretching Term . . . . . . . . . . . . . . . 291
Electrostatic and van der Waals
Cutoff Terms . . . . . . . . . . . . . . . . . . . . . . . . 291
Pi Orbital SCF Computation . . . . . . . . . . . 291
Appendix I: MOPAC . . . . . . . . . . . . . 293
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293
MOPAC Background . . . . . . . . . . . . . . . . . 293
Potential Functions Parameters . . . . . . . . . . . . 293
Adding Parameters to MOPAC . . . . . . . . . . . . 294
Using Keywords . . . . . . . . . . . . . . . . . . . . . . . . . 294
Automatic Keywords . . . . . . . . . . . . . . . . . . 294
Additional Keywords . . . . . . . . . . . . . . . . . . 295
Specifying the Electronic Configuration . . . . 296
Even-Electron Systems . . . . . . . . . . . . . . . . 297
Ground State, RHF . . . . . . . . . . . . . . . . . 297
Ground State, UHF . . . . . . . . . . . . . . . . . 298
Excited State, RHF . . . . . . . . . . . . . . . . . 298
Excited State, UHF . . . . . . . . . . . . . . . . . 298
Odd-Electron Systems . . . . . . . . . . . . . . . . 298
Ground State, RHF . . . . . . . . . . . . . . . . . 298
Ground State, UHF . . . . . . . . . . . . . . . . . 298
Excited State, RHF . . . . . . . . . . . . . . . . . 299
Excited State, UHF . . . . . . . . . . . . . . . . . 299
Sparkles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
Introduction . . . . . . . . . . . . . . . . . . . . 301
About ChemFinder . . . . . . . . . . . . . . . . . . . . . . . 301
Whats New in ChemFinder 10? . . . . . . . . . . . 301
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
CambridgeSoft
Chapter 13: ChemFinder Basics . . . . 303
The ChemFinder GUI . . . . . . . . . . . . . . . . . . . . 303
The ChemFinder Toolbars . . . . . . . . . . . . . 306
Main Toolbar. . . . . . . . . . . . . . . . . . . . 306
Form Toolbar . . . . . . . . . . . . . . . . . . . . 306
Search Toolbar . . . . . . . . . . . . . . . . . . 307
Record Toolbar . . . . . . . . . . . . . . . . . . 307
Text Toolbar . . . . . . . . . . . . . . . . . . . . 307
The Status Bar . . . . . . . . . . . . . . . . . . . . . . . . 307
GUI Improvements in ChemFinder 10 . . . . . 308
Find and Replace 308
Struct=Name from the Context Menu. 308
Opening ChemFinder . . . . . . . . . . . . . . . . . . . . 309
Using ChemFinder with Databases . . . . . . . . 309
The Database Model . . . . . . . . . . . . . . . . . . 310
Understanding Forms and Databases . . 311
Chapter 14: ChemFinder Tutorials . . 313
Sample Databases 313
Tutorial 1: Creating Forms . . . . . . . . . . . . . . . . 313
Creating Data Boxes . . . . . . . . . . . . . . . . . . 314
Editing Data Boxes . . . . . . . . . . . . . . . . . . . 315
Deleting Data Boxes 316
Creating and Saving a Form . . . . . . . . . . . . 316
Tutorial 2: Opening a Database . . . . . . . . . . . . 317
Connecting a Database to a Form . . . . . . 317
Assigning Fields to Data Boxes . . . . . . . . . 318
Tutorial 3: Creating Your Own Database . . . 319
Adding Records. . . . . . . . . . . . . . . . . . . . . . . 320
Tutorial 4: Searching a Database . . . . . . . . . . . 321
Opening the Demo Database . . . . . . . . . . 322
Text Searching . . . . . . . . . . . . . . . . . . . . . . . . 323
Formula Searching . . . . . . . . . . . . . . . . . . 323
Name Searching . . . . . . . . . . . . . . . . . . . . 325
Numerical Searching . . . . . . . . . . . . . . . . . . 325
Substructure Searching . . . . . . . . . . . . . . . . 326
Combined Searching . . . . . . . . . . . . . . . . . . 327
Tutorial 5: Reaction Queries . . . . . . . . . . . . . . . 327
Opening A Specific Database . . . . . . . . . . 327
Searching for Reactants . . . . . . . . . . . . . . . . 328
Searching for Products . . . . . . . . . . . . . . . . 328
Searching by Reaction Type . . . . . . . . . . . . 329
Search Over List . . . . . . . . . . . . . . . . . . . . . . 330
Tutorial 6: Using BioViz . . . . . . . . . . . . . . . . . . 330
Tutorial 7: Working with Subforms . . . . . . . . . 332
Creating a Subform . . . . . . . . . . . . . . . . . . . . 332
Chapter 15: Creating and Editing
Forms . . . . . . . . . . . . . . . . . . . . . . . . . 335
Selecting a Database . . . . . . . . . . . . . . . . . . . . . . 335
Opening an Existing Chemical Database . 335
Selecting the Data to Display . . . . . . . . . . . 336
Opening a Secured MS Access Database . 337
Creating a Database . . . . . . . . . . . . . . . . . . . 337
Creating Forms Automatically. . . . . . . . . . . . . . 338
Saving a Form . . . . . . . . . . . . . . . . . . . . . . . . 339
Creating Forms Manually . . . . . . . . . . . . . . . . . . 340
Using the Form Tools . . . . . . . . . . . . . . . . . 340
Creating a New Form . . . . . . . . . . . . . . . . . . 340
Using the Grid . . . . . . . . . . . . . . . . . . . . . . . 340
Creating Boxes . . . . . . . . . . . . . . . . . . . . . . . . 340
Creating Frames . . . . . . . . . . . . . . . . . . . . . . . 341
Creating Boxes with Frames . . . . . . . . . . . . 341
Automatic Labels . . . . . . . . . . . . . . . . . . . 342
Adding Plain Text . . . . . . . . . . . . . . . . . . . . . 342
Adding a Button . . . . . . . . . . . . . . . . . . . . . . 343
Adding a Checkbox. . . . . . . . . . . . . . . . . . . . 343
Adding Pictures . . . . . . . . . . . . . . . . . . . . . . . 343
Creating and Editing Tabs . . . . . . . . . . . . . . 344
Creating Forms with the Database Tree . . . . . 344
Setting Box Properties. . . . . . . . . . . . . . . . . . . . . 345
Setting Data Box Styles . . . . . . . . . . . . . . . . 345
Viewing Structures . . . . . . . . . . . . . . . . . . . . 346
Viewing Structures in Chem3D Format 347
Setting Fixed and Live Data . . . . . . . . . . . .348
Adding a Data Box Menu . . . . . . . . . . . . . . 348
Adding Scroll Bars. . . . . . . . . . . . . . . . . . . . . 349
Hiding Data Boxes . . . . . . . . . . . . . . . . . . . . 349
Customizing Text . . . . . . . . . . . . . . . . . . . . . 349
Customizing Fonts . . . . . . . . . . . . . . . . . . 349
Customizing Numbers . . . . . . . . . . . . . . . 350
Setting Color . . . . . . . . . . . . . . . . . . . . . . . . . . 351
Editing Forms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
Selecting Objects on a Form . . . . . . . . . . . . 352
Moving Objects 352
Resizing Objects . . . . . . . . . . . . . . . . . . . . . . 352
Deleting Objects . . . . . . . . . . . . . . . . . . . . . . 353
Reversing and Restoring Changes . . . . . . . 353
Chem & BioOffice 2006 /Contents
Ordering Objects . . . . . . . . . . . . . . . . . . . . . .353
Aligning and Distributing Objects . . . . . . .354
Changing the Layout of an Existing Form . . .354
Securing Forms . . . . . . . . . . . . . . . . . . . . . . . . . . .356
Setting Security Options . . . . . . . . . . . . . . .356
Disabling Security . . . . . . . . . . . . . . . . . . . . .360
Overriding Security . . . . . . . . . . . . . . . . . . . .360
Chapter 16: Relational Data and
Subforms . . . . . . . . . . . . . . . . . . . . . . 361
Accessing Relational Data Using Subforms . 361
Creating a Subform . . . . . . . . . . . . . . . . . . . . . . .361
Subform Generator . . . . . . . . . . . . . . . . . . . .361
Generating Subforms Automatically . .362
Subform Changes in ChemFinder 9 . . . . .362
Changing the Layout of an Existing
Subform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .364
Working with Subforms . . . . . . . . . . . . . . . . . . .365
Searching a Subform . . . . . . . . . . . . . . . . . . .365
Viewing Subform Data in a Table . . . . . . . . . .365
Using Scripts in Subforms . . . . . . . . . . . . . .365
Chapter 17: Working with Data. . . . . 367
Overview 367
Opening Databases . . . . . . . . . . . . . . . . . . . . . . .367
Read-Only Access . . . . . . . . . . . . . . . . . . . . .367
Multi-user Access. . . . . . . . . . . . . . . . . . . . . .367
Secured Access . . . . . . . . . . . . . . . . . . . . . . . .368
Browsing Databases . . . . . . . . . . . . . . . . . . . . . . .369
The Data Table . . . . . . . . . . . . . . . . . . . . . . .369
R-Group Tables . . . . . . . . . . . . . . . . . . . . .370
Creating a Database . . . . . . . . . . . . . . . . . . . . . . .371
Creating Tables . . . . . . . . . . . . . . . . . . . . . . .372
Deleting Tables . . . . . . . . . . . . . . . . . . . . . . .372
Attaching Tables from Other
Applications . . . . . . . . . . . . . . . . . . . . . . . . .373
Attaching Files from a File-Based
Database . . . . . . . . . . . . . . . . . . . . . . . . . .373
Attaching Files from a Non File-Based
Database . . . . . . . . . . . . . . . . . . . . . . . . . .373
Creating Fields . . . . . . . . . . . . . . . . . . . . . . . .374
Deleting Fields . . . . . . . . . . . . . . . . . . . . . . . .376
Adding Multiple Structures . . . . . . . . . . . . .376
 Adding Structures to Non-Chemical
Databases . . . . . . . . . . . . . . . . . . . . . . . . . . . 377
Backing up Databases . . . . . . . . . . . . . . . . . 377
Moving Databases . . . . . . . . . . . . . . . . . . . . 377
Administrator
Creating a Portal Database . . . . . . . . . . . . . . . . 377
Entering Data into a Database . . . . . . . . . . . . . 378
Clearing the Form. . . . . . . . . . . . . . . . . . . . . 378
Adding New Data. . . . . . . . . . . . . . . . . . . . . 378
Committing the New Data . . . . . . . . . . . . . 379
Duplicating Records. . . . . . . . . . . . . . . . . . . 379
Undoing Data Entry . . . . . . . . . . . . . . . . . . 379
Editing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
Editing Data . . . . . . . . . . . . . . . . . . . . . . . . . 380
Sorting Data . . . . . . . . . . . . . . . . . . . . . . . . . . 380
Sorting Fields . . . . . . . . . . . . . . . . . . . . . . 380
Sorting from the Data Table . . . . . . . . . 380
Sorting in Reverse Order . . . . . . . . . . . . 380
Sorting Languages Other Than English 381
Resetting the Database . . . . . . . . . . . . . . 381
Editing Structures . . . . . . . . . . . . . . . . . . . . . 381
Working with Structures Using
ChemDraw . . . . . . . . . . . . . . . . . . . . . . . . 382
Viewing Models using Chem3D . . . . . . 383
Styled Text . . . . . . . . . . . . . . . . . . . . . . . . . . . 383
Undoing Changes . . . . . . . . . . . . . . . . . . . . . 384
Redoing Changes . . . . . . . . . . . . . . . . . . . . . 384
Deleting Data . . . . . . . . . . . . . . . . . . . . . . . . 384
Changing the Database Scheme . . . . . . . . . . . . 384
Chapter 18: Visualizing Data
With BioViz. . . . . . . . . . . . . . . . . . . . . 385
Improvements in Version 10 . . . . . . . . . . . . . . 385
Better Selecting And Mouse-overs . . . . . . 385
More plotting flexibility . . . . . . . . . . . . . . . . 385
Details Window. . . . . . . . . . . . . . . . . . . . . . . 386
Removal of Empty Points . . . . . . . . . . . . . 386
Histogram Improvements . . . . . . . . . . . . . 386
Creating a Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
BioViz Options . . . . . . . . . . . . . . . . . . . . . . . 388
Statistical Analysis . . . . . . . . . . . . . . . . . . . . . . . . 389
Cleaning Up the PlotSorting and Filtering . 390
Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 390
Filter Slider Adjustment . . . . . . . . . . . . . 391
Plotting Searches . . . . . . . . . . . . . . . . . . . . . . . . . 392
CambridgeSoft
Synchronization of Plots . . . . . . . . . . . . . . . 392
Changing the Display . . . . . . . . . . . . . . . . . . . . . 393
Chapter 19: Importing and Exporting
Data. . . . . . . . . . . . . . . . . . . . . . . . . . . 395
Supported File Formats 395
Importing Data . . . . . . . . . . . . . . . . . . . . . . . . . . 395
Importing Structures 395
Importing Structure Data and Reaction
Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
Using Log Files . . . . . . . . . . . . . . . . . . . . . 398
Reading a Structure . . . . . . . . . . . . . . . . . . . 398
Drag and Drop . . . . . . . . . . . . . . . . . . . . . 399
Importing Text Files . . . . . . . . . . . . . . . . . . 399
Exporting Data Files . . . . . . . . . . . . . . . . . . . . . . 400
Saving Structures. . . . . . . . . . . . . . . . . . . . . . 401
Exporting an ASCII File . . . . . . . . . . . . . . . 401
Exporting a Word file . . . . . . . . . . . . . . . . . 401
Export to SDFile . . . . . . . . . . . . . . . . . . . . . 402
Chapter 20: Searching . . . . . . . . . . . . 403
Text Searches . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403
Numeric Searches . . . . . . . . . . . . . . . . . . . . . . . . 404
Molecular Formula Searches . . . . . . . . . . . . . . . 404
Date Searches . . . . . . . . . . . . . . . . . . . . . . . . . . . . 405
Find List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 405
Structure Searches . . . . . . . . . . . . . . . . . . . . . . . . 406
Search Type . . . . . . . . . . . . . . . . . . . . . . . . . . 406
Normal Searching . . . . . . . . . . . . . . . . . . . 406
Exact Searching . . . . . . . . . . . . . . . . . . . . 406
Similarity Searching . . . . . . . . . . . . . . . . . 407
Substructure Searching . . . . . . . . . . . . . . . . 407
Fragment Searching . . . . . . . . . . . . . . . . . 407
Full Structure Searching . . . . . . . . . . . . . . . 408
Stereochemistry . . . . . . . . . . . . . . . . . . . . 408
3D Properties . . . . . . . . . . . . . . . . . . . . . . 408
Searching with R-Groups . . . . . . . . . . . . . . 408
Alternative Groups . . . . . . . . . . . . . . . . . 408
Defining an Alternative Group . . . . . . . 409
Reaction Searches . . . . . . . . . . . . . . . . . . . . . . . . 410
Reaction Centers . . . . . . . . . . . . . . . . . . . . . . 410
Atom-to-Atom Mapping . . . . . . . . . . . . . . . 411
Searching for Reactants . . . . . . . . . . . . . . . . 412
Searching for Products . . . . . . . . . . . . . . . . 412
 Searching for Intermediates . . . . . . . . . . . .412
Combined Searches . . . . . . . . . . . . . . . . . . . . . . . 412
SQL Searches . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
Searching Procedures . . . . . . . . . . . . . . . . . . . . . 413
Setting Search Type Preferences . . . . . . . .413
Setting Search Details Preferences . . . .414
Setting Stereochemical Search
Preferences . . . . . . . . . . . . . . . . . . . . . . . . 415
Entering Query Mode . . . . . . . . . . . . . . . . . 416
Entering and Submitting a Query . . . . . . . 416
Stopping a Search . . . . . . . . . . . . . . . . . . . . . 417
Refining a Search . . . . . . . . . . . . . . . . . . . . . . 417
Entering a Structural Query . . . . . . . . . . . .417
Using the Current Molecule as a Query 418
Finding the Current Molecule . . . . . . . .418
Entering a Reaction Query . . . . . . . . . . . . . 418
Special Structure Searches . . . . . . . . . . . . . . . . . 419
Managing Queries . . . . . . . . . . . . . . . . . . . . . . . . 421
The Queries context menu . . . . . . . . . . . . . 422
Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
Saving and Restoring Lists . . . . . . . . . . . . . 423
Saving a Hit List . . . . . . . . . . . . . . . . . . . . 424
Restoring a Hit List . . . . . . . . . . . . . . . . . 424
Search Examples. . . . . . . . . . . . . . . . . . . . . . . . . . 425
Working with Multiple Hit Lists . . . . . . 425
Using Atom Lists . . . . . . . . . . . . . . . . . . . 426
Atom Types and Bond Types . . . . . . . .426
Searching Fullerenes . . . . . . . . . . . . . . . . . 426
Searching Link Nodes and Multivalent
Rs (MVRs) . . . . . . . . . . . . . . . . . . . . . . . . 426
Searching More Than One Substructure 427
Chapter 21: Customizing ChemFinder429
Setting Preferences . . . . . . . . . . . . . . . . . . . . . . . . 429
Display Preferences . . . . . . . . . . . . . . . . . . . . 429
Structure Display . . . . . . . . . . . . . . . . . . . . 429
Using Keyboard Shortcuts . . . . . . . . . . . 430
Scaling Structures . . . . . . . . . . . . . . . . . . . 430
Framing Pictures . . . . . . . . . . . . . . . . . . . . 430
Grid Spacing . . . . . . . . . . . . . . . . . . . . . . . . 430
Color Preferences . . . . . . . . . . . . . . . . . . . . . 430
General Preferences . . . . . . . . . . . . . . . . . . . 431
Structure Registration Options . . . . . . . 431
ChemFinder Opening Options . . . . . . . 431
Chem & BioOffice 2006 /Contents
Setting the Recent File List Size . . . . . . .432
Customizing the Favorites Tree . . . . . . . . . . . .432
Customizing Toolbars . . . . . . . . . . . . . . . . . . . . .433
Using the Periodic Table. . . . . . . . . . . . . . . . . . .434
ChemFinder Automation Language (CAL) . .435
Getting CAL Help . . . . . . . . . . . . . . . . . . . . .435
Creating a Script . . . . . . . . . . . . . . . . . . . . . . .435
Debugging a Script . . . . . . . . . . . . . . . . . . . .436
Trigger Scripts . . . . . . . . . . . . . . . . . . . . . . . .437
Communicating with Other Applications . . . .437
Using Scripts . . . . . . . . . . . . . . . . . . . . . . . . . .437
Using Visual Basic . . . . . . . . . . . . . . . . . . . . .438
Using Microsoft Access with ChemFinder439
Chapter 22: ChemFinder/Oracle . . . 441
Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .441
Opening an Oracle Database . . . . . . . . . . . . . . .442
Searching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .443
Handling Lists . . . . . . . . . . . . . . . . . . . . . . . . . . .443
Setting Oracle Preferences . . . . . . . . . . . . . . . . .444
Updating and Adding Data . . . . . . . . . . . . . . . .444
Loading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .445
Indexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .446
CAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .447
Chapter 23: ChemFinder/Office. . . . 449
The ChemFinder/Office Graphical User
Interface (GUI) . . . . . . . . . . . . . . . . . . . . . . . . . . .449
Selecting Files to Search . . . . . . . . . . . . . . . . . . .450
Selecting Files From the File Menu . . . . . .450
Selecting Files With the Look In Tab . . . .450
Searching by Chemical Structure . . . . . . . . . . .451
Searching by Multiple Properties . . . . . . . . . . .452
Browsing Search Results . . . . . . . . . . . . . . . . . . .453
Saving Files or Data Sources . . . . . . . . . . . . . . .454
Saving Search Results as .sdf Files . . . . . . .454
Saving Data Sources as .dsd Files . . . . . . .454
Saving Lists of Directory Paths as
.dsd Files . . . . . . . . . . . . . . . . . . . . . . . . . . . .454
Searching .dsd Files . . . . . . . . . . . . . . . . . . . . . . .455
Sending a File to Another Application . . . . . .455
Refining Your Search . . . . . . . . . . . . . . . . . . . . .457
 Using the Search Tools . . . . . . . . . . . . . . . . 457
Refining Your Query With the Search
Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
Changing ChemFinder/Office Settings . . . . . 459
Administrator
Customizing the ChemFinder/Office
Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 459
Changing the ChemFinder/Office
Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . 460
Chapter 24: Using ChemFinder/Office
with CombiChem . . . . . . . . . . . . . . . . 461
CombiChem Overview . . . . . . . . . . . . . . . . 461
Working with Reaction Templates . . . . . . . . . 461
Reaction Template Basics . . . . . . . . . . . . . . 461
Entering a Template . . . . . . . . . . . . . . . . . . . . . . 461
Using ChemDraw or the ChemDraw
ActiveX control: . . . . . . . . . . . . . . . . . . . . . 462
Using a ChemFinder database: . . . . . . . . . 462
Appendix J: Structural Query Features465
General Properties . . . . . . . . . . . . . . . . . . . . . . . 465
Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465
Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465
Substituents . . . . . . . . . . . . . . . . . . . . . . . . . . 466
Charges and Radicals . . . . . . . . . . . . . . . . . . 466
Isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467
Stereochemistry . . . . . . . . . . . . . . . . . . . . . . . 467
Relative Tetrahedral Stereochemistry . 468
MDL File Formats . . . . . . . . . . . . . . . . . . 468
Normalization . . . . . . . . . . . . . . . . . . . . . . . . 469
Atom Properties . . . . . . . . . . . . . . . . . . . . . . . . . 469
Special Atom Types . . . . . . . . . . . . . . . . . . . 469
Atom Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . 469
Atom Not-Lists . . . . . . . . . . . . . . . . . . . . . . . 470
Substituents: Exactly . . . . . . . . . . . . . . . . . . 470
Substituents: Up To . . . . . . . . . . . . . . . . . . . 470
Substituents: Free Sites . . . . . . . . . . . . . . . . 471
Implicit Hydrogens . . . . . . . . . . . . . . . . . . . 471
Unsaturation . . . . . . . . . . . . . . . . . . . . . . . . . 471
Bond Properties . . . . . . . . . . . . . . . . . . . . . . . . . . 472
Special Bond Types . . . . . . . . . . . . . . . . . . . 472
Topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472
Reaction Center. . . . . . . . . . . . . . . . . . . . . . . 472
CambridgeSoft
Appendix K: Formula Input Rules . . 475
Rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475
Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475
Appendix L: Similarity Rules . . . . . . . 477
Complete Structure Similarity . . . . . . . . . . . . . . 477
Substructure Similarity . . . . . . . . . . . . . . . . . . . . 478
Appendix M: CAL Commands . . . . . 479
New in ChemFinder 479
CAL Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 479
Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . 479
Box Creation Commands . . . . . . . . . . . . . . . . . 480
Box Manipulation Commands . . . . . . . . . . . . . 481
Program Execution Commands . . . . . . . . . . . . 482
General Commands . . . . . . . . . . . . . . . . . . . . . . 483
File Commands . . . . . . . . . . . . . . . . . . . . . . . . . . 484
Database Commands . . . . . . . . . . . . . . . . . . . . . 484
Variable Commands . . . . . . . . . . . . . . . . . . . . . . 485
Environment Variables . . . . . . . . . . . . . . . . . . . 487
Script-Only Commands . . . . . . . . . . . . . . . . . . . 487
Appendix N: CS Oracle Cartridge . . 491
Pre-Setup Procedures 491
Fast-Move Caching Scheme . . . . . . . . . . . . . . . 491
Configuration Via CF_SETTINGS Table . . . 492
Working with Reaction Templates . . . . . . . . . 495
Reaction Template Basics . . . . . . . . . . . . 495
Chapter 25: CombiChem/Excel . . . . 495
Working with CombiChem/Excel . . . . . . . . . 495
Initializing CombiChem/Excel . . . . . . . . . 495
Using Help . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
Using CombiChem/Excel with secured
databases like ChemACX: . . . . . . . . . . . . . 496
Creating a New CombiChem Workbook 497
Adding a Reaction Template to the
Reaction Worksheet . . . . . . . . . . . . . . . . . . 498
Processing the Reaction Template . . . . . . 498
Working with Reactant Lists . . . . . . . . . . . 499
Searching Databases . . . . . . . . . . . . . . . . 499
 Reactant List Format . . . . . . . . . . . . . . . . . . 500
Structure Column . . . . . . . . . . . . . . . . . . . 500
Use (Y/N) . . . . . . . . . . . . . . . . . . . . . . . . . 500
Other Data . . . . . . . . . . . . . . . . . . . . . . . . . 500
Creating Experiments . . . . . . . . . . . . . . . . . . 500
Using the Products Only Option . . . . . 501
Working With Experiments . . . . . . . . . . . .501
Configuring Plates . . . . . . . . . . . . . . . . . . . 501
Assigning Plates . . . . . . . . . . . . . . . . . . . . . 502
Browsing Plates . . . . . . . . . . . . . . . . . . . . . 502
Viewing Related Structures . . . . . . . . . . . 502
Using CombiChem with ChemFinder/Office503
Chapter 26: Introducing
E-Notebook 10.0 . . . . . . . . . . . . . . . . . 505
New Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . 505
Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 506
About the E-Notebook Guide . . . . . . . . . . . . . 508
Getting Started in E-Notebook . . . . . . . . . . . .508
Logging In . . . . . . . . . . . . . . . . . . . . . . . . . . . . 508
Start Menu Login . . . . . . . . . . . . . . . . . . . 508
Logging in with Internet Explorer . . . .509
Navigation Overview . . . . . . . . . . . . . . . . . . 509
Security Overview . . . . . . . . . . . . . . . . . . . . . 509
E-Notebook Overview . . . . . . . . . . . . . . . . . . . . 510
Chapter 27: Working with E-Notebook513
Notebooks, Pages, Experiments, and Other
Collections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513
Working with the User Collection . . . . . . . . . . 514
Adding a New Collection to the User
Collection. . . . . . . . . . . . . . . . . . . . . . . . . . . . 514
Adding a Reference within the User
Collection. . . . . . . . . . . . . . . . . . . . . . . . . . . . 514
Browsing up to the User Group . . . . . . . .515
Working with Notebooks . . . . . . . . . . . . . . . . . . 515
Creating a Notebook . . . . . . . . . . . . . . . . . . 515
Working with Pages and Experiments . . . . . . 516
Creating a Page or Experiment . . . . . . . . . 516
Creating a Page or Experiment from
a Template . . . . . . . . . . . . . . . . . . . . . . . . . . . 516
Closing and Reopening Pages and
Experiments . . . . . . . . . . . . . . . . . . . . . . . . . 516
Working with the Inbox . . . . . . . . . . . . . . . . . . . 517
Chem & BioOffice 2006 /Contents
Working with Folders . . . . . . . . . . . . . . . . . . . . .517
Creating a Folder . . . . . . . . . . . . . . . . . . . . . .517
Adding a Reference to the Folder . . . . . . .517
Working with the User Configuration
Folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .518
Working with Reactants Collections . . . . . . . .518
Adding a New Reactant to an E
xisting Reactant Collection . . . . . . . . . . . .518
Adding a New Reactant Collection . . . . . .519
Working with Table of Contents . . . . . . . . . . .519
Hiding Columns . . . . . . . . . . . . . . . . . . . . . . .519
Showing Columns . . . . . . . . . . . . . . . . . . . . .520
Sorting Items in the TOC . . . . . . . . . . . . . .520
Working with Templates. . . . . . . . . . . . . . . . . . .520
Working with MS Office Sections,
Reactions, and other Sections . . . . . . . . . . . . . .521
Reaction Sections . . . . . . . . . . . . . . . . . . . . . .521
Captured Image Sections . . . . . . . . . . . . . . .521
Ancillary Data Sections . . . . . . . . . . . . . . . .522
Table Sections . . . . . . . . . . . . . . . . . . . . . . . .522
Spectrum and Spectra Sections. . . . . . . . . .522
MS Word Sections . . . . . . . . . . . . . . . . . . . . .522
MS Excel Spreadsheet Sections . . . . . . . . .522
Send2ENotebook and Send2File . . . . . . . . . . .523
Working with Send2ENotebook . . . . . . . . . . .523
Working with Send2File . . . . . . . . . . . . . . . . . . .525
Working Offline . . . . . . . . . . . . . . . . . . . . . . . . . .526
Chapter 28: E-Notebook Features . . 527
Browsing the Collection Tree . . . . . . . . . . . . . .527
Showing and Hiding Collections . . . . . . . .528
Hiding the Collection Tree . . . . . . . . . . . . .528
Limiting Collection Browsing . . . . . . . . . . .528
Browsing from Home. . . . . . . . . . . . . . . . . .529
Browsing at a Higher Level . . . . . . . . . . . . .529
Browsing the Entire Collection Tree . . . .530
E-Notebook Workflows . . . . . . . . . . . . . . . . . . .530
Reactions in E-Notebook . . . . . . . . . . . . . .530
Drawing and Analyzing Reactions . . . .531
Drawing a Structure or Reaction . . . . . .531
Expanding the Drawing Window . . . . .531
Working with ISIS/ Draw . . . . . . . . . . . . . .531
Drawing a Structure or Reaction . . . . . .531
 Working with the Name=Struct Feature 532
Working with the Reaction Toolbar . . . . . 532
Adding Structures with the
Reaction Toolbar . . . . . . . . . . . . . . . . . . 533
Administrator
Filtering Acronyms with the
Reaction Toolbar . . . . . . . . . . . . . . . . . . 534
Defining a New Acronym with
the Reaction Toolbar . . . . . . . . . . . . . . . 535
Deleting a Structure with the
Reaction Toolbar . . . . . . . . . . . . . . . . . . 535
Working with the Stoichiometry Table . . 535
Adding Information to the
Stoichiometry Table . . . . . . . . . . . . . . . . 536
Removing Reactants and Products
from the Stoichiometry Table . . . . . . . 537
Working with Salts and Solvates
in a Reaction Section . . . . . . . . . . . . . . . 538
Working With Batch Explorer. . . . . . . . . . 538
Panning Experiments in Batch
Explorer . . . . . . . . . . . . . . . . . . . . . . . . . . 540
Flipping Experiments in Batch
Explorer . . . . . . . . . . . . . . . . . . . . . . . . . . 540
Saving Experiments as Bitmap in
Batch Explorer . . . . . . . . . . . . . . . . . . . . 541
Copying Experiments in Batch
Explorer . . . . . . . . . . . . . . . . . . . . . . . . . . 541
Printing Experiments in Batch
Explorer . . . . . . . . . . . . . . . . . . . . . . . . . . 542
Selecting Experiments in Batch
Explorer . . . . . . . . . . . . . . . . . . . . . . . . . . 543
Working with Autotext . . . . . . . . . . . . . . . . 543
Inserting Reactants and Products
with AutoText . . . . . . . . . . . . . . . . . . . . . 543
Adding Items from the AutoText
Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 544
Inserting Links with Autotext . . . . . . . . 545
Inserting Custom Autotext . . . . . . . . . . 546
Creating New Autotext Definitions . . . 546
Working with Solvents in a Reaction
Section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 548
Using the Inbox . . . . . . . . . . . . . . . . . . . . . . . . . . 549
Working Offline . . . . . . . . . . . . . . . . . . . . . . 550
Working With the Offline Folder . . . . . 550
Creating an Offline Folder . . . . . . . . . . . 551
CambridgeSoft
Chapter 29: Working with Data in
E-Notebook . . . . . . . . . . . . . . . . . . . . 553
Working with Chemical Structure Data . . 553
Drawing a Structure . . . . . . . . . . . . . . . . . 553
Expanding the Drawing Window . . . . . 554
Working with Images in Chemical
tructure Fields . . . . . . . . . . . . . . . . . . . . . . . 554
Inserting an Image a Structure . . . . . . . 554
Annotating the Image . . . . . . . . . . . . . . . 554
Working with Database Tables . . . . . . . . . 554
Working with MS Excel Spreadsheets . . . 555
Importing an MS Excel document . . . . 555
Working with Captured Image Sections . 556
Importing and Exporting a PDF File . 556
Importing an Image File . . . . . . . . . . . . . 557
Annotating an Image File . . . . . . . . . . . . 557
Working with Image Viewer Sections . . . 557
Importing and Exporting an Image File 558
To export the Image file: . . . . . . . . . . . . 558
Working with MS Word Sections . . . . . . . 558
Working with MS PowerPoint Slideshow
Sections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 559
Importing and Exporting an
MS PowerPoint slideshow . . . . . . . . . . 559
Working with Property Lists . . . . . . . . . . . 560
Adding Properties to Property Lists . . 561
Removing Properties from a Property
List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 561
Setting and Editing Values in a
Property List . . . . . . . . . . . . . . . . . . . . . . 561
Working with Enumerated Lists in
Property Lists . . . . . . . . . . . . . . . . . . . . . 562
Working with Numerical Units in
Property Lists . . . . . . . . . . . . . . . . . . . . . 563
Creating a Reference within a
Property List . . . . . . . . . . . . . . . . . . . . . . 564
Working with Spectrum and Spectra
Sections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 566
Adding a Spectrum . . . . . . . . . . . . . . . . . 567
Replacing a Spectrum . . . . . . . . . . . . . . . 567
Zooming in on a Spectrum Peak . . . . . 567
Other Fields in a Spectrum Section . . . 567
Working with Styled Text . . . . . . . . . . . . . . 568
Working with Subsections . . . . . . . . . . . . . 568
Working with Subsections in Button
 View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 569
Working with Ancillary Data Sections . . . 569
Working with Table Sections . . . . . . . . . . . 570
Adding Columns and Rows to a Table 570
Removing Columns and Rows
from a Table . . . . . . . . . . . . . . . . . . . . . . . 571
Organizing Columns and Rows
in a Table . . . . . . . . . . . . . . . . . . . . . . . . . . 572
Resizing Columns and Rows in a Table 573
Pivoting a Table . . . . . . . . . . . . . . . . . . . . . 573
Adding Information to a Table Cell . . . 573
Working with Structures and Images
in Tables . . . . . . . . . . . . . . . . . . . . . . . . . . 573
Changing Information in a Table Cell . 575
Working with Numerical Units in
Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575
Creating a Reference within a Table
Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575
Blocking of References in Tables . . . . . 576
Validation of Values in Tables . . . . . . . . 576
Working with URL Displays . . . . . . . . . . . . 577
Rendering in E-Notebook . . . . . . . . . . . . . . . . . 577
Exporting . . . . . . . . . . . . . . . . . . . . . . . . . . . . 577
Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579
E-Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . 580
Signing and Closing . . . . . . . . . . . . . . . . . 580
Reviewing a Document . . . . . . . . . . . . . . 581
Countersigning a Document . . . . . . . . . 581
Chapter 30: Working with Sections
and Collections . . . . . . . . . . . . . . . . . . 583
Working with Sections . . . . . . . . . . . . . . . . . . . . 583
Creating a Section . . . . . . . . . . . . . . . . . . . . . 583
Changing a Section . . . . . . . . . . . . . . . . . . . . 583
Removing a Section . . . . . . . . . . . . . . . . . . . 584
Moving a Section within a Collection . . . . 584
Renaming a Section . . . . . . . . . . . . . . . . . . . . 584
Duplicating a Section within a Collection 585
Duplicating a Section between Collections585
Exporting Sections to MS Word . . . . . . . .585
Printing Sections . . . . . . . . . . . . . . . . . . . . . . 585
Working with Collections . . . . . . . . . . . . . . . . . . 585
Behaviors of Collections in E-Notebook. 586
Auto-Numbered Collections . . . . . . . . . 586
Collections that Cannot be Deleted . . . 586
Chem & BioOffice 2006 /Contents
Collections that Cannot be
Deleted if Modified . . . . . . . . . . . . . . . . .587
Collections that Cannot be
Renamed . . . . . . . . . . . . . . . . . . . . . . . . . .587
Copying Collections that
Contain References . . . . . . . . . . . . . . . . .587
Creating a Collection. . . . . . . . . . . . . . . . . . .588
Organizing Collections . . . . . . . . . . . . . . . . .588
Moving Collections within a
Container Collection . . . . . . . . . . . . . . . .588
Moving Collections between
Container Collections . . . . . . . . . . . . . . .589
Creating a Reference within the
Collection Tree . . . . . . . . . . . . . . . . . . . . .589
Duplicating a Collection within a
Container Collection . . . . . . . . . . . . . . . .590
Copying a Collection . . . . . . . . . . . . . . . .591
Renaming a Collection . . . . . . . . . . . . . . .591
Deleting a Collection . . . . . . . . . . . . . . . .591
Viewing Collection Properties . . . . . . . . . .592
Importing and Exporting Collections . . . .593
Importing a Collection . . . . . . . . . . . . . . .593
Exporting a Collection . . . . . . . . . . . . . . .593
Changing Collection Security Properties .593
Collection Security . . . . . . . . . . . . . . . . . .594
Transition Security . . . . . . . . . . . . . . . . . .595
Performing a Collection Transition . . . . . .597
Exporting a Collection or Section to
MS Word . . . . . . . . . . . . . . . . . . . . . . . . . . . .597
Printing Collections . . . . . . . . . . . . . . . . . . . .597
Printing Multiple Collections at Once .597
Performing a Collection Transition . . . . . . . . .598
Working with Form Tools . . . . . . . . . . . . . . . . .598
The New Section Tool . . . . . . . . . . . . . . . . .598
The Duplication Collection Tool . . . . . . . .599
The New Child Collection Tool . . . . . . . . .599
The New Sibling Collection Tool . . . . . . .600
Chapter 31: Changes and Audit Trail 601
Working with the Changes Icon. . . . . . . . .601
Saving Changes to a Collection . . . . . . . . .601
Clicking the Changes Icon . . . . . . . . . . .602
Selecting Annotate Last Change
from the Collection Menu . . . . . . . . . . .602
Saving Changes by Browsing to
 Another Collection . . . . . . . . . . . . . . . . . 602
Saving Changes through Autosave . . . . 602
Saving Changes through Backup
and Restore . . . . . . . . . . . . . . . . . . . . . . . 602
Administrator
Annotation of Changes . . . . . . . . . . . . . . . . 603
Providing Required Annotation . . . . . . 603
Providing Unprompted, Optional
Annotation . . . . . . . . . . . . . . . . . . . . . . . . 604
Working with the History Pane . . . . . . . . . 604
Specifying an Annotation through
the History Pane . . . . . . . . . . . . . . . . . . . 605
Visual Display of Changes . . . . . . . . . . . . . 606
Chapter 32: Searching . . . . . . . . . . . . 609
Conducting a Search . . . . . . . . . . . . . . . . . . . . . . 609
Working with Query Results . . . . . . . . . . . 609
Viewing Items in a Results List . . . . . . . 609
Saving a Results List . . . . . . . . . . . . . . . . 610
Customizing the Display of Search
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . 610
Saving a Query . . . . . . . . . . . . . . . . . . . . . 610
Running a Saved Query . . . . . . . . . . . . . 610
Refining a Search . . . . . . . . . . . . . . . . . . . . . 611
Using the E-Notebook Search Types . . . 611
Searching for Sections . . . . . . . . . . . . . . . 612
Collections Search . . . . . . . . . . . . . . . . . . 613
Chemical Structure Search . . . . . . . . . . . 614
General Query Properties . . . . . . . . . . . . . . 615
Atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 615
Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 616
Substituents . . . . . . . . . . . . . . . . . . . . . . . . 616
Charges and Radicals . . . . . . . . . . . . . . . . 617
Isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . 617
Atom Properties . . . . . . . . . . . . . . . . . . . . . . 617
Special Atom Types . . . . . . . . . . . . . . . . . 617
Atom Lists . . . . . . . . . . . . . . . . . . . . . . . . . 618
Substituents: Exactly . . . . . . . . . . . . . . . . 618
Substituents: Up To . . . . . . . . . . . . . . . . . 618
Substituents: Free Sites . . . . . . . . . . . . . . 619
Unsaturation . . . . . . . . . . . . . . . . . . . . . . . 619
Bond Properties . . . . . . . . . . . . . . . . . . . . . . 620
Special Bond Types . . . . . . . . . . . . . . . . . 620
Topology . . . . . . . . . . . . . . . . . . . . . . . . . . 620
Reaction Center . . . . . . . . . . . . . . . . . . . . 620
Reaction Searching . . . . . . . . . . . . . . . . . . . . 621
CambridgeSoft
Reaction Centers . . . . . . . . . . . . . . . . . . . 621
Atom-to-Atom Mapping . . . . . . . . . . . . 622
Searching for Reactants . . . . . . . . . . . . . . 622
Searching for Products . . . . . . . . . . . . . . 623
Searching with the Search Location Field . . . 623
Searching with Collection Attributes . . . . . . . 623
Searching with the Property Query and
Table Query Fields . . . . . . . . . . . . . . . . . . . . . . . 624
Adding Properties to the Field . . . . . . . . . 625
Removing Properties from the Field . . . . 625
Search Options . . . . . . . . . . . . . . . . . . . . . . . 625
Searching for Text with the Query Text Field626
Basic Text Searching . . . . . . . . . . . . . . . . . . 626
Exact Phrase Matching . . . . . . . . . . . . . . 627
Wildcard Searching . . . . . . . . . . . . . . . . . 627
Advanced Text Searching . . . . . . . . . . . . . . 627
Escape Characters . . . . . . . . . . . . . . . . . . 627
ABOUT . . . . . . . . . . . . . . . . . . . . . . . . . . . 628
AND (&) . . . . . . . . . . . . . . . . . . . . . . . . . . 628
EQUIValence (=) . . . . . . . . . . . . . . . . . . 629
Fuzzy (?) . . . . . . . . . . . . . . . . . . . . . . . . . . . 629
MINUS (-) . . . . . . . . . . . . . . . . . . . . . . . . . 630
NEAR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630
NOT (~) . . . . . . . . . . . . . . . . . . . . . . . . . . 631
OR (|) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 632
Soundex (!) . . . . . . . . . . . . . . . . . . . . . . . . . 632
Stem ($) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633
Chapter 33: Introducing CombiChem
for E-Notebook. . . . . . . . . . . . . . . . . . 635
Setting up the Generic Reaction . . . . . . . . . . . 635
Adding a Generic Reaction . . . . . . . . . . . . 635
Preparing a Reaction from an Existing
Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . 636
Managing CombiChem Reactants . . . . . . . . . . 637
Adding Reactants from a Chemical
Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 637
Importing Reactants from a Chemical
Database . . . . . . . . . . . . . . . . . . . . . . . . . . 637
Adding Reactants Manually . . . . . . . . . . 638
Checking Reaction Sites . . . . . . . . . . . . . . . 639
Editing Reactants . . . . . . . . . . . . . . . . . . . . . 639
Removing Reactants from a CombiChem
Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 640
 Removing a Selected Reactant . . . . . . . . 640
Removing All Reactants from a
CombiChem Library . . . . . . . . . . . . . . . . 640
Enumerating and Managing CombiChem
Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 640
Working with the Enumeration Template640
Creating an Enumeration Template . . . 640
Showing an Enumeration Template . . . 641
Updating an Enumeration Template . . 641
Removing an Enumeration Template . 641
Enumerating Products . . . . . . . . . . . . . . . . . 642
Enumerating All of the Products
of a Generic Reaction . . . . . . . . . . . . . . . 642
Enumerating Selected Products of
a Generic Reaction . . . . . . . . . . . . . . . . . 642
Exporting Products to an SD File . . . . . . . 642
Removing Products from a CombiChem Library
643
Using the CombiChem Navigator and
Structure Window . . . . . . . . . . . . . . . . . . . . . . . . 643
Using the CombiChem Navigator . . . . . . . 643
Using the Navigator when in
Products Mode . . . . . . . . . . . . . . . . . . . . . 644
Using the Navigator in Reactants Mode 644
Viewing and Hiding the Docked
CombiChem Navigator . . . . . . . . . . . . . 645
Viewing the Navigator as a Floating
Palette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 645
Docking the Navigator at Another
Location . . . . . . . . . . . . . . . . . . . . . . . . . . . 645
Using the Structure Window. . . . . . . . . . . . 646
Viewing and Hiding the Docked
CombiChem Structure Window . . . . . 646
Viewing the Structure Window
as a Floating Palette . . . . . . . . . . . . . . . . 647
Docking the Structure Window at
Another Location . . . . . . . . . . . . . . . . . . 647
Managing Plate Layout and Structure
Palette Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . 648
Editing Structure Palette Display Settings 648
Editing Reactant Layout Settings . . . . . . . . 648
Editing Product Layout Settings . . . . . . . .649
Specifying Empty Wells in the Plate . . . 650
Changing the Size of the Plate . . . . . . . . 650
Chem & BioOffice 2006 /Contents
Changing the Grouping Order . . . . . . . .651
Setting Product Grid Options . . . . . . . . . .651
Chapter 34: Miscellaneous Topics . . 653
Using the Session Manager . . . . . . . . . . . . . . . .653
Ending a Session . . . . . . . . . . . . . . . . . . . . . .653
Refreshing E-Notebook . . . . . . . . . . . . . . . . . . .654
Viewing User Information . . . . . . . . . . . . . . . . .654
Chapter 35: Managing Section
Types and Forms . . . . . . . . . . . . . . . . 655
Creating a New Section Type . . . . . . . . . . . . . .655
Managing Fields within a Section Type . . . . . .656
Adding a Field to a Section Type . . . . . . . .656
Managing Summary Fields in a Table of
Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . .657
Managing Form Tools . . . . . . . . . . . . . . . . . . . . .658
Adding a Form Tool to a Section Type . .658
Viewing and Editing the Properties
of a Form Tool . . . . . . . . . . . . . . . . . . . . . . .659
Removing a Form Tool from a
Section Type . . . . . . . . . . . . . . . . . . . . . . . . .660
Managing the Standard Form Tools . . . . .660
Managing the Next Step Form Tool . . .661
Managing the New Section Form Tool 661
Managing the New Subsection
Section Form Tool . . . . . . . . . . . . . . . . .661
Managing the Spectrum Form Tool . . .662
Managing the Active Document
Form Tool . . . . . . . . . . . . . . . . . . . . . . . . .662
Managing the Insert Reference
Form Tool . . . . . . . . . . . . . . . . . . . . . . . . .663
Managing the Print Multiple
Form Tool . . . . . . . . . . . . . . . . . . . . . . . . .663
Managing Section Listeners . . . . . . . . . . . . . . . .663
Adding a Section Listener to a
Section Type . . . . . . . . . . . . . . . . . . . . . . . . .664
Viewing and Editing the Properties
of a Section Listener . . . . . . . . . . . . . . . . . .664
Removing a Section Listener from a
Section Type . . . . . . . . . . . . . . . . . . . . . . . . .665
Managing the Standard Section Listeners 666
Managing the Required Section
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . .666
 Managing the Fixed Section Name
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 666
Managing the Audit Section Listener . 666
Configuring a Form . . . . . . . . . . . . . . . . . . . . . . 666
Administrator
Configuring a New Form . . . . . . . . . . . . . . 667
Setting the Fields in Boxes . . . . . . . . . . . 668
Reconfiguring an Existing Form . . . . . . . . 669
Adding a Field to an Existing Form . . 669
Rearranging Boxes in a Form . . . . . . . . 670
Deleting a Box from a Form . . . . . . . . . 670
Showing and Hiding the Max Button
for a Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . 671
Hiding the Max Button . . . . . . . . . . . . . . 671
Showing the Max Button . . . . . . . . . . . . 671
Showing and Hiding the Name of a Box 672
Hiding the Box Name . . . . . . . . . . . . . . . 672
Showing the Name of a Box . . . . . . . . . 673
Resizing Boxes in a Form . . . . . . . . . . . . . . 673
Changing the Weight of a Box . . . . . . . 673
Changing the Dimensions of a Box
Manually . . . . . . . . . . . . . . . . . . . . . . . . . . 674
Clearing Fields when Configuring a Form675
Hiding Fields and Boxes when
Configuring a Form . . . . . . . . . . . . . . . . . . 675
Hiding a Box . . . . . . . . . . . . . . . . . . . . . . . 675
Hiding Fields in a Form . . . . . . . . . . . . . 676
Changing Box Orientation . . . . . . . . . . . . . 676
Managing Export Templates for Section
ypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 677
Creating the Export Template for a
Section Type. . . . . . . . . . . . . . . . . . . . . . . . . 678
Editing the Export Template for a
Section Type. . . . . . . . . . . . . . . . . . . . . . . . . 678
Section Metadata Tags . . . . . . . . . . . . . . 679
Standard Field Types . . . . . . . . . . . . . . . . 679
Page Breaks . . . . . . . . . . . . . . . . . . . . . . . . 681
Chapter 36: Managing Commands . . 683
Managing Collection Commands. . . . . . . . . . . 683
Adding a Command to a Collection
Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 683
Viewing and Editing the Properties of a
Collection Command . . . . . . . . . . . . . . . . . 684
Removing a Command from a
Collection Type . . . . . . . . . . . . . . . . . . . . . . 684
CambridgeSoft
Managing the Standard Collection
Commands . . . . . . . . . . . . . . . . . . . . . . . . . . 685
Managing the Export to MS Word
Collection Command . . . . . . . . . . . . . . . 685
Managing the Export to PDF
Collection Command . . . . . . . . . . . . . . . 685
Managing the Print Collection
Command . . . . . . . . . . . . . . . . . . . . . . . . . 686
Managing Section Commands . . . . . . . . . . . . . 686
Adding Commands to a Section Type . . . 686
Viewing and Editing the Properties of a
Section Command . . . . . . . . . . . . . . . . . . . 686
Removing a Command from a Section
ype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 687
Managing the Standard Section
Commands . . . . . . . . . . . . . . . . . . . . . . . . . . 687
Managing the Export to MS Word
Section Command . . . . . . . . . . . . . . . . . 687
Managing the Print Section Command 688
Chapter 37: Managing Rendering in
E-Notebook . . . . . . . . . . . . . . . . . . . . 689
Configuring a Rendering Template . . . . . . . . . 689
Designing a Rendering Template . . . . . . . . . . . 690
Rendering Tags . . . . . . . . . . . . . . . . . . . . . . . 691
Templates for Headers and Footers . . . . . 691
Section Metadata Tags . . . . . . . . . . . . . . . . . 692
Managing the MS Word Section Renderers. . 692
Managing the Fixed Text After Word
Renderer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 692
Managing the Full History Word Renderer693
Managing the Tracked History Word
Renderer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 693
Managing the Standard Field Renderers . . . . . 694
Managing the Fixed Table Field Renderer694
Managing the NonBlank Property
Field Renderer . . . . . . . . . . . . . . . . . . . . . . . 694
Managing the One Property Value
Field Renderer . . . . . . . . . . . . . . . . . . . . . . . 694
Managing the One Table Value Field
Renderer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 694
Managing the Property Value Field
Renderer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 695
 Chapter 38: Managing Fields . . . . . . 697
Managing Field Listeners . . . . . . . . . . . . . . . . . . 697
Adding a Field Listener . . . . . . . . . . . . . . . . 697
Managing Generic Field Listeners . . . . . . . 698
Managing the Block User Edit Field
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 698
Managing the Block Edit Cell Field
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 698
Managing the Copy Default Field
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 699
Managing Data Fields . . . . . . . . . . . . . . . . . . . . . 699
Managing Active Document Fields . . . . . . 699
Managing Active Document Field
Listeners . . . . . . . . . . . . . . . . . . . . . . . . . . 700
Managing the Prevent External
Link Active Document Field Listener 700
Managing the Extract Links
Document Listener . . . . . . . . . . . . . . . . . 700
Managing AutoText Fields . . . . . . . . . . . . . 700
Managing AutoText Field Listeners . . . . . 702
Managing the AutoText Color Field
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 702
Managing Chemical Structure Fields . . . . . 702
Managing Chemical Structure Field
Listeners . . . . . . . . . . . . . . . . . . . . . . . . . . 703
Configuring E-Notebook with
ISIS/Draw Tool . . . . . . . . . . . . . . . . . . . 704
Managing Database Table Fields . . . . . . . . 705
Creating a Database Table Field . . . . . . 705
Configuring a Database Table Field . . . 705
Managing Database Value Fields . . . . . . . . 707
Configuring a Database Value Field . . . 708
Managing Excel Fields . . . . . . . . . . . . . . . . . 708
Managing Break Link Excel Listener . . 709
Managing Hide Addins Excel Listener 709
Managing Remove Macros Field
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 710
Managing PowerPoint Fields . . . . . . . . . . . 710
Managing Context Sensitive Help Fields . 710
Managing Captured Image Fields . . . . . . . 711
Managing Property Lists . . . . . . . . . . . . . . . 712
Creating a Property List . . . . . . . . . . . . . . 713
Managing Enumerated Values in
Property Lists . . . . . . . . . . . . . . . . . . . . . . 714
Chem & BioOffice 2006 /Contents
Modifying Properties without
Obscuring Data . . . . . . . . . . . . . . . . . . . .716
Managing Database Values in
Property Lists . . . . . . . . . . . . . . . . . . . . . .716
Managing Enumerated Values in
Property Lists . . . . . . . . . . . . . . . . . . . . . . . .718
Editing an Enumerated Values List: . . .718
Managing Property List Listeners . . . . . . .719
Managing the Formula Listener . . . . . . .720
Managing the Block Reference In
State Property List Listener . . . . . . . . . .721
Managing the Person Property List
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . .721
Managing the Chemical Properties
Property List Listener . . . . . . . . . . . . . . .722
Managing the Validate Value Property
List Listener . . . . . . . . . . . . . . . . . . . . . . .722
Managing Spectrum Fields . . . . . . . . . . . . .722
Managing Stored Document Fields . . . . . .723
Managing Subsection Fields . . . . . . . . . . . .723
Managing Subsection Field Listeners . .725
Managing the Button View
Subsection Listener . . . . . . . . . . . . . . . . .725
Managing the Hide Tools
Subsection Listener . . . . . . . . . . . . . . . . .725
Managing Table Fields . . . . . . . . . . . . . . . . .725
Creating a Table Field . . . . . . . . . . . . . . .726
Configuring the Appearance of a Table 727
Managing Database Values in Tables . .728
Managing Enumerated Values in Tables 729
Managing Table Listeners . . . . . . . . . . . .730
Managing URL Display Fields . . . . . . . . . .732
Managing Search Fields . . . . . . . . . . . . . . . . . . . .733
Chemical Query Fields . . . . . . . . . . . . . . . . .733
Collection Query Fields . . . . . . . . . . . . . . . .734
Collection Type Query Fields . . . . . . . . . . .735
Join Type Fields . . . . . . . . . . . . . . . . . . . . . . .735
Property Query Fields . . . . . . . . . . . . . . . . .736
Query Text Fields . . . . . . . . . . . . . . . . . . . . .736
State Query Fields . . . . . . . . . . . . . . . . . . . . .737
Table Query Fields . . . . . . . . . . . . . . . . . . . .737
Unannotated Version Query Fields . . . . . .738
Search Location Fields . . . . . . . . . . . . . . . . .738
Managing the Add-In Configuration . . . . . . . .739
 Changing a Field Type . . . . . . . . . . . . . . . . . 740
Adding a new Field Type . . . . . . . . . . . . . . 740
Deleting a Field Type. . . . . . . . . . . . . . . . . . 740
Time Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . 740
Administrator
Managing Units in Property Lists and Tables 741
Specification of Units . . . . . . . . . . . . . . . . . 743
Entry of data . . . . . . . . . . . . . . . . . . . . . . . . . 743
Chapter 39: Managing Collection
Types . . . . . . . . . . . . . . . . . . . . . . . . . . 745
Creating a New Collection Type . . . . . . . . . . . 746
Adding a Section Type to a Collection Type. 747
Having a Section Appear by Default . . . . 748
Removing a Section Type from a Collection
Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 748
Managing Contained Collection Types. . . . . . 749
Adding a Contained Collection Type . . . . 749
Changing the Relationship between a
Contained Collection Type and the
arent Collection Type . . . . . . . . . . . . . . . . . 750
Removing a Contained Collection Type
from a Collection Type . . . . . . . . . . . . . . . 750
Managing Contained Reference Types . . . . . . 750
Adding a Contained Reference Type . . . . 751
Changing the Relationship between a
Contained Reference Type and the
Parent Collection Type . . . . . . . . . . . . . . . 752
Removing a Contained Reference
Type from a Collection Type . . . . . . . . . . 752
Configuring Relationships to Unspecified
Types of Collections . . . . . . . . . . . . . . . . . . . . . . 752
Managing Collection Listeners . . . . . . . . . . . . . 753
Adding a Collection Listener to a
Collection Type . . . . . . . . . . . . . . . . . . . . . . 753
Viewing and Editing the Properties
of a Collection Listener . . . . . . . . . . . . . . . 754
Removing a Collection Listener from a
Collection Type . . . . . . . . . . . . . . . . . . . . . . 754
Managing the Standard Collection
Listeners . . . . . . . . . . . . . . . . . . . . . . . . . . . . 755
Managing the Auto Number Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 755
Managing the Audit Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 756
CambridgeSoft
Managing the Change Display
Collection Listener . . . . . . . . . . . . . . . . . 756
Managing the Clear Value Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 756
Managing the Delete Spawn Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 757
Managing the Parent Prefix Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 757
Managing the Database Procedure
Collection Listener . . . . . . . . . . . . . . . . . 757
Managing the Fixed Name Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 757
Managing the Offline Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 758
Managing the Owner Full Control
Collection Listener . . . . . . . . . . . . . . . . . 758
Managing the No Create Offline
Collection Listener . . . . . . . . . . . . . . . . . 758
Managing the Parent Prefix Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 758
Managing the Prevent Reference Copy
Collection Listener . . . . . . . . . . . . . . . . . 759
Managing the Prevent Delete when
Referenced Collection Listener . . . . . . 759
Managing the Refresh Database Table
Privilege Change Collection Listener . 759
Managing the Section List Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 760
Managing the Security Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 760
Managing the Sequence Collection
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 760
Managing the Unduplicatable
Collection Listener . . . . . . . . . . . . . . . . . 761
Managing the Unique Child
Collection Listener . . . . . . . . . . . . . . . . . . 761
Managing the User Collection Listener 761
Managing Templates . . . . . . . . . . . . . . . . . . . . . . 761
Managing Collection Type Form Tools. . 762
Managing the Duplicate Collection
Form Tool . . . . . . . . . . . . . . . . . . . . . . . . 762
Managing the Structure Form Tool . . . 762
Managing the Next Step Form Tool . . 763
Managing the New Section Form Tool 763
Managing the New Child Collection
 Form Tool . . . . . . . . . . . . . . . . . . . . . . . . . 763
Managing the New Sibling Collection
Form Tool . . . . . . . . . . . . . . . . . . . . . . . . . 763
Managing Search Types . . . . . . . . . . . . . . . . . . . 764
Creating a Search Type . . . . . . . . . . . . . . . . . 764
Managing the Standard Search Engines . .765
Collection Search Engine . . . . . . . . . . . .766
Section Search Engine . . . . . . . . . . . . . . . 766
Chemical Structure Search Engine . . . .766
Creating a Search Form . . . . . . . . . . . . . . . . 766
Viewing and Editing the Properties
of a Search Engine . . . . . . . . . . . . . . . . . . . . 767
Managing States and Transitions . . . . . . . . . . . 768
Adding States to a Collection Type . . . . . . 768
Configuring a Transition between States . 769
Managing Transition Listeners . . . . . . . . . . 770
Associating a Transition Listener
with a Transition . . . . . . . . . . . . . . . . . . . 770
Viewing and Editing the Properties
of a Transition Listener . . . . . . . . . . . . . 771
Removing a Transition Listener
from a Transition . . . . . . . . . . . . . . . . . . 771
Managing the Standard Transition
Listeners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 772
Managing the Annotate Transition
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 772
Managing the Change Display
Transition Listener . . . . . . . . . . . . . . . . . 772
Managing Change Security Transition
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 773
Managing Confirm Transition Listener 773
Managing the Export Transition
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 773
Managing the Final Print Transition
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . . 773
Managing the Locked Container
Transition Listener . . . . . . . . . . . . . . . . . 774
Managing the Print Transition Listener 774
Managing the Required Non-Blank
Properties Transition Listener . . . . . . . 774
Managing the Required Rows
Transition Listener . . . . . . . . . . . . . . . . . 775
Managing the Required Properties
Transition Listener . . . . . . . . . . . . . . . . . 775
Chem & BioOffice 2006 /Contents
Managing the Sign Version Transition
Listener . . . . . . . . . . . . . . . . . . . . . . . . . . .775
Managing the Unlocked Contents
Transition Listener . . . . . . . . . . . . . . . . .775
Managing the View Signed Versions
Transition Listener . . . . . . . . . . . . . . . . .776
Configuring Change Control Options . . . . . . .776
Managing Visual Display of Changes . . . .776
Enabling Visual Display of Changes
from Collection Creation Onward . . .777
Enabling Visual Display of Changes
with a Transition . . . . . . . . . . . . . . . . . . .777
Configuring Annotation Options . . . . .778
Configuring Autosave . . . . . . . . . . . . . . .779
Managing Export Templates of Collection
Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .779
Creating and Editing the Export
Templates for a Collection Type . . . . . . .780
Creating the Export Templates for a
Collection Type . . . . . . . . . . . . . . . . . . . .780
Editing the Header and Footer
Information . . . . . . . . . . . . . . . . . . . . . . . .781
Chapter 40: User Administration . . . 783
Creating a User . . . . . . . . . . . . . . . . . . . . . . . . . . .783
Creating a User Group . . . . . . . . . . . . . . . . . . . .784
Changing a User's Properties . . . . . . . . . . . . . . .784
Changing the Security Properties of a
User Collection . . . . . . . . . . . . . . . . . . . . . . .784
Chapter 41: Managing E-Notebook
Security . . . . . . . . . . . . . . . . . . . . . . . . 787
Managing Collection Security . . . . . . . . . . . . . .787
Collection Security. . . . . . . . . . . . . . . . . . . . .788
Transition Security. . . . . . . . . . . . . . . . . . . . .791
Managing the Security Properties of a
Collection Type . . . . . . . . . . . . . . . . . . . . . . . . . . .792
Collection Type Security . . . . . . . . . . . . . . .793
Managing the Security Properties of a
Section Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . .796
Section Type Security . . . . . . . . . . . . . . . . . .796
Using the Session Manager . . . . . . . . . . . . . . . .798
Ending a Session . . . . . . . . . . . . . . . . . . . . . .799
 Chapter 42: Summary of the
Standard Add-Ins . . . . . . . . . . . . . . . . 801
Collection Listeners . . . . . . . . . . . . . . . . . . . . . . 801
Transition Listeners . . . . . . . . . . . . . . . . . . . . . . 802
Administrator
Section Listeners . . . . . . . . . . . . . . . . . . . . . . . . . 802
Form Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 802
Search Engines . . . . . . . . . . . . . . . . . . . . . . . . . . . 803
Field Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 803
Field Listeners . . . . . . . . . . . . . . . . . . . . . . . . . . . 804
Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 805
Rendering Add-ins . . . . . . . . . . . . . . . . . . . . . . . 806
Chapter 43: Using the Batch
Import Facility . . . . . . . . . . . . . . . . . . 807
<batch>. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 807
<import> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 807
<target> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 807
<collectionType> . . . . . . . . . . . . . . . . . . . . . . . . 807
<childReference> . . . . . . . . . . . . . . . . . . . . . . . . 807
<source> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 808
<log> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 808
<alert> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 808
CambridgeSoft
<refresh> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 808
Appendix O: Technical Support . . . . 809
Serial Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . 809
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . 809
Performance . . . . . . . . . . . . . . . . . . . . . . . . . . 810
System Crashes . . . . . . . . . . . . . . . . . . . . . . . 810
Appendix P: Accessing the
CambridgeSoft Web Site . . . . . . . . . . 811
Registering Online . . . . . . . . . . . . . . . . . . . . . . . . 811
Accessing the Online ChemDraw Users
Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 812
Accessing CambridgeSoft Technical Support 812
Finding Information on ChemFinder.com . . 812
Finding Chemical Suppliers on ACX.com . . . 813
Finding ACX Structures and Numbers . . . . . 813
ACX Structures . . . . . . . . . . . . . . . . . . . . . . . 813
ACX Numbers . . . . . . . . . . . . . . . . . . . . . . . 814
Browsing ChemStore.com . . . . . . . . . . . . . . . . . 814
Browsing CambridgeSoft.com . . . . . . . . . . . . . 815
Using the ChemOffice SDK . . . . . . . . . . . . . . . 815
Chem & BioOffice Introduction
Overview
This Users Manual provides information about
Chem3D, ChemFinder, CombiChem/Excel,
E-Notebook, and related Desktop Addins. The
Desktop Addins incorporate features of
ChemDraw, ChemFinder, and Chem3D into
Microsoft Office applications promoting data
sharing within organizations that have standardized
on MS Office for word processing and
spreadsheets.
Section I describes Chem3D. Section II describes
ChemFinder and its addin, ChemFinder/Office.
Section III describes CombiChem/Excel, and
Section IV describes E-Notebook.
NOTE: You can use the CombiChem engine as a Microsoft
Excel add-in or with E-Notebook, ChemFinder/Office,
and other applications.
About Chem3D
Chem3D is an application designed to enable
scientists to model chemicals. It combines powerful
building, analysis, and computational tools with a
easy-to-use graphical user interface, and a powerful
scripting interface.
Chem3D provides computational tools based on
molecular mechanics for optimizing models,
conformational searching, molecular dynamics, and
calculating single point energies for molecules.
About ChemFinder
ChemFinder is a database management system for
anyone who works with chemical information. It
provides a place to store chemical structures,
Chem & BioOffice 2006/
physical properties, notes, and tables of data. It
takes the place of that box of index cards youve
been using to jot notes about interesting molecules
and reactions, but does it much better! With
ChemFinder, you can search through data
efficiently and quickly, and you can organize the
data instantly.
ChemFinder is integrated with the following
CambridgeSoft products:
ChemDraw
Chem3D
ChemDraw/Excel
ChemFinder/Office
ChemFinder/Office
ChemFinder/Office helps you to build databases
by extracting information from various sources.
With ChemFinder/Office you can browse Word
documents or Excel spreadsheets to find chemical
structures. You can also browse ChemFinder
databases and ChemDraw, Isis/Draw, or SD files.
In addition to browsing, ChemFinder/Office can
search these files by chemical structure or formula,
or by molecular weight.
About CombiChem/Excel
Using the CombiChem engine you can perform the
following tasks:
Add combinatorial library syntheses to Excel
workbooks and other documents.
Search for reactants (starting materials) in avail-
able chemicals databases and import them into
a document.
Chem & BioOffice Introduction 23
About Chem3D
 Choose which reactants to use to create
product libraries (experiments).
Find related structures in reactant and product
listings.
Administrator
Assign reactants and products to automated
synthesis well plates.
Calculate properties of reactants and products
to determine which ones might be the most
desirable.
About E-Notebook
Use E-Notebook instead of your paper laboratory
notebook. With E-Notebook, you can make notes
about experiments, projects, reactions, and other
laboratory tasks and data. You can create MS Word,
MS Excel, spectra, table, and reaction sections for
your data. You can also see the notes of other
people who share the E-Notebook database. You
control access to E-Notebook with the
E-Notebook Administrator.
About This Users Guide
This Users Manual contains information for the
Chem & BioOffice 2006 desktop applications for
Windows. It assumes that you are familiar with the
basics of your Windows operating system. If you
are not, please refer to your system manual before
using the applications. Some of the material
describes tasks that must be performed in
conjuction with other integrated CambridgeSoft
products. The material on the Addins describes
tasks that must be performed in conjuction with
Microsoft Excel or Word. If you are not familiar
with these products, please consult the relevant
Users Manual for more detailed information.
The chapters in this guide are organized by task.
They are intended to help you familiarize yourself
with the ChemOffice applications and start using
them as quickly and efficiently as possible. New
users should read the Basics chapter in each section
24Chem & BioOffice Introduction
to get an overview of the product and how it works.
Chapter 2 in each section, Tutorials, demonstrates
most of the features of the application. Perform the
tutorials in the order they are presented.
Experienced users can skip to Chapter 3 and the
subsequent chapters, which provide more detailed
information.
Conventions
The following notations are used throughout this
users guide:
Ultra The Ultra symbol indicates that a feature is
available in the Ultra version only.
Pro The Pro symbol indicates that a feature is
available in both the Pro and Ultra versions.
Features that are available in the Standard version
are not indicated by a symbol.
NOTE: Notes such as this are used to highlight
information supplemental to the main text.
Shortcut key sequences are indicated with a + sign,
for example: Use the command: Ctrl+H to toggle
hidden Hydrogens and lone pairs.
A bold font is used to indicate that you are to take
a particular action, for example: From the Help
Menu, choose Help Contents.
Additional Information
Additional sources of ChemOffice information are:
The Quick Reference Cards.
The Help system
CambridgeSoft Web Pages.
http://www.cambridgesoft.com/support
CambridgeSoft
About E-Notebook
Quick Reference Card
For Access
The ChemOffice Quick Reference Cards are information
located in the back of the manual. The cards about
provide summaries of ChemOffice Desktop
Application commands and features. Because many Software Devel- http://sdk.cambridge-
of the instructions require knowledge of the opers kit soft.com/
interface elements, use the Quick Reference card as
you perform the tutorials in Chapter 2: Tutorials.
Purchasing http://chemstore.cambridge-
CambridgeSoft soft.com/
Help System products and
ChemOffice applications provide some or all of the chemicals
following types of Help:
HelpAn HTML reference guide. Installation and System
Context-sensitive Help Help topics Requirements
related to user interface objects. To access
Before installation, see the ReadMeFirst and any
Context sensitive Help type Shift+F1.
other ReadMe documents on the installation CD-
ToolTipsShort descriptions of user inter- ROM.
face objects displayed by pointing.
Status BarThe lower left corner of the GUI Microsoft Windows Requirements
displays useful information as you work.
Windows 2000 or XP
CambridgeSoft Web Pages Microsoft Office add-ins require Office
The following table contains the addresses of 2000, 2003, or XP
ChemDraw-related web pages. Screen resolution must be 800 x 600 or higher.
ChemDraw plug-ins/ActiveX controls support
For Access Microsoft IE 6.x, Netscape 7.x and 8.x, Mozilla
information
1.x, and Firefox 1.x.
about
The Chem3D ActiveX control supports Microsoft
Technical Support http://www.cambridge- IE 6.x, Netscape 7.x and 8.0, Mozilla 1.x, and
soft.com/services Firefox 1.x.

ChemDraw Plugin http://www.cambridge- NOTE: Windows XP Service Pack 2 includes security

soft.com/services/documen-
tation/chemdrawplugin/
Chem3D http://www.cambridge-
ActiveX control soft.com/services/documen-
tation/chem3dcontrol/
features that automatically block active content. This means
that by default, Internet Explorer blocks ChemDraw and
Chem3D ActiveX controls. To activate them, you must
choose the option to allow blocked content from the bar
appearing under the address bar notifying you that the
security settings have blocked some of the content of the page.
IE does not remember this information, so you must repeat

Chem & BioOffice 2006/ Chem & BioOffice Introduction 25

Additional Information
 the activation each time you access the page.
If you visit a site frequently, you can add it to the list of
trusted sites in IEs security settings.
Administrator
Site License Network Installation Instruc-
tions
If you have purchased a site license, please see the
following web site for network installation

instructions:
http://www.cambridgesoft.com/services/sl/

26Chem & BioOffice Introduction CambridgeSoft

Additional Information
Section I Chem3D: Introduction
About Chem3D
Chem3D is an application designed to enable
scientists to model chemicals. It combines powerful
building, analysis, and computational tools with a
easy-to-use graphical user interface, and a powerful
scripting interface.
Chem3D provides computational tools based on
molecular mechanics for optimizing models,
conformational searching, molecular dynamics, and
calculating single point energies for molecules.
COEA
Initially developed for Chem3D third-party
interfaces (MOPAC, Gaussian, etc.), COEA
(ChemOffice Extension Architecture) is a
compatible, extendable architecture that can:
Allow any ChemOffice application to perform
calculations using MOPAC, Gaussian, or other
COEA driver.
Allow third-party software providers to embed
their products in CambridgeSoft products.
About CS MOPAC
CS MOPAC is an implementation of the well
known semi-empirical modeling application
MOPAC, which takes advantage of the easy-to-use
interface of Chem3D. CS MOPAC currently
supports MOPAC 2002.
There are two CS MOPAC options available with
Chem3D 10:
MOPAC Ultra
Chem & BioOffice 2006 /Chem3D
MOPAC Pro
MOPAC Ultra is the full MOPAC implementation,
and is only available as an optional addin. The CS
MOPAC Ultra implementation provides support
for previously unavailable features such as
MOZYME and PM5 methods.
MOPAC Pro allows you to compute properties,
perform simple (and some advanced) energy
minimizations, optimize to transition states, and
compute properties. The CS MOPAC Pro
implementation supports MOPAC sparkles, has an
improved user interface, and provides faster
calculations. It is included in some versions of
Chem3D, or may be purchased as an optional
addin. Contact CambridgeSoft sales or your local
reseller for details.
CAUTION
If you have CS MOPAC installed on your computer from
a previous Chem3D or ChemOffice installation,
upgrading to version 10 will remove your existing
MOPAC installation. See the ReadMe for instructions
on saving your existing MOPAC menu extensions.
See Chapter 9, MOPAC Computations on
page 171 for more information on using CS
MOPAC.
About Gaussian
Gaussian is a cluster of programs for performing
semi-empirical and ab initio molecular orbital (MO)
calculations. Gaussian is not included with CS
Chem3D, but is available from SciStore.com,
http://scistore.cambridgesoft.com/software/.
Introduction 27
 When Gaussian is correctly installed, Chem3D New Gaussian Interface
communicates with it and serves as a graphical Predicting Spectra
front end for Gaussians text-based input and
Multi-step Jobs
output.
Partial Optimizations
Administrator

Chem3D is compatible with Gaussian 03 for Input Template

Windows, and requires the 32-bit version.
Advanced Mode
About Jaguar Support for DFT Methods
New SCHRDINGER Jaguar Interface
SCHRDINGER Jaguar is a high-performance
ab initio package for both gas and solution phase Hydrogen Bonding and Polar Hydrogen
simulations, with particular strength in treating Display
metal containing systems. It is a practical quantum Partial Surfaces
mechanical tool for solving real-world problems. Displaying Group Labels
The new Chem3D interface is the only Windows Displaying Measurements
platform GUI for Jaguar. The Demo Toolbar
Image Format Features
Whats New in Chem3D Embedding Models in Other Applications
10? Background Effects and Images
The major emphasis in Chem3D 10 development More Browser Support
was on improving support for calculations. The
following is a list of Chem3D enhancements in For Users of Chem3D 9
Chem & BioOffice 2006:
The following table lists things that have changed or
Enhancements to Chem3D 10 include: moved on the Chem3D 10.GUI.

Feature Chem3D 9 Chem3D 10

Preferences dialog box: on the General tab on the Picture tab

Image export settings

Preferences dialog box: GUI tab Collapse Single Top Level Fragment
Collapse Fragments With Only One
Child

Preferences dialog box: Popup Group Name

tab

28 Introduction CambridgeSoft
Whats New in Chem3D 10?
Feature Chem3D 9 Chem3D 10

Preferences dialog box: Chem- Do Cleanup When Synchronizing

Draw tab

Model Settings dialog box: Hydrogen Bonds

Model Display Modes
Lone Pairs

Model Settings dialog box: Atom Display tab Atom & Bond tab

Bond Size

Model Settings dialog box: Colors and Fonts tab: Background tab
Background

Model Settings dialog box: Highlighted Selected Color

Colors and Fonts tab:

Model Display toolbar Background Effect tool

Residue Label tool

File Menu Import (SDFiles and SYBYL)

Print Preview

View Menu Start Spinning Model Demo Demo toolbar (spinning and
rocking demos, with settings)
Spectrum Viewer

Structure Menu>Measurements Display Distance

Display Bond Angle

Display Dihedral

Chem & BioOffice 2006 /Chem3D Introduction 29

For Users of Chem3D 9
 Feature Chem3D 9 Chem3D 10

Structure Menu Set Target Fragment

Administrator

Clear Target Fragment

Fast Overlay

Unmap Atoms

Show Atom Map Labels

Calculations Menu Dihedral Driver

Surfaces Menu Advanced Molecular Surfaces

Model Explorer: Atom Serial Numbers These settings only appear at the
Context Menu (at Fragment or atom level.
AtomSymbols
Group level)
Atom Dots

Model Explorer: Group Labels

Context Menu
Export to File

Context Menu>Select Select All options

Context Menu>Select> Selects new atoms; deselects orig- Selects new atoms; original atom
Select Atoms Within Distance of inal atom remains selected
Selection or Select Atoms Within
Radius of Selection Centroid

Context Menu>Select> Selects new atoms; original atom Selects new atoms; deselects orig-
Select Atoms Within Distance of remains selected inal atom
Selection or Select Atoms Within
Radius of Selection Centroid
(with Shift key held down)

Context Menu>Visibility Objects are still selected after Objects automatically deselected
change after change

30 Introduction CambridgeSoft
For Users of Chem3D 9
Feature Chem3D 9 Chem3D 10

Context Menu Set Bond Angle Measurement or Set Display Bond Angle Measurement
when selecting atoms that define a Dihedral Measurement or Display Dihedral Measurement
bond angle or a dihedral

For Users of Chem3D The Measurements table has been augmented

Versions 6 to 8
Many features of Chem3D changed in version 9.
Please note the following:
The rotation bars are now dynamic rather than
permanently displayed. See Rotation Bars on
page 34 for details.
Internal rotations have changed. See Rotating
Models on page 119 for details on how to
perform internal rotations.
by three other tables: the Model Explorer, the
Cartesian Coordinates table, and the Z-Matrix
table. See The Model Explorer on page 48,
and Model Coordinates on page 48for more
details.
Menus and toolbars have changed. Consult the
relevant sections of the manual for details.

Chem & BioOffice 2006 /Chem3D Introduction 31

For Users of Chem3D 9
Administrator

32 Introduction CambridgeSoft
For Users of Chem3D 9
Chapter 1: Chem3D Basics
The Graphical User Inter-
face
The Graphical User Interface (GUI) is the part of
Chem3D that you interact with to perform tasks.
The GUI consists of a model window, menus,
toolbars and dialog boxes. It can also include up to
three optional panels that display Output and
Comments boxes, the Model Explorer and tables
(Cartesian coordinates, Z-Matrix, and
Measurement), and the ChemDraw Panel. At the
bottom of the GUI is a Status bar which displays
information about the active frame of your model
and about hidden atoms in your model. The GUI is
shown in Rotation mode with the dynamic Rotation
bars showing, the ChemDraw panel open, and the
Tables panel set to Auto-Hide.
Figure 1-1: Chem3D GUI

Building Toolbar Computation Toolbar Model Display Toolbar ChemDraw Panel

tab
Title bar
Menu bar
Standard
Toolbar

Active
Window
Tab

Model
Explorer tab

Model window

Status bar

Model Window the model, it appears in the Output window or the

Status bar.
The Model window is the work space where you do
your modeling. If there is textual information about

Chem & BioOffice 2006 /Chem3D Chem3D Basics 33

 The following table describes the objects in the Click on a bar and drag to rotate a model around
Model window. that axis. The Rotate About a Bond bar is only
active when a bond or dihedral is selected. Freehand
Object Description rotation is accomplished by dragging in the main
Administrator

window. The cursor changes to a hand when

Model area The workspace where a molec- you are in freehand rotation mode.
ular model is viewed, built,
You can turn off the display (but not the function)
edited, or analyzed. The origin
of the bars with the Show Mouse Rotation Zones
of the Cartesian axes (0,0,0) is
checkbox on the GUI tab of the Preferences dialog
always located at the center of
box (File > Preferences).
this window, regardless of how
the model is moved or scaled. Model display window tabs now have context
The Cartesian axes do not move menus (right-click menus) for saving and closing.
relative to the window.
Figure 2: Window tab context menus

Active Window Chem3D 10 can open multiple

tab models simultaneously. The tab
selects the active window.

Rotation Bars
Chem3D 9 introduces dynamic (auto-hide) rotation
bars. The rotation bars only appear on your screen Preferences Dialog Box
when you are actually using them. To view the GUI customization now includes style options,
dynamic rotation bars you must do two things: window settings, and Model Explorer display
options. The VS 2005 (Whidbey) style option
Activate rotation mode by selecting the Track-
includes smart docking of toolbars. Change settings
ball tool. on the GUI tab of the Preferences dialog box.
Mouse over the rotation bar area.
Figure 1-2: Rotation bars
Z-axis X-axis

Bond axis Y-axis

34 Chem3D Basics CambridgeSoft

Figure 3: GUI Preferences dialog
Menus and Toolbars
All Chem3D commands and functions can be
accessed from the menus or toolbars. The toolbars
contain icons that offer shortcuts to many
commonly used functions. You can activate the
Toolbars you want from the Toolbars submenu of
the View menu.
Toolbars can be attached to any side of the GUI, or
can be torn off and placed anywhere on the
screen for convenience.
TIP: Most Toolbar commands are duplicated from the
menus, and are intended as a convenience. If you only use a
command infrequently, you can save clutter by using the menu
commands.
The File Menu
In addition to the usual File commands, you use the
File menu to access the Chem3D Templates and
Preferences, and the Model Settings.
Import FileImport MOL2 and SD files into
Chem3D a document. The import utility accu-
rately preserves model coordinates.
Chem & BioOffice 2006 /Chem3D
Model SettingsDisplays the Model
Settings dialog box. Set defaults for display
modes and colors, model building, atom and
ligand display, atom labels and fonts, movie and
stereo pair settings, and atom/bond popup
label information.
PreferencesDisplays the Preferences
dialog box. Set defaults for image export,
calculation output path, OpenGL settings and
including hydrogens in CDX format files.
Sample FilesAccesses example models.
The Edit Menu
In addition to the usual Edit functions, you can use
the Edit menu to copy the model in different
formats, to clear the model window, and to select all
or part of the model.
Copy asPuts the model on the Clipboard in
ChemDraw format, as a SMILES string, or in
bitmap format.
Copy As ChemDraw StructurePuts the
model on the Clipboard in CDX format. You
may only paste the structure into an application
that can accept this format, for example Chem-
Draw, ChemFinder, or Chem3D.
Copy As SMILESPuts the model on the
Clipboard as a SMILES string. You may only
paste the structure into an application that can
accept this format.
Copy As PicturePuts the model on the
Clipboard as a bitmap. You may only paste the
structure into an application that can accept
bitmaps.
NOTE: The application you paste into must recognize the
format. For example, you cannot paste a ChemDraw
structure into a Microsoft Word document.
Paste SpecialPreserves coordinates when
pasting a Chem3D model from one document
to another.
Chem3D Basics 35
 ClearClears the model window of all struc-
tures.
Select AllSelects the entire model.
Select FragmentIf you have selected an
Administrator
atom, selects the fragment that atom belongs
to.
The View Menu/Model Display Toolbar
Use the View menu to select the view position and
focus, as well as which toolbars, tables, and panels
are visible. The Model Display submenu of the
View menu duplicates all of the commands in the
Model Display toolbar.
View PositionThe View Position submenu
gives you options for centering the view, fitting
the window, and aligning the view with an axis.
View FocusThe View Focus submenus is
used to set the focus. See View Focus on
page 107
Model DisplayDuplicates the Model
Display toolbarContains tools to control the
display of the model. These tools are dupli-
cated on the View menu..
Show Atom LabelsA toggle switch to
display or hide the atom labels.
Show Serial NumbersA toggle switch to
display or hide the atom numbers.
Show Atom DotsDisplays or hides atom
dot surfaces for the model. The dot surface is
based on VDW radius or Partial Charges, as
set in the Atom Display table of the Model
Settings dialog box.
Show Atom SpheresDisplays or hides
atom spheres for the model. The radius is
based on VDW radius or Partial Charges, as
set in the Atom Display table of the Model
Settings dialog box.
Show Hs and LpsA toggle switch to
display or hide hydrogen atoms and lone
pairs.
36 Chem3D Basics
Red and Blue glassesA toggle switch to
set the display for optimal viewing with red-
blue 3D glasses to create a stereo effect.
Stereo PairsA toggle switch to enhance
three dimensional effect by displaying a
model with two slightly different
orientations. It can also create orthogonal
(simultaneous front and side) views. The
degree of separation is set on the Stereo View
tab of the Model Settings dialog box.
PerspectiveA toggle switch to create a
perspective rendering of the model by
consistent scaling of bond lengths and atom
sizes by depth. The degree of scaling is
controlled by the Perspective Field of View
slider on the Model Display tab of the Model
Settings dialog box.
Depth FadingA toggle switch to create a
realistic depth effect, where more distant
parts of the model fade into the background.
The degree of fading is controlled by the
Depth Fading Field of View slider on the
Model Display tab of the Model Settings
dialog box.
Model AxesDisplays or hides the Model
axes.
View AxesDisplays or hides the view
axes.
NOTE: When both axes overlap and the Model axes
are displayed, the View axes are not visible.
Background ColorDisplays the
Background color select toolbar. Dark
backgrounds are best for viewing protein
ribbon or cartoon displays. Selecting red-
blue or Chromatek 3D display will
automatically override the background color
to display the optimal black background.
Background colors are not used when
printing, except for Ribbon displays. When
saving a model as a GIF file, the background
CambridgeSoft
 will be transparent, if you have selected that
option for Image Export in the Preferences
dialog box.
Color BySelects the model coloring
scheme. See Coloring Displays on page 79
for more information.
ToolbarsClick the name of a toolbar to
select it for display. Click again to deselect. You
can attach a toolbar to any side of the GUI by
dragging it to where you want it attached. If
you are using a floating toolbar, you can change
its shape by dragging any of its edges.
Standard toolbarContains standard file,
edit, and print tools. The commands are
duplicated on the File and Edit menus.
Building toolbarContains the Select,
Translate, Rotate, and Zoom tools in
addition to the model building tools
bonds, text building tool, and eraser. These
tools are not duplicated on any menu. This
toolbar is divided into safe and unsafe
tools. The four safe tools on the left
control only the view they do not affect
the model in any way. This includes the new
safe select tool and the new translate
tool . The old select tool is now
called the Move tool. Although it can also be
used to select, its primary use is to move
atoms and fragments.
Model Display toolbarContains tools to
control the display of the model. These tools
are duplicated on the View menu.
Surfaces toolbarContains tools to
calculate and display a molecular surface.
Molecular Surface displays provide
information about entire molecules, as
opposed to the atom and bond information
provided by Structure displays.
Movies toolbarContains tools for the
creation and playback of movies. Chem3D
movies are animations of certain
Chem & BioOffice 2006 /Chem3D
visualization operations, such as iterations
from a computation. They can be viewed in
Chem3D, or saved in Windows AVI movie
format. The commands are reproduced on
the Movie menu.
Calculation toolbarPerforms MM2
minimization from a desktop icon. The
spinning- arrow icon shows when any
calculation is running, and the Stop icon can
be used to stop a calculation before its
preset termination.
Status barDisplays the Status bar, which
displays information about the active frame
of your model.
CustomizeDisplays the Customize
dialog box. Customizing toolbars is a
standard MS Windows operation, and is not
described in Chem3D documentation.
Model ExplorerDisplays a hierarchical tree
representation of the model. Most useful when
working with complex molecules such as
proteins, the Model Explorer gives you highly
granular control over the model display.
ChemDraw PanelDisplays the ChemDraw
Panel. Use the ChemDraw Panel to build mole-
cules quickly and easily with familiar Chem-
Draw drawing tools. You can import, export,
edit, or create small molecules quickly and
easily using the ChemDraw ActiveX tools
palette.
Cartesian TableDisplays the Cartesian
Coordinates table. Cartesian Coordinates
describe atomic position in terms of X-, Y-,
and Z-coordinates relative to an arbitrary
origin.
Z-Matrix TableDisplays the internal coor-
dinates, or Z-Matrix, table. Internal coordi-
nates are the most commonly used coordinates
for preparing a model for further computation.
Chem3D Basics 37
 Measurements TableDisplays the
Measurements table.The Measurements table
displays bond lengths, bond angles, dihedral
angles, and ring closures.
Administrator
Parameters TablesDisplays a list of
external tables that are used by Chem3D to
construct models, perform computations and
display results.
Output BoxDisplays the Output box,
which presents textual information about the
model, iterations, etc.
Comments BoxDisplays the Comments
box, a place for user comments that is stored
with the file.
Dihedral ChartOpens the window
displaying results of Dihedral Driver MM2
computation. See Tutorial 5: Mapping
Conformations with the Dihedral Driver on
page 62 for more information.
Status BarDisplays or hides the Status Bar.
Start Spinning Model DemoSpins the
model on the Y axis. Use stop calculation
on the Calculations toolbar to stop the demo.
Full ScreenActivates the full screen display.
The Structure Menu
The Structure menu commands populate the
Measurements table and control movement of the
model.
The Measurements submenu
Set MeasurementsSets a
measurementbond length, angle, or
distanceaccording to what is selected.
Bond LengthsDisplays bond lengths in
the Measurements Table. The Actual values
come from the model and the Optimal
values come from the Bond Stretching
Parameters external table.
38 Chem3D Basics
Bond AnglesDisplays bond angles in the
Measurements Table. The Actual values
come from the model and the Optimal
values come from Angle Bending
Parameters and other external tables.
Dihedral AnglesDisplays dihedral angles
in the Measurements Table. The Actual
values come from the model and the
Optimal values come from Angle Bending
Parameters and other external tables.
ClearClears the entire Measurement
table. If you only want to clear part of the
table, select the portion you want to clear,
and choose Delete from the context menu.
The Model Position submenu
Center Model on OriginResizes and
centers the model in the model window after
a change to the model is made.
Center Selection on OriginResizes and
centers the selected portion of the model in
the model window.
Align Model With X AxisWhen two
atoms are selected, moves them to the X-
axis.
Align Model With Y-axisWhen two
atoms are selected, moves them to the Y-
axis.
Align Model With Z-axisWhen two
atoms are selected, moves them to the Z-
axis.
Align Model With XY PlaneWhen
three atoms are selected, moves them to the
XY-plane.
Align Model With XZ PlaneWhen
three atoms are selected, moves them to the
XZ-plane.
Align Model With YZ PlaneWhen
three atoms are selected, moves them to the
YZ-plane.
CambridgeSoft
The Reflect Model submenu
Through XY PlaneReflects the model
through the XY plane by negating Z
coordinates. If the model contains any chiral
centers this will change the model into its
enantiomer. Pro-R positioned atoms will
become Pro-S and Pro-S positioned atoms
will become Pro-R. All dihedral angles used
to position atoms will also be negated.
Through XZ PlaneReflects the model
through the XZ plane by negating Y
coordinates. If the model contains any chiral
centers this will change the model into its
enantiomer. Pro-R positioned atoms will
become Pro-S and Pro-S positioned atoms
will become Pro-R. All dihedral angles used
to position atoms will also be negated.
Through YZ PlaneReflects the model
through the YZ plane by negating X
coordinates. If the model contains any chiral
centers this will change the model into its
enantiomer. Pro-R positioned atoms will
become Pro-S and Pro-S positioned atoms
will become Pro-R. All dihedral angles used
to position atoms will also be negated.
Invert Through OriginReflects the
model through the origin, negating all
Cartesian coordinates. If the model contains
any chiral centers this will change the model
into its enantiomer. Pro-R positioned atoms
will become Pro-S and Pro-S positioned
atoms will become Pro-R. All dihedral
angles used to position atoms will also be
negated.
The Set Z-Matrix submenu
Set Origin Atom(s) fileSets the selected
atom(s) as the origin of the internal
coordinates. Up to three atoms may be
selected. Setting Measurements on page
107
Chem & BioOffice 2006 /Chem3D
Position by DihedralsPositions an atom
relative to three previously positioned atoms
using a bond distance, a bond angle, and a
dihedral angle. For more information on
changing the internal coordinates see
Setting Dihedral Angles on page 108.
Position by Bond AnglesPositions an
atom relative to three previously positioned
atoms using a bond distance and two bond
angles. For more information on changing
the internal coordinates see Setting Bond
Angles on page 108.
Detect StereochemistryScans the model
and lists the stereocenters in the Output box.
InvertInverts the isomeric form. For
example, to invert a model from the cis- form
to the trans- form, select one of the stereo
centers and use the Invert command.
Deviation from PlaneWhen you select four
or more atoms, outputs the RMS deviation
from the plane to the Output window.
Add CentroidAdds a centroid to a selected
model or fragment. At least two atoms must be
selected. The centroid and bonds to the
selected atoms are displayed, and bond
lengths can be viewed in the tool tips. To delete
a centroid, select it and press the Delete or
Backspace key.
RectifyFills the open valences for an atom,
usually with hydrogen atoms. This command is
only useful if the default automatic rectification
is turned off in the Model Settings dialog box.
Clean UpCorrects unrealistic bond lengths
and bond angles that may occur when building
models, especially when you build strained ring
systems.
OverlayThe Overlay submenu provides all
of the commands to enable you to compare
fragments by superimposing one fragment in a
model window over a second fragment. Two
types of overlay are possible: quick, and mini-
Chem3D Basics 39
 mization. See Tutorial 6: Overlaying Models Figure 1-4: The Building toolbar
on page 63, and Comparing Models by
Overlay on page 134 for information on each Safe Select tool (view only)
overlay type.
Administrator

Translate tool
DockThe Dock command enables you to
position a fragment into a desired orientation Trackball tool
and proximity relative to a second fragment. Rotation Dial activator
Each fragment remains rigid during the
docking computation. Zoom tool

The Standard Toolbar Move tool

The Standard toolbar contains tools for standard Single Bond tool
Windows functions, including up to 20 steps of
Undo and Redo. Double Bond tool

Figure 1-3: The Standard toolbar Triple Bond tool

New File Uncoordinated Bond tool

Open File
Save File Text tool

Eraser tool
Copy
Cut
Paste
The Rotation Dial, activated by clicking the arrow
Undo under the Trackball tool, lets you rotate a model an
exact amount. Select an axis, then drag the dial or
type a number into the box.
Redo
Figure 1-5: The Rotation dial
Print

About Chem3D

The Building Toolbar

For detailed descriptions of the tools see Building
The Building toolbar contains tools that allow you With the Bond Tools on page 97, Rotating
to create and manipulate models. The tools are Models on page 119, and Resizing Models on
shown below. page 124.

40 Chem3D Basics CambridgeSoft

The Model Display Toolbar
The Model Display toolbar contains tools for all of
the Chem3D display functions. The Model type and
Background color tools activate menus that let you
choose one of the options. All of the remaining
tools are toggle switchesclick once to activate;
click again to deactivate.
Figure 1-6: The Model Display toolbar
The Surfaces Toolbar
The Surfaces toolbar controls the display of
molecular surfaces. In most cases, you will need to
do either an Extended Hckel, MOPAC, or
Gaussian calculation before you can display
surfaces.
Figure 1-7: The Surfaces toolbar

Model type Surface

Solvent radius
Background Color

Stereo Visualization Display mode

Red-Blue Stereo
Color Mapping
Chromatek Stereo

Perspective Surface color

Depth Fading
Resolution

Model Axes
HOMO/LUMO selection
View Axes

Isovalues
Atom labels

Atom numbers
Color A

Full screen mode

Color B
Spinning model demo

For more information on Surfaces, see Molecular

Surface Displays on page 84.

Chem & BioOffice 2006 /Chem3D Chem3D Basics 41

 The Movie Toolbar Figure 1-9: The Demo toolbar

The Movie toolbar controls the creation and

playback of animations. You can animate certain
visualization operations, such as iterations from a
Administrator

computation, by saving frames in a movie. Movies

can be saved as Windows AVI video files. Spin Rock Axis Speed Amplitude Stop

Figure 1-8: The Movie toolbar Set the Speed and the rocking Amplitude. Choose
and axis. In addition to the X, Y, and Z axes, you
Play
may select a bond to spin or rock, and use the
Selected option. Stop the demo by either clicking
Stop the Spin or Rock button a second time, or use the
Stop button.
First frame
The Calculation Toolbar
Previous Frame The Calculation toolbar provides a desktop icon for
performing the most common calculation, MM2
Position minimization. It also provides a Stop button and a
calculation running indicator that work with all
calculations.
Next frame
Figure 1-10:The Calculation toolbar
Last frame

Calculation indicator
Delete

MM2 minimization
Delete all

Stop button
Properties

The ChemDraw Panel

For more information on Movies, see Creating
and Playing Movies on page 139.
The Demo Toolbar
A new Demo toolbar lets you set properties for
spinning and rocking models.
Chem3D 10 makes it easier than ever to create or
edit models in ChemDraw. The ChemDraw panel is
activated from the View menu. By default it opens
on the right side of the GUI, but like the toolbars
you can have it float or attach it anywhere you
like.

42 Chem3D Basics CambridgeSoft

Figure 1-11: The ChemDraw panel The Model Information
Close panel
Auto-Hide
Panel
The Model information panel contains information
Synchronize about the model in the top-most tabbed window
Draw > 3D add
and its display. You can display one or more of the
Draw>3D following tables in the area:
replace
Model Explorer
3D>Draw
Measurements
Clean up
structure Cartesian Coordinates
Clear Z-Matrix table
Lock Tables are linked to the structure so that selecting
Name=Struct an atom, bond, or angle in either will highlight both.
Numerical values in the tables can be edited or cut
and pasted to/from other documents (text or Excel
worksheets), and the changes are displayed in the
structure.
ChemDraw
ActiveX tool
All of the tables have an Auto-hide feature to
palette minimize their display. For more information on
Model Tables, see Model Coordinates on page
Use the 3D > Draw icon to drag a Chem3D model 48.
into the ChemDraw panel. Figure 1-12: The Z-Matrix table
To create a model in ChemDraw, click in the Column Field Name Cell
ChemDraw panel to activate the ChemDraw Record
Heading
Selector Column Divider
toolbar. Use the Draw>3D Add or Draw>3D Replace
icons to put the model in Chem3Dor select the
Synchronize icon to draw in both simultaneously.
You can also create a model by typing the name of
a compoundor a SMILES stringinto the
Name=Struct box. When you finish editing, add
or replace your Chem3D model by clicking the
appropriate icon.

Chem & BioOffice 2006 /Chem3D Chem3D Basics 43

 The following table describes the elements of the 1. Right-click in the window and choose Export.
Measurement table. A Save As dialog box appears.
2. Enter a name for the file, select a file format
Table Element Description (.html or .txt) and click Save.
Administrator

Column Heading Contains field names
describing the information in
the table.
Record Selector Used to select an entire
record. Clicking a record
selector highlights the corre-
sponding atoms in the model
window.
Field Name Identifies the type of infor-
mation in the cells with
which it is associated.
Column Divider Used to change the width of
the column by dragging.
Cell Contains one value of one
field in a record. All records
in a given table contain the
same number of cells.
To save information with the clipboard:
1. Select the text you want to save.
2. Right-click in the window and choose Copy.
Alternately, you can choose Select All from the
context menu.
3. Paste into the document of your choice.
You must use Copy Paste to restore information
from a saved file.
You can remove information from the Output
window without affecting the model.
To remove messages:
1. Select the text you want to delete.
2. Do one of the following:
From the context menu, choose Clear.
Press the Delete or Backspace key.
The Comments window gives you a place to add
notes and comments about the model. When you
save a model, comments are also saved.

The Output and Comments Model Building Basics

Windows
The Output and Comments boxes are typically
found at the bottom of the GUI window. You can
have them float if you wish, or move them to
another side of the window. You can select Auto-
hide to minimize them.
Calculations on models and other operations
produce messages that are displayed in the Output
window.You can save the information in the
Output window either directly or using the
clipboard. To save information directly:
As you create models, Chem3D applies standard
parameters from external tables along with user-
selected settings to produce the model display.
There are several options for selecting your desired
display settings: you can change defaults in the
Model Settings dialog box, use menu or toolbar
commands, or use context-sensitive menus (right-
click menus) in the Model Explorer. You can also
view and change model coordinates.
Internal and External Tables
Chem3D uses two types of parameter tables:

44 Chem3D Basics CambridgeSoft

Model Building Basics
 Internal tablesContain information about a To view an external table:
specific model. Point to Parameter Tables on the View menu,
Examples of internal tables are: then choose the table to view.

TIP: You can superimpose multiple tables if you

Measurements table
attach them to an edge of the GUI. One table will be
Z-Matrix table visible and the others will display as selection tabs.
Attached tables have the Auto-hide feature.
Internal coordinates table
To auto-hide a table:
External tablesContain information used
Push the pin in the upper right corner of the
by all models.
table.
Examples of external tables are: The table minimizes to a tab when you are not
using it.
Elements, Atom Types, and Substructures
tables that you use to build models. The Model Setting Dialog
Torsional Parameters tables that are used by Box
Chem3D when you perform an MM2 The Chem3D Model Settings dialog box allows
computation. you to configure settings for your model.
Tables that store data gathered during To open the Chem3D Model Settings dialog box:
Dihedral Driver conformational searches. From the File menu, choose Model Settings.
Standard MeasurementsStandard The Model Settings dialog box appears:
measurements are the optimal (or equilibrium) Figure 1-13: The Settings dialog box
bond lengths and angles between atoms based on
their atom type. The values for each particular atom
type combination are actually an average for many
compounds each of which have that atom type (for
example, a family of alkanes). Standard
measurements allow you to build models whose 3D
representation is a fair approximation of the actual
geometry when other forces and interactions
between atoms are not considered.

For more information on External Tables, see

Parameter Tables on page 251.

To view an internal table:

Choose the table from the View menu.

Chem & BioOffice 2006 /Chem3D Chem3D Basics 45

Model Building Basics
 The settings are organized into tabbed panels. To
select a control panel, click one of the tabs at the
top of the dialog box.
Administrator
In the Model Settings dialog box, select the
Atom Labels tab, and check the box next to
Show Element Symbols and Show Serial
Numbers.

Model Display
The serial number for each atom is assigned in the
The model of ethane shown below displays the order of building. However, you can reserialize the
cylindrical bonds display type (rendering type) with atoms. For more information see Setting Serial
the element symbols and serial numbers for all Numbers on page 109.
atoms.
The element symbol comes from the Elements
Figure 1-14: Model display table. The default color used for an element is also
Atom serial numbers defined in the Elements table. For more
Element symbols information, see Coloring by Element on page 79
and The Elements on page 254.

Model Data Labels

When you point to an atom, information about the
atom appears in a model label pop-up window. By
default, this information includes the element
symbol, serial number, atom type, and formal
charge.

Figure 1-15 shows the model label for the C(1)

To specify the rendering type do one of the atom of ethane.
following:
Figure 1-15: Atom labels
From the View menu, point to Model Display,
then Display Mode, and select a rendering type.
Activate the Model Display toolbar, click the
arrow next to the Model Display icon ,
and select a rendering type.
In the Model Settings dialog box, choose
Model Display, and select a rendering type.

To specify the display of serial numbers and

element symbols, do one of the following:
On the View menu, point to Model Display,
then click Show Serial Number or Show Atom
Label.
Activate the Model Display toolbar and click
the Atom Labels and Serial Numbers icons.

46 Chem3D Basics CambridgeSoft

Model Building Basics
The model data changes when you point to a bond If you select four contiguous atoms the dihedral
instead of an atom. angle appears in the model label. If you select two
bonded or non-bonded atoms, the distance
Figure 1-16 shows the model label for the bond
between those atoms appears.
between C(1) and C(2).
Figure 1-16: Bond labels To specify what information appears in atom, bond,
and angle labels:

In the Model Settings dialog box, select the

Pop-up Info tab, then select the information you
want to display.

Atom Types

Atom types contain much of the Chem3D chemical

The model data changes to reflect the atoms that
are selected in the model. For example, when three
contiguous atoms H(3)-C(1)-C(2) are selected, the
model label includes the atom you point to and its
atom type, the other atoms in the selection, and the
angle.
Figure 1-17: Model label
these atoms are selected
they are displayed in yellow
in Chem3D
intelligence for building models with reasonable 3D
geometries. If an atom type is assigned to an atom,
you can see it in the model data when you point to
it. In the previous illustration of pointing
information, the selected atom has an atom type of
C Alkane.
An atom that has an atom type assigned has a
defined geometry, bond orders, type of atom used
to fill open valences (rectification), and standard
bond length and bond angle measurements
(depending on the other atoms making up the
bond).
The easiest way to build models uses a dynamic
assignment of atom types that occurs as you build.
For example, when you change a single bond in a
model of ethane to a double bond, the atom type is
automatically changed from C Alkane to C Alkene.
In the process, the geometry of the carbon and the
number of hydrogens filling open valences changes.

You can also build models without assigning atom

types. This is often quicker, but certain tasks, such
as rectification or MM2 Energy Minimization, will
also correct atom types because atom types are
required to complete these tasks.

Chem & BioOffice 2006 /Chem3D Chem3D Basics 47

Model Building Basics
 To assign atom types as you build:
In the Chem3D Model Settings dialog box,
select the Model Build tab, then check the
Correct Atom Types checkbox.
Administrator
To assign atom types after building:
Select the atom(s) and use the Rectify command
on the Structure menu.
Atom type information is stored in the Atom Types
table. To view the Atom Types table:
From the View menu, select Parameter Tables,
then select atom types.xml.
Rectification
Rectification is the process of filling open valences
of the atoms in your model, typically by adding
hydrogen atoms.
To rectify automatically as you build, do the
following:
In the Chem3D Model Settings dialog box,
select the Model Build tab, then check the
Rectify checkbox.
If you activate automatic rectification in the Model
Settings dialog box, you have the option of
showing or hiding hydrogens. If you turn off
automatic rectification, the Show Hs and Lps
command on the Model Display submenu of the
View menu is deactivated, and you will not have the
option of displaying hydrogens.
Bond Lengths and Bond Angles
You can apply standard measurements (bond
lengths and bond angles) automatically as you build
or apply them later. Standard measurements are
determined using the atom types for pairs of
bonded atoms or sets of three adjacent atoms, and
are found in the external tables Bond Stretching
Parameters.xml and Angle Bending Parameters.xml.
48 Chem3D Basics
The Model Explorer
The Model Explorer allows users to explore the
hierarchical nature of a macromolecule and alter
properties at any level in the hierarchy. Display
modes and color settings are easy to control at a
fine-grained level. Properties of atoms and bonds
are easy to access and change.
The Model Explorer is designed as a hierarchical
tree control that can be expanded/collapsed as
necessary to view whatever part of the model you
wish. Changes are applied in a bottom-up manner,
so that changes to atoms and bonds override
changes at the chain or fragment level. You can
show/hide/highlight features at any level. Hidden
or changed features are marked in the hierarchical
tree with colored icons, so you can easily keep track
of your edits. See Working With the Model
Explorer on page 136 for more information.
Model Coordinates
Each of the atoms in your model occupies a
position in space. In most modeling applications,
there are two ways of representing the position of
each atom: internal coordinates and Cartesian
coordinates. Chem3D establishes internal and
Cartesian coordinates as you build a model.
Z-matrix
Internal coordinates for a model are often referred
to as a Z-matrix (although not strictly correct), and
are the most commonly used coordinates for
preparing a model for further computation.
Changing a Z-matrix allows you to enter relations
between atoms by specifying angles and lengths.
You display the Z-Matrix table by selecting it from
the View menu. You can edit the values within the
table, or move atoms within the model and use the
Set Z-matrix submenu of the Structure menu. You
CambridgeSoft
Model Building Basics
can copy and paste tables to text (.txt) files or Excel Figure 1-19: Cartesian coordinates
spreadsheets using the commands in the context
(right-click) menu.
Figure 1-18 shows an example of the internal
coordinates (Z-matrix) for ethane:7
Figure 1-18: Internal coordinates

The Measurements Table

Cartesian Coordinates
Cartesian coordinates are also commonly accepted
as input to other computation packages. They
describe atomic position in terms of X-, Y-, and
Z-coordinates relative to an arbitrary origin. Often,
the origin corresponds to the first atom drawn.
However, you can set the origin using commands in
the Model Position submenu of the Structure menu.
Instead of editing the coordinates directly in this
table, you can save the model using the Cartesian
Coordinates file format (.cc1 or .cc2), then edit that
file with a text editor. You can also copy and paste
the table into a text file or Excel worksheet using
the commands in the context (right-click) menu.
The Measurements table displays bond lengths,
bond angles, dihedral angles, and ring closures.
When you first open a Measurements Table, it will
be blank.
To display data in a Measurements Table:
From the Structure menu, point to Measure-
ments, then select the information you wish to
display.
Figure 1-20 shows the display of Bond Lengths and
Bond Angles for ethane:
Figure 1-20: The Measurements table

NOTE: If you do edit coordinates in the table, remember to

turn off Rectify and Apply Standard Measurements in
the Model Build panel of the Model Settings dialog while you
edit so that other atoms are not affected.

An example of the Cartesian coordinates for ethane

is shown in Figure 1-19.

If you edit the Actual field, you change the value in

the model, and see atoms in the model move.

Chem & BioOffice 2006 /Chem3D Chem3D Basics 49

Model Building Basics
 If you edit the Optimal value, you apply a constraint. To delete records:
These values are used only in Clean Up (on the
Structure menu) and MM2 computations. Select the records and click Delete on the
context menu.
Administrator

Deleting Measurement Table Data

You can isolate the information you in the
Measurements table by deleting the records that
you do not want to view. For example, you could
display bond lengths, then delete everything except
the carbon-carbon bonds. This would make them
easier to compare.
Deleting records in a Measurements table does
not delete the corresponding atoms.
To clear the entire table:
On the Measurement submenu of the Struc-
ture menu, select Clear.

50 Chem3D Basics CambridgeSoft

Model Building Basics
Chapter 2: Chem3D Tutorials
Overview From the File menu, open the Model Settings
dialog box. Click the Reset button.
The following section gives detailed examples of
some general tasks you can perform with Chem3D. Open a new model window if one is not already
For examples of MOPAC calculations, see Chapter opened. To view models as shown in this tutorial,
9, MOPAC Computations on page 171. select Cylindrical Bonds from the drop-down menu
of the Model Display mode tool on the Model
In this section: Display toolbar.
Tutorial 1: Working with ChemDraw on Figure 2-21: Setting the model display mode
page 51.
Tutorial 2: Building Models with the Bond
Tools on page 52.
Tutorial 3: Building Models with the Text
Building Tool on page 56.
Tutorial 4: Examining Conformations on
page 59. The installation default for the ChemDraw panel is
Tutorial 5: Mapping Conformations with the activated, hidden. You should see a tab labeled
Dihedral Driver on page 62. ChemDraw on the upper right side of the GUI.
Tutorial 6: Overlaying Models on page 63. Figure 2-22: The ChemDraw tab
Tutorial 7: Docking Models on page 65.
Tutorial 8: Viewing Molecular Surfaces on
page 68. ChemDraw tab
Tutorial 9: Mapping Properties onto
Surfaces on page 69.
Tutorial 10: Computing Partial Charges on
page 71.

Tutorial 1: Working with If you do not see the tab:

ChemDraw
The following tutorial introduces model building
with Chem3D. It assumes that no defaults have
been changed since installation. If what you see is
not like the description, you may need to reset the
defaults. To reset defaults:
1. From the View menu, select ChemDraw Panel.
The ChemDraw Panel opens in its default
position, attached to the right edge of the
model window.
If the tab is visible:

Chem & BioOffice 2006 /Chem3D Chem3D Tutorials 51

Tutorial 1: Working with ChemDraw
 2. Click the ChemDraw tab to open the panel.
TIP: The panel default is Auto-hide. If you want the
panel to stay open, push the pin on the upper right.
Administrator
You can turn off the hot linking by clicking the
Synchronize button. If you do this, you will need to
use the 3D>Draw and Draw>3D buttons to copy
models between the windows.

pin
Figure 2-24: ChemDraw panel functions
Synchronize Draw>3D replace Name=Struct
Cleanup text box
3. Click in the ChemDraw panel it.
A blue line appears around the ChemDraw
Panel model window, and the ChemDraw tools Draw>3D add 3D>draw Clear Lock
palette appears.
4. On the ChemDraw tools palette, select the TIP: Use Ctrl+A to select the model you want to copy.
Benzene Ring tool.
5. Click in the panel to place a benzene ring.
Tutorial 2: Building
The ChemDraw structure is converted into a
3D representation. Models with the Bond
Figure 2-23: Creating a 3D model from the Chem- Tools
Draw panel
Draw ethane using a bond tool.
1. Click the Single Bond tool .
2. Point in the model window, drag to the right
and release the mouse button.
A model of ethane appears. When you rotate
the model in a later step, you will see the other
hydrogen.
Figure 2-25: Ethane model

You can work with the model in Chem3D. The 2D

and 3D models are hot-linked, so any change in one
changes the other:
1. Double-click one of the hydrogens in the 3D
model.
A text box appears. NOTE: If you are using default settings, hydrogens are
displayed automatically.
2. Type OH in the text box, then hit the Enter key.
3. A phenol molecule is displayed in both the To see the three-dimensionality of your model you
Chem3D model window and the ChemDraw can perform rotations using the Trackball tool. The
window. Trackball Tool mimics a sphere in which your

52 Chem3D Tutorials CambridgeSoft

Tutorial 2: Building Models with the Bond Tools
model is centered. You can rotate your model by 3. Release the mouse button when the model is
rotating the sphere. You have a choice of free-hand orientated approximately like this:
rotation, or rotating around the X, Y, or Z axis.
Figure 2-26: Orienting a model
To perform free-hand rotation of the model with
the Trackball tool:

1. Click the Trackball tool .

2. Point near the center of the model window and
hold down the mouse button.
3. Drag the cursor in any direction to rotate the
model.
Examine the atoms and bonds in the model using
CAUTION the Select tool.

Users familiar with earlier versions of Chem3D should be 1. Click the Select tool .
aware of changed behavior: the Trackball tool rotates the
2. Move the pointer over the far left carbon.
view only, it does not change the atoms Cartesian
coordinates.
NOTE: Depending on how much you rotated the
model, the far left carbon might be C(2).
To rotate around an axis:
An information box appears next to the atom
1. Move the cursor to the edge of the model you are pointing at. The first line contains the
window. atom label. In this case, you are pointing to
C(1). The second line contains the name of the
As you mouse over the edge of the window, the atom type, C Alkane.
rotation bars will appear.
Figure 2-27: Viewing the atom label
NOTE: Rotation bars are only available when you
are using the Trackball tool.

2. Drag on one of the bars to rotate the model on

that axis.
One of the bars is labeled Rotate About Bond.
You wont be able to select that one. Youll
cover rotating around bonds later.

TIP: Once you start dragging, you dont have to stay

within the rotation bars boundaries. Your model will
only rotate around the chosen axis no matter where you
3. Move the pointer over the C-C bond to display
drag your mouse.
its bond length and bond order.

Chem & BioOffice 2006 /Chem3D Chem3D Tutorials 53

Tutorial 2: Building Models with the Bond Tools
 Figure 2-28: Viewing bond length
Administrator
To display information about angles, select several
atoms.
1. Click C(1), then Shift+click C(2) and H(7).
2. Point at any of the selected atoms or bonds.
The angle for the selection appears.
Figure 2-29: Viewing bond angles
To display information about contiguous atoms:
1. Hold the Shift key and select four contiguous
atoms.
2. Point at any portion of the selection.
The dihedral angle formed by those four atoms
is displayed.
54 Chem3D Tutorials
Figure 2-30: Viewing a dihedral angle
Change the ethane model to an ethylene model.
1. Click the Double Bond tool .
2. Drag the mouse from C(1) to C(2).
3. Point to the bond.
The bond length decreases and the bond order
increases.
Figure 2-31: Changing the bond length by changing
bond order
Continue to build on this model to build
cyclohexane.
1. Click the Select tool .
2. Click the double bond.
3. Right click, point to Bond(s), then to Order, and
choose Single Bond.
The bond order is reduced by one.
Hide the hydrogens to make it easier to build.
CambridgeSoft
Tutorial 2: Building Models with the Bond Tools
 On the Model Display submenu of the View Figure 2-34: Viewing model data when closing a ring
menu, deselect Show Hs and Lps.
The hydrogens are hidden.

Add more atoms to the model:

1. Click the Single Bond tool .

2. Drag upward from the left carbon.

3. Another C-C bond appears.

Figure 2-32: Building with the bond tool: step 1

2. Release the mouse button to close the ring.

Figure 2-35: Building cyclohexane with the bond tool

4. Continue adding bonds until you have 6

carbons as shown below.
Figure 2-33: Building with the bond tool: step 5

Add serial numbers and atom labels.

1. On the Model Display submenu of the View

menu, select Show Serial Numbers, or click the
Serial Number icon on the Model Display
toolbar.
2. On the Model Display submenu of the View
menu, select Show Atom Labels, or click the
Create a ring: Atom Label icon on the Model Display
toolbar.
1. Drag from one terminal carbon across to the
other. NOTE: The serial numbers that appear do not reflect
a normal ordering because you started with a smaller
The pointing information appears when you
model and built up from it.
drag properly.

Chem & BioOffice 2006 /Chem3D Chem3D Tutorials 55

Tutorial 2: Building Models with the Bond Tools
 You can reserialize the atoms as follows:
1. Select the Text Building tool . Computations on page 157 andAppendix H:
2. Click the first atom.
Administrator
A text box appears on the atom.
Figure 2-36: Adding atom labels and numbers
3. Type the number you want to assign to this
atom (1 for this example).
4. Press the Enter key.
The first atom is renumbered as (1).
5. Double-click each of the atoms in the order
you want them to be numbered.
Each time you double-click an atom to serialize
it, the new serial number is one greater than the
serial number of the previously serialized atom.
6. From the Model Display submenu of the View
menu, choose Show Hs and Lps and examine
the model using the Trackball Tool . 2. Locate and select the file, tut1, that you created
The hydrogens appear as far apart as possible.
Because you built the structure by using bond tools,
you may have distorted bond angles and bond
lengths.
To correct for distorted angles and lengths:
1. From the Edit menu, choose Select All.
All of the atoms in the model are selected.
2. From the Structure menu, choose Clean Up
Structure.
To locate an energy minimum for your structure
which represents a stable conformation of your
model, click the MM2 Minimize Energy tool
on the Calculation toolbar.
56 Chem3D Tutorials
Tutorial 3: Building Models with the Text Building Tool
For more information about MM2 and energy
minimization see Chapter 8, MM2 and MM3
MM2.
After the minimization is complete:
1. From the File menu, choose Save.
2. Select a directory in which to save the file.
3. Type tut1 in the text box at the bottom of the
dialog box.
4. Click Save.
5. Click the model window to activate it.
6. From the File menu, choose Close Window.
Tutorial 3: Building
Models with the Text
Building Tool
This tutorial illustrates alternative methods to build
models using the Text Building Tool. You will start
by opening the file you saved in the first tutorial:
1. From the File menu, choose Open.
in the previous tutorial.
3. Click Open.
Replacing Atoms
To change one element into another:
1. Click the Text Building tool .
2. Click a hydrogen atom attached to C(1).
A text box appears.
3. Type C.
NOTE: Element symbols and substructure names are
case sensitive. You must type an uppercase C to create a
carbon atom.
4. Press the Enter key.
CambridgeSoft
 The hydrogen attached to C(1) is changed to a Using Labels to Create
carbon. The valence is filled with hydrogens to
form a methyl group because Automatic
Models
Rectification is turned on. You can also create models by typing atom labels
You dont have to select the Text tool in order to (element symbols and numbers) into a text box.
use it. Double-clicking with any other tool selected Figure 2-37: Creating a model with the text box
has the same effect as single-clicking with the Text CH3
tool. To demonstrate this, lets replace two more H2 H
hydrogens using an alternative method: H3C C C C CH3
H

1. Select the Trackball tool so that you can OH

rotate your model to get a better view of what
you are building.
2. Double-click two more hydrogens to change
them to methyl groups.
TIP: Notice that the C you entered previously in the
Text tool remains as the default until you change it. You only
have to double-click, and press the Enter key.
Now, refine the structure to an energy minimum to
take into account the additional interactions
imposed by the methyl groups by clicking the MM2
tool on the Calculation toolbar.
When the minimization is complete:
1. From the File menu, choose Save As.
2. Type tut2a.
To build the model of 4-methyl-2-pentanol shown
above:
1. From the File menu, choose New, or click the
new file tool on the Standard toolbar.
2. Click the Text Building tool .
3. Click in the empty space in the model window.
A text box appears where you clicked.
4. In the text box, type
CH3CH(CH3)CH2CH(OH)CH3.
You type labels as if you were naming the
structure: pick the longest chain of carbons as
the backbone, and specify other groups as
substituents. Enclose substituents in
parentheses after the atom to which they are
attached.
5. Press the Enter key.

3. Select a directory in which to save the file.
4. Click Save.
Save a copy of the model using a different name:
1. From the File menu, choose Save As.
2. Type tut2b.
3. Select a directory in which to save the file.
4. Click Save.
Well be using these two copies of your model in
later tutorials.
TIP: The Text building tool will also accept structures in
SMILES notation, either typed in or cut and pasted from
other documents.
Another, simpler, way of building this model is to
type Pentane in the Name=Struct text box then
modify the appropriate hydrogens.
Refine the model as follows.
1. Click the Select tool
2. Select the model by dragging diagonally across
it.

Chem & BioOffice 2006 /Chem3D Chem3D Tutorials 57

Tutorial 3: Building Models with the Text Building Tool
 3. From the Structure menu, choose Clean Up. Using Substructures
If you want a more accurate representation of a low
Labels are useful to build simple structures.
energy conformation, optimize the geometry of the
However, if you make larger, more complex
model by clicking the MM2 tool on the
Administrator

structures, you will find it easier to use a

Calculation toolbar.
combination of labels and pre-defined
To specify text equivalent to the structure of substructures.
1,2-dimethyl cyclopentane shown below:
Over 200 substructures are pre-defined in
Figure 2-38: More complex models with the text box Chem3D. These substructures include the most
H2
C
commonly used organic structures.
H 2C CH2
TIP: Pre-defined substructures are listed in the
CH CH substructures.xml file. You can view the list by pointing to
Parameter Tables on the View menu and selecting
H 3C CH3 Substructures. Text typed in the text box is case sensitive.
You must type it exactly as it appears in the Substructures
1. From the File menu, choose New. table.
2. Click the Text Building tool .he
3. Click in the empty space in the model window. Build a model of nitrobenzene:
4. Type CH(CH3)CH(CH3)CH2CH2CH2. 1. From the File menu, choose New.
5. Press the Enter key. 2. Click the Text Building tool .
The trans-isomer appears. 3. Click the empty space in the model window.
6. Select the model and choose Clean Up from the 4. Type Ph(NO2) in the text box.
Structure menu. 5. Press the Enter key.
TIP: You dont have to click the Select tool every time A model of nitrobenzene appears.
you want to select something. Just hold down the letter S The substructure in this example is the phenyl
on your keyboard while working with any building tool, group. Substructures are defined with specific
and you temporarily activate the Select tool. attachment points for other substituents. For
phenyl, the attachment point is C(1).
You cannot specify stereochemistry when you build
models with labels. The structure of 1,2-dimethyl Build a peptide model:
cyclopentane appears in the trans conformation.
1. From the File menu, choose New.
To obtain the cis-isomer: 2. Click the Text Building tool .
1. Click the Select tool . 3. Click an empty space in the Model window.

2. Select C(1). A text box appears.

3. From the Structure menu, choose Invert. 4. Type H(Ala)12OH.

The cis-isomer appears. You can rotate the 5. Press the Enter key.
molecule to see the differences between the 6. Rotate this structure to see the alpha helix that
isomers after you invert the molecule. forms.

58 Chem3D Tutorials CambridgeSoft

Tutorial 3: Building Models with the Text Building Tool
Change the model display type:
1. Click the arrow on the right side of the
Model Display Mode tool on the Model
Display toolbar.
2. Select Wire Frame as the Model Type.
TIP: You can also click on the icon. Successive clicks
cycle through the Display Mode options.
3. Select the Trackball tool , and rotate the
model so you are viewing it down the center of
the helix as shown in Figure 2-39.
Figure 2-39: Rotating a model with the trackball
4. Use the Model Display Mode tool to choose
Ribbons as the Model Type to see an alternative
display commonly used for proteins.
Figure 2-40: Ribbon display
Chem & BioOffice 2006 /Chem3D
Tutorial 4: Examining
Conformations
This tutorial uses steric energy values to compare
two conformations of ethane. The conformation
with the lower steric energy value represents the
more likely conformation.
Build ethane:
1. Draw a single bond in the ChemDraw panel.
A model of ethane appears.
2. View the Measurements table:
a. From the Structure menu, point to
Measurements, then choose Bond Lengths.
b. From the Structure menu, point to
Measurement, then choose Bond Angles.
NOTE: If the Measurements table appears along side
the Model Explorer, you can stack the windows by
locking the Model Explorer window open and dragging
the Measurements table on top of it.
The information you chose appears in the
Measurements table. The measurements in the
Actual and Optimal columns are nearly
identical. The Actual column represents the
measurements for the model in the active
window. The Optimal measurements (for bond
lengths and bond angles only) represent the
standard measurements in the Bond Stretching
and Angle Bending parameter tables.
Chem3D Tutorials 59
Tutorial 4: Examining Conformations
 Figure 2-41: Angle Bending parameter tables
Administrator
Chem3D shows the most common conformation
of a molecule. You can rotate parts of a molecule,
such as a methyl group, to see other conformations.
Rotate the orientation of the model to obtain a
Newman projection (viewing the model along a
bond.) This orientation helps clarify the
conformations of ethane.
To rotate a methyl group on an ethane model:
1. Click the Trackball tool .
When you mouse over the edges of the model
window, the Rotation Bars appear.
Only the X- and Y-rotation bars are active.
These Rotations bars are always active because
they are not dependent on any atoms being
selected.
2. Click the X-Axis rotation bar and drag to the
right.
As you drag, the status bar shows details about
the rotation.
3. Stop dragging when you have an end-on view
of ethane.
60 Chem3D Tutorials
This staggered conformation, where the
hydrogens on adjoining carbons are a
maximum distance from one another (which
represents the global minimum on a potential
energy plot) represents the most stable
conformation of ethane.
Figure 2-42: Ethane in stable conformation
To examine this result numerically, calculate the
steric energy of this conformation then compare it
to a higher energy (eclipsed) conformation.
1. From the Calculations menu, point to MM2,
then choose Compute Properties.
The Compute Properties dialog box appears.
The Properties tab should show Pi Bond Orders
and Steric Energy Summary selected as the
default. If it does not, select them.
TIP: Use Shift-click to select multiple properties.
2. Click Run.
The Output box appears beneath the model
window, with Steric Energy results displayed.
The last line displays the total energy.
NOTE: The values of the energy terms shown are
approximate and may vary slightly based on the type of
processor used to calculate them.
To obtain the eclipsed conformation of ethane,
rotate a dihedral angle (torsional angle). Rotating a
dihedral angle is a common way of analyzing the
conformational space for a model.
CambridgeSoft
Tutorial 4: Examining Conformations
To view dihedral angles: Figure 2-44: Rotating a dihedral angle

1. From the Structure menu, point to

Measurement, then choose Dihedral Angles.
All of the models dihedral angles are added to
the bottom of the Measurements table.
2. Click the H(3)-C(1)C(2)-H(8) dihedral record to
select the corresponding atoms in the model.

NOTE: Although the serial numbers and element

symbols are shown in the Measurements table, they do
not appear in your model. In the Measurements table, notice that the dihedral
for H(3)-C(1)-C(2)-H(8) is now minus 0 degrees, as
To help keep visual track of the atoms as you shown in the model.
change the dihedral angle you can display the serial
numbers and element symbols for the selected Figure 2-45: The Measurements table
atoms.
From the Model Display submenu of the View
menu, select Show Serial Numbers and Show
Element Symbols.

1. Click the arrow next to the Trackball tool, and

tear off the rotation dial by dragging on the
blue bar at the top.
Figure 2-43: The Rotation dial

trackball To compute steric energy:

local axis rotation
1. From the Calculations menu, point to MM2,
dihedral rotation then choose Compute Properties.
dihedral, move other
side NOTE: The property tab defaults should remain as
The Rotation dial should show the angle of the in the previous calculation.
selected dihedral, approximately 60, and
dihedral rotation should be selected. 2. Click Run.

2. Grab the green indicator button, and rotate the The final line in the Output box appears as in
dial to 0.0. Figure 2-46.

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Tutorial 4: Examining Conformations
 Figure 2-46: The Output box
Administrator
NOTE: The values of the energy terms can vary slightly
based on the type of processor used to calculate them.
The steric energy for the eclipsed conformation
(~3.9 kcal/mole) is greater in energy than that of
the staggered conformation (~1 kcal/mole),
indicating that the staggered configuration is the
conformation that is more likely to exist.
NOTE: As a rule, steric energy values should only be used
for comparing different conformations of the same model.
Tutorial 5: Mapping
Conformations with the
Dihedral Driver
The dihedral driver allows you to map the
conformational space of a model by varying one or
two dihedral angles. At each dihedral angle value,
the model is energy minimized using the MM2
force field and the steric energy of the model is
computed and graphed. After the computation is
complete you can view the data to locate the models
with the lowest steric energy values and use these as
starting points for further refinement in locating a
stationery point.
To use the dihedral driver:
1. Select the bond in your model that defines the
dihedral angle of interest.
2. Choose Dihedral Driver from the Calculations
menu.
The Dihedral Driver window opens. When the
computation is completed, a graph is displayed
showing the energy (kcal) vs. theta (angle of
rotation).
62 Chem3D Tutorials
Tutorial 5: Mapping Conformations with the Dihedral Driver
To view the conformation at any given point:
1. Point to a location (specific degree or energy
setting) inside the Dihedral Driver Window.
A dashed-line box appears. As you move the
mouse, the box moves to define a specific point
on the graph.
Figure 2-47: Using the dihedral driver
2. Click on the point of interest.
The model display rotates the dihedral to the
selected conformation.
NOTE: The dihedral is rotated in 5 degree increments
through 360 degrees for a total of 72 conformations to
produce the graph. You can view the minimized energy values
for each point in the Output window.
To rotate the other dihedral angle (other end of the
bond):
Right-click in the Dihedral Driver window and
choose Exchange.
Rotating two dihedrals
To rotate two dihedrals:
1. Use Shift+click to select two adjacent bonds.
In this case, the middle atoms position remains
fixed
2. Choose Dihedral Driver from the Calculations
menu.
The Dihedral Driver window opens. When the
computation is completed, a graph is displayed
showing theta 1 vs. theta 2.
CambridgeSoft
Figure 2-48: Two dihedrals in the dihedral driver
NOTE: The graph is the result of rotating one angle
through 360 in 15 increments while holding the other
constant. The second angle is then advanced 15 and the
operation is repeated.
To view the conformation at any given point:
Click any block in the graph.
The model display rotates both dihedrals to the
selected conformation.
Customizing the Graph
You can use the context menu to set the rotation
interval used for the computation. You can also
select display colors for the graph, background,
coordinates, and labels.
You also use the context menu to copy the graph,
or its data set, to other applications, or to save the
data.
Ultra Tutorial 6: Over-
laying Models
Overlays are used to compare structural similarities
between models, or conformations of the same
model. Chem3D provides two overlay techniques:
a Fast Overlay algorithm
the traditional do it by hand method based
on minimization calculations
Chem & BioOffice 2006 /Chem3D
This tutorial describes the Fast Overlay method.
For the Minimization Method, see Comparing
Models by Overlay on page 134. The
Minimization Method is more accurate, but the Fast
Overlay algorithm is more robust. In both tutorial
examples, you will superimpose a molecule of
Methamphetamine on a molecule of Epinephrine
(Adrenalin) to demonstrate their structural
similarities.
1. From the File menu, choose New Model.
Open the Model Explorer if it is not already
open.
2. Choose the Text tool from the Building
Toolbar and click in the model window.
A text box appears.
3. Type Epinephrine and press the Enter key.
A molecule of Epinephrine appears.
TIP: If you leave out the upper case E, Chem3D
will display an Invalid Label error message.
4. Click in the model window again to open
another text box.
5. Select the entire word Epinephrine, replace it
with Methamphetamine, and press the Enter
key.
The list of atoms in the Model Explorer is
replaced with two Fragment objects, labeled
Epinephrine and Methamphetamine.
Figure 2-49: Two fragments
Fragment Labels
Chem3D Tutorials 63
Tutorial 6: Overlaying Models
 The two fragments are hopelessly jumbled together Figure 2-52: Rotating fragments prior to alignment
at this point, so you might want to separate them
before you proceed.
1. Click one of the fragment names in the Model
Administrator

Explorer.
The entire fragment is selected.
Figure 2-50: Selecting a fragment

At this point, you have to decide which of the

fragments will be the target. In this simple example,
with only two compounds, it doesnt really matter.
You might, however, have cases where you want to
overlay a number of compounds on a specific
target. Chem3D allows multiple overlays. The
Model Explorer makes it easy to hide compounds
you are not actively working with, and to display any
2. Click the Move Objects tool. combination of compounds you want.
3. Drag the selected fragment away from the 1. Click the Epinephrine fragment to select it.
other fragment. 2. Point to Overlay on the context (right-click)
Figure 2-51: Dragging a fragment menu, and click Set Target Fragment.
Figure 2-53: Setting the target

A box or oval indicates the position of the

fragment while you are moving it. The icon on the fragment changes to a target.
TIP: You can rotate a fragment separately from the
whole model by selecting at least one atom in it and using
the Shift key with the trackball tool. Try this to re-
orient the fragments as in the illustration below.

64 Chem3D Tutorials CambridgeSoft

Tutorial 6: Overlaying Models
Figure 2-54: Model Explorer with target selected
3. Select the Methamphetamine fragment.
TIP: The check in the box next to Methamphetamine
does not mean that it is selected, it means that it is
visible. (Try it. This is how you work with multiple
overlays.) You must click on the fragment name for the
Fast Overlay command to become active.
4. Choose Fast Overlay from the Overlay
submenu on the context menu.
The fragments are overlaid. The numbers show
the serial numbers of the target atoms that the
matching overlay atoms correspond to.
TIP: You can designate a group, rather than the entire
fragment, as the target. In some cases, this will give more
useful results.
Figure 2-55: Overlaid fragments
To turn off the Fast Overlay mode:
Choose Clear Target Fragment from the Overlay
submenu.
Chem & BioOffice 2006 /Chem3D
Tutorial 7: Docking
Models
The Dock command enables you to position a
fragment into a desired orientation and proximity
relative to a second fragment. Each fragment
remains rigid during the docking computation.
The Dock command is available when two or more
distances between atoms in one fragment and
atoms in a second fragment are specified. These
distances are entered into the Optimal field in the
Measurements table.
You can use docking to simulate the association of
regions of similar lipophilicity and hydrophilicity on
two proximate polymer chains. There are four
steps:
A. Build a polymer chain:
1. Open a new Model window and select the Text
Building tool.
2. Click in the model window.
A text box appears.
3. Type (AA-mon)3(C2F4)4(AA-mon)3H in the
text box.
4. Press the Enter key.
A polyacrylic acid/polytetrafluoroethylene
block copolymer appears in the model window.
The text, (AA-mon)3, is converted to a polymer
segment with three repeat units of acrylic acid.
The text, (C2F4)4, is converted to a polymer
segment with four repeat units of
tetrafluoroethylene.
B. Build a copy of the chain:
Double-click in the model window well above
and to the right of the first polyacrylic
acid/polytetrafluoroethylene block copolymer
molecule.
Chem3D Tutorials 65
Tutorial 7: Docking Models
 A second polymer molecule appears above the 1. In the Model Explorer, select C(6) in
first polyacrylic acid/polytetrafluoroethylene Fragment 1.
block copolymer molecule. Hint: Its in the AA-mon 2 group.
C. Orient the chains: 2. Locate the C(98) atom in Fragment 2
Administrator

(AA-mon 12 group) and Ctrl-click to select it

1. Click in the empty space in the model window
to deselect any atoms in the model window.
2. Click the arrow on the Trackball tool to open
the Rotation Dial tool.
3. Select the Y axis, and drag the dial to show 55.
TIP: To get exactly 55 you will probably have to edit
the value in the number box. After editing, you must
press the Enter key. The value displayed in the right
corner of the dial should be the same as in the number
box.
The resulting model appears as shown in Figure 2-
56 (the second model may appear in a different
position on your computer):
Figure 2-56: Docking models I
also.
3. In the Structure menu, point to Measurements
and choose Set Distance Measurement.
The Measurements table opens, (if it is already
open as a tabbed window, it becomes active)
displaying the C(98)-C(6) pair.
4. Click the Optimal cell.
5. Type 5 and press the Enter key.
The optimal distance between C(6) and C(98)
is specified as 5.000.
To have a reasonable dock, you must specify at least
four atom pairs. Repeat steps 1 through 5 for
matching atom pairs throughout the fragments. For
example, if you choose one pair from each group
your list might look like the following:

Atoms Actual Optimal

C(1)-C(93) 21.2034 5.0000

C(98)-C(6) 21.1840 5.0000

C(104)-C(12) 21.2863 5.0000

C(108)-C(16) 21.1957 5.0000

C(22)-C(114) 20.6472 5.0000

C(28)-C(120) 20.7001 5.0000

D. set optimal distances between atoms in the
two fragments:
C(34)-C(126) 20.1410 5.0000
The Optimal distance determines how closely
the molecules dock. In this tutorial, you will set C(133)-C(41) 20.3559 5.0000
the distance to 5.

66 Chem3D Tutorials CambridgeSoft

Tutorial 7: Docking Models
 Figure 2-58: Recording iterations
Atoms Actual Optimal

C(45)-C(137) 20.3218 5.0000

C(50)-C(142) 20.4350 5.0000

Ignore the distances in the Actual cell because they

iteration
depend on how the second polymer was positioned values
relative to the first polymer when the second
polymer was created.

To begin the docking computation:

Note that while the docking computation proceeds,
1. From the Structure menu, choose Dock.
one molecule remains stationary and the second
The Dock dialog box appears. molecule moves.

Figure 2-57: The Dock dialog box To stop the docking computation before it reaches
its preset RMS values, click Stop Calculation
on the Calculation toolbar. Both docking and
recording are stopped.

The Status bar displays the values describing each

iteration of the docking computation.

Figure 2-59 shows the docked polymer molecules.

Figure 2-59: Docked polymers

2. Type 0.100 for the Minimum RMS Error value
and 0.010 for the Minimum RMS Gradient.

The docking computation stops when the RMS

Error or the RMS Gradient becomes less than
the Minimum RMS Error and Minimum RMS
Gradient value.

3. Click Display Every Iteration.

This allow you to see how much the fragments

have moved after each iteration of the docking
computation.
To save the iterations as a movie, click Record Each
Iteration.
The following illustration shows the distances
between atom pairs at the completion of the
docking computation. The distances in the Actual
cell are close to the distances in the Optimal cell.

Chem & BioOffice 2006 /Chem3D Chem3D Tutorials 67

Tutorial 7: Docking Models
 Figure 2-60: The measurements table for docked poly- To view the Highest Occupied Molecular Orbital
mers (HOMO):
4. From the Surfaces menu, point to Choose
Surface, and select Molecular Orbital.
Administrator

5. From the Surfaces menu, point to Molecular

Orbital to see the HOMO/LUMO options.
Select HOMO (N=6).
The pi bonding orbital surface appears.
Figure 2-61: Pi bonding orbital surface

Your results may not exactly match those described

here. The relative position of the two fragments or
molecules at the start of the docking computation
can affect your results. For more accurate results,
lower the minimum RMS gradient.

Tutorial 8: Viewing
Molecular Surfaces
Frontier molecular orbital theory says that the
highest occupied molecular orbitals (HOMO) and
lowest unoccupied molecular orbitals (LUMO) are
the most important MOs affecting a molecules
reactivity. This tutorial examines the reactivity of
double bonds by looking at the simplest molecule
containing a double bond, ethene.
Create an ethene model:
NOTE: You may need to rotate the molecule to view
the orbitals.
To view the Lowest Unoccupied Molecular Orbital
(LUMO):
1. From the Surfaces menu, point to Molecular
Orbital to see the HOMO/LUMO options.
Select LUMO (N=7).
The pi antibonding orbital surface appears.
Figure 2-62: Pi antibonding orbital surface

1. From the File menu, choose New.

2. Draw a double bond in the ChemDraw panel.

A molecule of ethene appears.

Before you can view the molecular orbital surface,
you must calculate it.

3. From the Calculations menu, point to

Extended Huckel and select Calculate Surfaces.

68 Chem3D Tutorials CambridgeSoft

Tutorial 8: Viewing Molecular Surfaces
These are only two of twelve different orbitals The propene radical is displayed.
available. The other ten orbitals represent various Figure 2-64: Propene radical model
interactions of sigma orbitals. Only the pi orbitals
are involved in the HOMO and the LUMO.
Because the HOMO and LUMO control the
reactivity of a molecule, you can conclude that it is
the pi bonding interactions of ethene that control
its reactivity. This is a specific case of a more general
rule: pi bonds are more reactive than sigma bonds.

Tutorial 9: Mapping
Properties onto Surfaces 4. From the Calculations menu, point to Gaus-
sian, and choose Minimize Energy.
5. In the Theory tab, set the Method to PM3, and
NOTE: This example is designed to demonstrate Gaussian the Wave Function to Open Shell (Unrestricted).
minimization. You can also do it using CS MOPAC or
6. Also in the Theory tab, set the Spin Multiplicity
Extended Hckel calculations.
to 2.
The allyl radical, CH2=CHCH2, is a textbook
NOTE: If you are doing this tutorial with CSMOPAC,
example of resonance-enhanced stabilization: there is no Spin Multiplicity setting.
Figure 2-63: The allyl radical
H H This molecule is intended to be a radical, and setting
C C
C
H
the Spin Multiplicity ensures that it is.
H
C
2 2 H
C
2 C
H
2
One of the best ways to view spin density is by
To examine Radicals with Spin Density surfaces: mapping it onto the Total Charge Density surface.
1. From the File menu, choose New. This allows you to see what portions of the total
charge are contributed by unpaired electrons, or
2. Type 1-propene in the ChemDraw
radicals.
Name=Struct text box.
A molecule of 1-propene appears. To view Spin Density mapped onto Total Charge
Density Surface:
Create a radical:
1. In the Properties tab, select Molecular Surfaces
1. Select the H9 hydrogen. and Spin Density (use Shift-click).
2. Press Delete. 2. Press Run.
A dialog box appears asking if you want to turn The calculation toolbar appears.
off rectification. Chem3D is chemically
Figure 2-65: The Calculation toolbar
intelligent, and knows that in most cases
carbon atoms have four substituents. Radicals
are one of the rare exceptions.
3. Click Turn Off Automatic Rectification.

Chem & BioOffice 2006 /Chem3D Chem3D Tutorials 69

Tutorial 9: Mapping Properties onto Surfaces
 When the calculation is finished, select the
Trackball tool and rotate the model back and forth.
It should be completely planar.
Figure 2-66: Viewing the minimized model
Administrator
2. On the Surfaces toolbar, point to Surface and
select Total Charge Density.
The icon changes to denote the surface
selected.

3. On the Surfaces toolbar, point to Display Mode

and choose Translucent.
4. On the Surfaces toolbar, point to Color
Mapping and choose Spin Density.
5. On the Surfaces toolbar, choose Isocharge.
The Isocharge tool appears.
Figure 2-68: Using the Isocharge tool

To complete this tutorial, you will need to adjust a

number of surface settings. For convenience,
activate the Surfaces toolbar.

1. From the View menu, point to Toolbars, and

choose Surfaces. 6. Set the isocharge to 0.0050. (The number in the
middle is the current setting.)
The Surfaces toolbar appears. Drag it into the
workspace for added convenience. NOTE: Isovalues are used to generate the surface. You
can adjust this value to get the display you want. The
Figure 2-67: The Surfaces toolbar
illustration below was made with the setting of 0.0050.
Surface
Figure 2-69: Viewing the total charge density surface
Solvent radius

Display mode

Color Mapping

Surface color

Resolution

HOMO/LUMO selection

Isovalues

Color A Most of the surface is grey, indicating that there is

no contribution to it from unpaired electrons. The
Color B
areas of red centered over each of the terminal

70 Chem3D Tutorials CambridgeSoft

Tutorial 9: Mapping Properties onto Surfaces
carbons is a visual representation of the expected
delocalization of the radicalthere is some radical
character simultaneously on both of these carbons.
Now, hide this surface:
Click the Surfaces icon to toggle the surface
off.
Determine the raw spin density alone, not mapped
onto the charge density surface.
1. On the Surfaces toolbar, point to Surface, and
select Total Spin Density.
2. From the Surfaces menu, point to Surfaces,
and choose Wire Mesh.
3. Set Isospin to 0.001.
Figure 2-70: Wire mesh surfaces
There is a large concentration of unpaired spin over
each of the terminal carbons and a small
concentration over the central hydrogen. This extra
little bit of spin density is not very significantyou
could not even see it when looking at the mapped
display earlier, but the calculations show that it is, in
fact, there.
Tutorial 10: Computing
Partial Charges
To compute the charge of a molecule, the number
of electrons contributed by each of its atoms can be
subtracted from the number of protons in the
nucleus of each of its atoms. Each atom of a
Chem & BioOffice 2006 /Chem3D
molecule contributes an integral charge to the
molecule as a whole. This integral contribution is
known as the formal charge of each atom.
Certain types of atoms in Chem3D deal with this
explicitly by having non-integral formal charges.
For example, the two oxygen atoms in nitro-
benzene each have charges of -0.500 because there
is one electron that is shared across the two N-O
bonds.
However, as shown above, electrons in molecules
actually occupy areas of the molecule that are not
associated with individual atoms and can also be
attracted to different atomic nucleii as they move
across different atomic orbitals. In fact, bonds are a
representation of the movement of these electrons
between different atomic nucleii.
Because electrons do not occupy the orbitals of a
single atom in a molecule, the actual charge of each
atom is not integral, but is based on the average
number of electrons in the model that are
occupying the valence shells of that atom at any
given instant. By subtracting this average from the
number of protons in the molecule, the partial
charge of each atom is determined.
Visualizing the partial charge of the atoms in a
molecule is another way to understand the model's
reactivity. Typically the greater the partial charge on
an atom, the more likely it is to form bonds with
other atoms whose partial charge is the opposite
sign.
Using the theories in Extended Hckel, MOPAC,
or Gaussian, you can compute the partial charges
for each atom. In the following example, the partial
charges for phenol are computed by Extended
Hckel.
1. From the File menu, choose New.
Click the Text Building tool , click in the
model window, type PhOH in the text box, and
press the Enter key.
Chem3D Tutorials 71
Tutorial 10: Computing Partial Charges
 A molecule of phenol is created.
To compute Extended Hckel charges:
From the Calculations menu, point to
Administrator
Extended Hckel and choose Calculate Charges.
Messages are added to the Output box, listing
the partial charge of each atom.
You can graphically display partial charges in the
following ways:
By coloring atoms.
By varying the size of atom spheres.
By varying the size of the dot surfaces.
To display partial charges:
1. From the File menu, choose Model Settings.
2. Click the Model Display tab.
3. Select the Color by Partial Charge radio button.
All of the atoms are colored according to a
scale from blue to white to red. Atoms with a
large negative partial charge are deep blue.
Atoms with a large positive partial charge are
deep red. As the magnitude of the charges
approaches 0, the color of the atom becomes
paler.
Figure 2-71: Coloring by partial charge
For phenol, the greatest negative charge is on the
oxygen atom. The greatest positive charge is on the
adjacent carbon atom (with the adjacent hydrogen
72 Chem3D Tutorials
atom a close second). The rest of the molecule has
relatively pale atoms; their partial charges are much
closer to zero.
In addition to color, you can vary the size of atom
spheres or dot surfaces by partial charge.
1. Select the Color By Element radio button in
Model Display tab of the Model Settings
dialog box.
2. Click the Atom Display tab.
3. Click the Show by Default checkbox in the Solid
Spheres section.
4. Select the Partial Charges radio button.
Figure 2-72: Varying atom sphere size as a function
of partial charge
In this representation, the oxygen atom and its two
adjacent atoms are large because they have relatively
large partial charges of opposite signs. The rest of
the atoms are relatively small.
You can display dot surfaces whose size is specified
by partial charge.
1. Click the VDW Radius radio button in the Solid
Spheres section.
1. Select the Show By Default check box in the Dot
Surfaces section.
2. Click the Partial Charges radio button.
CambridgeSoft
Tutorial 10: Computing Partial Charges
Figure 2-73: Dot surface size as a function of partial
charge
Chem & BioOffice 2006 /Chem3D
In this representation, the oxygen atom and its two
adjacent atoms have large dot surface clouds
around them because they have relatively large
partial charges of opposite signs. The rest of the
atoms are relatively small. Their dot surfaces are
obscured by the solid spheres. If another molecule
were to react with this molecule, it would tend to
react where the large clouds are, near the oxygen
atom.
Chem3D Tutorials 73
Tutorial 10: Computing Partial Charges
Administrator

74 Chem3D Tutorials CambridgeSoft

Tutorial 10: Computing Partial Charges
Chapter 3: Displaying Models
Overview Ribbons
Cartoons
You can display molecular models in several ways,
depending on what information you want to learn To change the default structural display type of a
from them. The atoms and bonds of a model can model:
take on different appearances. These appearances 1. From the File menu, choose Model Settings.
are generically termed rendering types, and the term
model display is used in Chem3D. Depending on the The Chem 3D Model Settings dialog box
type of molecule, certain model displays may offer appears.
advantages by highlighting structural features of 2. Select the Model Display tab.
interest. For example, the Ribbons model display The Model Display control panel of the Chem
might be the option of choice to show the 3D Model Settings dialog box appears.
conformational folding of a protein without the
Figure 3-1: The Model Display control panel
distracting structural detail of individual atoms.
Model display options are divided into two general
types: Model
Display
Structure displays Tab
Molecular surface displays

Structure Displays
Structures are graphical representations based on
the traditional physical three-dimensional
molecular model types. The following structure Default
display types are available from Model Display view Model
of the Chem 3D Model Settings dialog box: Type

Wire Frame
Sticks
Ball and Stick
Cylindrical Bonds
Space Filling 3. Set the new options.

Chem & BioOffice 2006 /Chem3D Displaying Models 75

 To change the structural display type of a model
temporarily: Model Type Description

1. Click the arrow on the Model Display tool ,

Ball and Stick Ball and Stick models
and select the display type.
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show bonds drawn as

Model Types thick lines and atoms are
drawn as filled spheres.
The following table describes the Chem3D model The atom spheres are
types: filled with color that
corresponds to the
Model Type Description element or position of
the atom.
Wire Frame Wire Frame models are
the most simple model Cylindrical Bonds Cylindrical Bond models
type. Bonds are displayed
are similar to Ball and
as pixel-wide lines.
Stick models except that
Atoms are not displayed
all bond types are drawn
explicitly, but each half of
as cylinders.
a bond is colored to
represent the element
color for the atom at that
end. Wire Frame models
are well suited for
extremely large models
such as proteins.

Sticks Stick models are similar

to Wire Frame, however,
the bonds are slightly
thicker. As this model
type is also fairly fast, it is
another good choice for
visualizing very large
models such as proteins.

76 Displaying Models CambridgeSoft

Model Type Description Model Type Description

Space Filling Space Filling models are Cartoons Cartoon models, like
more complex to draw Ribbon models, show
and slowest to display. large protein molecules
Atoms are scaled to in a form that highlights
100% of the van der secondary and tertiary
Waals (VDW) radii speci- structure.
fied in the Atom Types
table. The following caveats
apply to the Ribbon and
NOTE: The VDW radii Cartoon model display
are typically set so that types:
overlap between
non-bonded atoms in They do not provide
space filling models pop-up information.
indicates a significant
They should be
(approximately 0.5
kcal/mole) repulsive printed as bitmaps.
interaction.
Displaying Solid Spheres
Ribbons Ribbons models show In Ball and Stick, Cylindrical Bond, and Space
large protein molecules Filling models, you can display the solid spheres
in a form that highlights representing atoms and control their size.in
secondary and tertiary individual atoms or all atoms.
structure. Ribbon models
can be colored by Group To display solid spheres by default on all atoms:
to help identify the
1. From the File menu, select Model Settings.
amino acid constituents.
Your model must have a 2. Select the Atom Display tab.
protein backbone in 3. In the Solid Spheres section, click the Show By
order to display ribbons. Default checkbox.

Chem & BioOffice 2006 /Chem3D Displaying Models 77

 Figure 3-2: Setting solid sphere display Solid Spheres Size%
Atom
Display The value of the Size% slider on the Atom Display
tab tab represents a percentage of the Covalent radius
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specified for each atom in the Elements Table. This

percentage ranges from 0 (small) to 100 (large).
Show solid
spheres by Thus, when the Atom Size is 100, the atoms are
default scaled to their maximum radii. The value of this
setting affects Ball and Stick and Cylindrical Bond
models.

Displaying Dot Surfaces

You can add dot surfaces to any of the model
display types like the stick model shown below:

To change the display of solid spheres in a model: Figure 3-3: Viewing dot surfaces

From the Model Display submenu of the View

menu, select or deselect Show Atom Dots.

Setting Solid Sphere Size

The maximum radius of the sphere that represents
an atom can be based on the Van der Waals (VDW)
Radius or Partial Charge. To specify which property
to use, select the radio button below the slider.

The VDW Radius is specified using the atom type

of the atom.
The dot surface is based on VDW radius or Partial
The Partial Charge is the result of a calculation:
Charges as set in the Atom Display table of the
Extended Hckel, MOPAC, or Gaussian. If you
Model Settings dialog box.
have not performed a calculation, the partial charge
for each atom is shown as 0, and the model will
To display dot surfaces by default on all atoms:
display as a Stick model. If you have performed
more than one calculation, you can specify the
1. In the Chem 3D Model Settings dialog box,
calculation to use from the Choose Result submenu
click the Atom Display tab.
on the Calculations menu.
2. In the Dot Surfaces area, click the Show By
When sizing by partial charge, the absolute value of Default checkbox.
the charge is used. An atom with a partial charge of
0.500 will have the same radius as an atom with a All atoms currently in the model window display
partial charge of -0.500. the selected option.

78 Displaying Models CambridgeSoft

You can vary the number of dots displayed in a 4. Close and Save the table.
surface by using the density slider. This is useful
when dot surfaces are applied to a very small or very NOTE: You must save the changes before they take
large models. effect.

To change the display of dot surfaces in a model:

From the Model Display submenu of the View
menu, select or deselect Show Atom Dots.
Coloring Displays
You can change the default for the way colors are
used to display your model in the Model Display tab
of the Model Settings control panel. To make a
temporary change, use the Color By... command on
the Model Display submenu of the View menu. The
choices are:
Coloring by Group
You may assign different colors to substructures
(groups) in the model.
To change a color associated with a group in the
active model:
1. In the Model Explorer, Right-click on the group
name and choose Select Color.
The Color dialog box appears.
2. Select the color to use and click OK.

Monochrome 3. Save the changes to the Model.

Partial Charge
Coloring by Partial Charge
Chain
When coloring by partial charge, atoms with a
Element highly negative partial charge are deep blue. Atoms
Group with a highly positive partial charge are deep red. As
Depth the partial charge gets closer to 0, the atom is paler.
Atoms with a 0 partial charge are white.
Two of the choices, Monochrome and Chain, are
only available for proteins displayed in the Ribbon The Partial Charge is the result of a calculation
or Cartoon mode. Extended Hckel, MOPAC, or Gaussian. If you
have not performed a calculation, the partial charge
Coloring by Element for each atom is 0. If you have performed more
Color by element is the usual default mode for small than one calculation, you can specify the calculation
to use in the Choose Result submenu of the
molecules. The default colors are stored in the
Calculations menu.
Elements Table.
Figure 3-4: Color by partial charge
To change the color of elements specified in the
Elements table:
1. From the View menu, point to Parameter
Tables, and choose Elements.
The Elements Table opens.
2. Double-click the Color field for an element.
The Color dialog box appears.
3. Select the color to use and click OK.

Chem & BioOffice 2006 /Chem3D Displaying Models 79

 Coloring by depth for Chromatek stereo
viewers
Chem3D supports color by depth for
Chromadepth stereo viewers. When you select
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Color by Depth, the model is colored so that objects
nearer the viewer are toward the red end, and
objects further from the viewer toward the blue
end, of the spectrum. This creates a stereo effect
when viewed with a Chromadepth stereo viewer.
The effect is best viewed with a dark background. If
you use the Chromatek icon on the Model
Display toolbar to activate this viewing option,
rather than the Color By Depth setting, the
background color is set automatically to black.
To set Color by Depth, do one of the following:
Select the Color by Depth radio button on the
Colors and Fonts tab of the Model Settings
dialog box.
Use the Color By option of the Model Display
submenu on the View menu.
Red-blue Anaglyphs
Chem3D supports viewing with red-blue 3D
glasses to create a stereo effect similar to that of the
Chromatek viewer.
To activate red-blue viewing:
1. From the Stereo and Depth tab of the Model
Settings dialog box, select Render Red/Blue
Anaglyphs.
2. Move the Eye Separation slider to adjust the
effect.
Figure 3-5: The eye separation slider
80 Displaying Models
To toggle the effect on or off:
From the Model Display submenu of the View
menu, choose Red&Blue.
Depth Fading3D enhancement:
The depth fading feature in Chem3D creates a
realistic depth effect, by making parts of the model
further from the viewer fade into the background.
Depth shading is activated by selecting the Depth
Fading checkbox on the Stereo and Depth tab of the
Model Settings dialog box, by selecting Depth
Fading from the Model Display submenu of the
View menu, or by clicking the Depth fading icon
on the Toolbar.
Perspective Rendering
Chem3D supports true perspective rendering of
models. This results in a more realistic depiction of
the model, with bond lengths and atom sizes
further from the viewer being scaled consistently.
The field of view slider adjusts the perspective
effect. Moving the slider to the right increases the
effect.
Figure 3-6: Depth fading settings
Depth Fading,
Perspective, &
field of view slider
CambridgeSoft
 CAUTION Coloring Individual Atoms
Moving the slider all the way to the left may make the You can mark atoms individually using the Select
model disappear completely. Color command in the Model Explorer.

To change an atom to a new solid color:

Coloring the Background 1. In the Model Explorer, select the atom(s) to
Window change.
2. From the context menu, choose Select Color.
Chem3D allows you to select a color for the
The Color dialog box appears.
background of your models. A black or dark blue
background can be particularly striking for ribbon 3. Select a color and Click OK.
displays intended for full color viewing, whereas a The color of the atom(s) changes to the new
light background is more suitable for print copy. color.
To change the default background color of the To remove a custom atom color from the model
model window: display:

1. In the Colors and Fonts tab of the Model 1. In the Model Explorer, select the atoms whose
Settings control panel, click Background Color. colors you want to change.

Figure 3-7: Background color settings 2. Right-click, point to Apply Atom Color and
choose Inherit Atom Color.
The custom colors are removed from the
selected atoms.

Displaying Atom Labels

Background
color You can control the appearance of element symbols
and serial numbers using the Atom Labels tab in the
Model Settings control panel, and the
corresponding commands in the Model Display
submenu of the View menu.

Setting Default Atom Label Display

Options
The Color dialog box appears.
To set the Element Symbols and Serial Numbers
2. Select a color and click OK. defaults:
1. On the Colors and Fonts tab of the Model
NOTE: The background colors are not saved in PostScript Settings dialog box, select the font, point size
files or used when printing, except when you use the Ribbons and color.
display.
2. Click the Set as Default button.

Chem & BioOffice 2006 /Chem3D Displaying Models 81

 All atoms currently in the model window Figure 5: Residue labels
display the selected options.
To toggle the Atom Labels or Serial Numbers at any
time, do one of the following:
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From the Model Display submenu of the View

menu, choose Show Atom Labels or Show Serial
Numbers.

Click the Atom Label or Serial Numbers

icon on the Model Display Toolbar.

Displaying Labels Atom by Atom

To display element symbols or serial numbers in
individual atoms:
1. In the Model Explorer, select the atom to
change.
2. On the context menu, point to Atom Serial
Number or Atom Symbol and choose Show...
Displaying Group Labels
You can display residue labels in protein structures.
The global setting for the model can be changed
with the new Residue button on the Model Display
toolbar. A more granular control is available with
the Group Labels command on the context menus
in the Model Explorer.
Figure 4: Setting Group Labels
Displaying Measurements
You can now display measurements in the model
view. By default, a measurement will display if you
add a single measurement from the Measurements
submenu of the Structure menu, but not if you
generate a set of measurements. You can select
which measurements to display by opening the
Measurements Window wide to show the Display
checkboxes.
Figure 6: Measurements window
Figure 3-8: Measurement display

82 Displaying Models CambridgeSoft

Using Stereo Pairs 2. Select Render Stereo Pairs to display two views
of the model next to each other.
Stereo Pairs is a display enhancement technique The right view is the same as the left view,
based on the optical principles of the Stereoscope, rotated about the Y-axis.
the late-Nineteenth century device for 3D viewing
3. Specify the Eye Separation (Stereo Offset) with
of photographs. By displaying two images with a
the slider. This controls the amount of Y-axis
slight displacement, a 3D effect is created.
rotation.
Stereo views can be either Parallel or Reverse (direct 4. Specify the degree of separation by clicking the
or cross-eyed). Some people find it easier to look Separation arrows.
directly, others can cross their eyes and focus on About 5% of the width is a typical separation
two images, creating an enhanced three dimensional for stereo viewing.
effect. In either case, the effect may be easier to
To select whether the views are cross-eyed or direct,
achieve on a printed stereo view of your model than
do one of the following:
on the screen. Keep the images relatively small, and
adjust the distance from your eyes. Select Reverse to rotate the right frame to the
left. If your left eye focuses on the right-hand
To set the Stereo Pairs parameters: model and your right eye focuses on the
left-hand model, the two stereo views can
1. Open the Model Settings dialog box, and overlap.
click the Stereo and Depth tab.
Select Parallel to rotate the right view further to
The stereo views control panel appears. the right.
Figure 3-9: Setting stereo viewing
Using Hardware Stereo
Graphic Enhancement
Chem3D 9.0 provides stereo graphics rendering for
hardware that has stereo OpenGL capabilities.
There are now a variety of stereo graphics cards,
stereo glasses, and 3D monitors that can be driven
by Chem3D. Hardware enhancement is enabled
from the OpenGL tab in the Chem3D Preferences
dialog, which you can access from the File menu.

Chem & BioOffice 2006 /Chem3D Displaying Models 83

 Figure 3-10: Setting hardware OpenGL settings
Administrator
Hardware
Stereo
Any 3D window opened after this mode is enabled
will utilize hardware graphics capabilities if they are
available and enabled.
NOTE: You must enable stereo in OpenGL in the
display adapter properties control, as well as in Chem3D
preferences, and select the correct mode for the glasses/monitor
you are using.
You can use depth fading and perspective with
hardware enhancement, but should not activate
other stereo modes.
TIP: The Eye Separation slider on the Stereo and
Depth tab of the Model Settings dialog box can be used to
control separation. You should select the Disabled radio
button when using hardware stereo.
84 Displaying Models
Figure 3-11: Setting eye separation
Molecular Surface
Displays
Molecular Surface displays provide information
about entire molecules, as opposed to the atom and
bond information provided by Structure displays.
Surfaces show information about a molecules
physical and chemical properties. They display
aspects of the external surface interface or electron
distribution of a molecule.
Unlike atom and bond data, Molecular Surface
information applies to the entire molecule. Before
any molecular surface can be displayed, the data
necessary to describe the surface must be calculated
using Extended Hckel or one of the methods
available in CS MOPAC or Gaussian. Under
MOPAC you must choose Molecular Surfaces as
one of the properties to be calculated.
CambridgeSoft
Molecular Surface Displays
There is one exception to the requirement that you
must perform a calculation before a molecular
surface can be displayed. Solvent Accessible
Surfaces
surfaces are automatically calculated from
To display a surface:
parameters stored in the Chem3D parameters
tables. Therefore, no additional calculations are
needed, and the Solvent Accessible command on the
Choose Surface submenu is always active.
Extended Hckel
Extended Hckel is a semi-empirical method that
can be used to generate molecular surfaces rapidly
for most molecular models. For this reason, a brief
discussion of how to perform an Extended Hckel
calculation is given here.
To compute molecular surfaces using the Extended
Hckel method:
From the Computations menu, point to
Extended Hckel, and choose Calculate
Surfaces.
NOTE: Before doing an Extended Hckel calculation,
Chem3D will delete all lone pairs and dummy atoms. You
will see a message to this effect in the Output window.
Displaying Molecular
1. Decide what surface type to display.
2. Perform a suitable calculation using Extended
Hckel, CS MOPAC, or Gaussian 03. Include
the Molecular Surfaces property calculation
whenever it is available.
NOTE: CS MOPAC and Gaussian
03 surfaces calculations are only available in Chem3D
Ultra.
Different calculation types can provide
different results. If you have performed more
than one calculation on a model, for example,
both an Extended Hckel and an AM1
calculation, you must choose which calculation
to use when generating the surface.
3. From the Calculations menu, point to Choose
Result and select one of your calculations.
4. From the Surfaces menu point to Choose
Surface, and select one of the surface types.

At this point, a calculation has been performed and NOTE: The Choose Surface commands are toggle
the results of the calculation are stored with the switchesclick once to display, click again to turn off the
model. display. You can display more than one surface at a
time. When a surface is displayed, its icon is
To compute partial charges using the Extended highlighted.
Hckel method:
Figure 3-12: Displayed surface
From the Computations menu, point to
Extended Hckel, and choose Calculate
Charges.

For each atom in the model, a message is created

listing the atom and its partial charge. If you have
selected Partial Charge in the Pop-up Information tab
of the Model Settings dialog box, then the partial
charges will appear as part of the pop-up
information when you point to an atom. Displayed surface

Chem & BioOffice 2006 /Chem3D Displaying Models 85

Molecular Surface Displays
 5. Adjust the display using the surface display
tools. Surface Extended MOPAC Gaussian
Type Hckel
TIP: If you are making a lot of adjustments to the
Administrator

display, activate the Surfaces toolbar and tear off the with Molec- Yes Yes Yes
specific tools you will be using often. ular Orbital
map
For a review of the surface display tools, see The
Surfaces Toolbar on page 41. with Spin No Yes Yes
Density
Not all surfaces can be displayed from all map
calculations. For example, a Molecular Electrostatic
Potential surface may be displayed only following a
with Partial Yes Yes Yes
Gaussian or MOPAC calculation. If a surface is
Charges
unavailable, the command is grayed out in the
submenu.
with Molec- No Yes Yes
To generate surfaces from MOPAC or Gaussian, ular Electro-
you must choose Molecular Surfaces as one of the static Poten-
properties calculated by these programs. The tial map
surface types and the calculations necessary to
display them are summarized in the following table. Total Spin No Yes Yes
Density
NOTE: Spin Density map requires that MOPAC or
Gaussian computations be performed with an open shell Molecular No Yes Yes
wavefunction. Electro-
static
Potential

Surface Extended MOPAC Gaussian Molecular Yes Yes Yes

Type Hckel Orbitals
a.
Calculated automatically from parameters
Solvent NA NA NA stored in the Chem3D parameters tables.
Accessiblea This surface is always available with no
further calculation.
Connolly Yes Yes Yes
Molecular
Setting Molecular Surface Types
Total Yes Yes Yes
Charge Chem3D offers four different types of surface
Density displays, each with its own properties. These types
are shown in the following table:

86 Displaying Models CambridgeSoft

Molecular Surface Displays
 Surface Type Description
Surface Type Description
Translucent The surface is
Solid The surface is displayed in solid
displayed as an opaque form, but is partially
form. Solid is a good transparent so you can
choice when you are also see the atoms and
interested in the details bonds within it.
of the surface itself, Translucent is a good
and not particularly compromise between
interested in the surface display styles.
underlying atoms and
bonds. Setting Molecular Surface Isovalues
Wire Mesh The surface is Isovalues are, by definition, constant values used to
displayed as a generate a surface. For each surface property, values
connected net of lines. can be calculated throughout space. For example,
Wire Mesh is a good the electrostatic potential is very high near each
choice when you want atom of a molecule, and vanishingly small far away
to focus on surface from it. Chem3D generates a surface by connecting
features, but still have all the points in space that have the same value, the
some idea of the atoms isovalue. Weather maps are a common example of
and bonds in the the same procedure in two dimensions, connecting
structure. locations of equal temperature (isotherms) or equal
pressure (isobars).
Dots The surface is
displayed as a series of To set the isovalue:
unconnected dots.
1. From the Surfaces menu, choose Isocontour.
Dots are a good choice
if you are primarily NOTE: The exact name of this command reflects the
interested in the type of isovalue in each window. For example, for Total
underlying structure Charge Density Surfaces, it is Isocharge.
and just want to get an
idea of the surface The Isocontour slider appears.
shape. Figure 3-13: Setting surface contour

2. Adjust the slider to the new isovalue.

The new isovalue is the middle value listed at
the bottom of the Isocontour tool.

Chem & BioOffice 2006 /Chem3D Displaying Models 87

Molecular Surface Displays
 Setting the Surface Resolution
The Surface Resolution is a measure of how
smooth the surface appears. The higher the
resolution, the more points are used to calculate the
Administrator
Setting Solvent Radius
The Solvent Radius can be set from 0.1 to 10
using the slider. The default solvent radius is 1.4 ,
which is the value for water. Radii for some

surface, and the smoother the surface appears. common solvents are shown in the following table:
However, high resolution values can also take a long
time to calculate. The default setting of 30 is a good
compromise between speed and smoothness. Solvent Radius ()
To set the resolution:
Water 1.4
1. From the Surfaces menu, choose Resolution.
The Resolution slider appears. Methanol 1.9
Figure 3-14: Setting surface resolution
Ethanol 2.2

Acetonitrile 2.3

2. Adjust the slider to the desired resolution. Acetone 2.4

The new resolution is the middle value listed at
the bottom of the Resolution tool. Ether 2.4
Setting Molecular Surface Colors
Pyridine 2.4
How you set the color depends on what type of
surface you are working with.
DMSO 2.5
For Solvent Accessible, Connolly Molecular, or
Total Charge Density surfaces, do the following: Benzene 2.6
1. On the Surfaces menu, choose Surface Color.
The Surface Color dialog box appears. Chloroform 2.7
2. Select the new color.
To set the solvent radius:
3. Click OK.
1. From the Surfaces menu, choose Solvent
For the other surface types, where you must specify Radius.
two colors, do the following.
The Radius slider appears.
1. On the Surfaces menu, choose Alpha Color or
Figure 3-15: Setting the surface radius
Beta Color.
The Alpha or Beta Color dialog box appears.
2. Select the new color.
3. Click OK.

88 Displaying Models CambridgeSoft

Molecular Surface Displays
 2. Adjust the slider to the desired resolution.
Amino Acid Hydrophobicity
The new radius is the middle value listed at the
bottom of the Radius tool. Cys 2.0

Setting Surface Mapping Trp 1.9

The Mapping Property provides color-coded Ala 1.6
visualization of Atom Colors, Group Colors,
Hydrophobicity, Partial Charges, or Electrostatic Thr 1.2
Potential (derived from partial charges)
superimposed upon the solvent-accessible surface. Gly 1.0

Surface Color is color you have chosen with the Ser 0.6 Middle (White)
Surface Color tool. Atom Color is based on the Pro 0.2
displayed atom colors, which may or may not be the
default element colors. Element Color is based on Tyr 0.7
the default colors in the Elements Table. Group
Color is based on the colors (if any) you specified His 3.0
in the Model Explorer when creating groups.
Gln 4.1
Hydrophobicity is displayed according to a
widely-used color convention derived from amino Asn 4.8
acid hydrophobicities1, where the most Glu 8.2
hydrophobic (lipophilic) is red and the least
hydrophobic (lipophobic) is blue. The following Lys 8.8
table shows molecule hydrophobicity.
Asp 9.2
Amino Acid Hydrophobicity Arg 12.3 Least hydrophobic (Blue)

Phe 3.7 Most hydrophobic (Red) The Partial Charges and Electrostatic Potential
(derived from the partial charges) properties are
Met 3.4
taken from the currently selected calculation. If you
Ile 3.1 have performed more than one calculation on the
model, you can specify which calculation to use
Leu 2.8 from the Choose Result submenu of the
Val 2.6 Calculations menu.
1. Engelman, D.M.; Steitz, T.A.; Goldman,
A., Identifying nonpolar transbilayer Partial Surfaces
helices in amino acid sequences of
membrane proteins, Annu. Rev. Bio- Scientists who study protein-ligand interactions are
phys. Biophys. Chem. 15, 321-353, often interested in generating a molecular surface of
1986. a protein that does not include ligand. Chem3D can

Chem & BioOffice 2006 /Chem3D Displaying Models 89

Molecular Surface Displays
 now generate partial Solvent Accessible and
Conolly surfaces, either by excluding ligands, or by
excluding selected parts of the model, or both.
To generate a partial surface:
Administrator
Solvent atoms are excluded by default, but may be
included with the checkbox. Hidden atoms (usually
hydrogens) may also be included or excluded.
Figure 9: Partial surface excluding solvent atoms

1. Click Advanced Molecular Surfaces on the

Surfaces menu.
Figure 7: Surfaces menu

After displaying a surface, you can set surface

transparency and reflectivity with the controls in
the middle of the dialog box. (These controls are
grayed out until a surface is displayed.) You can
color the surface by atom, element, or group color,
or by group hydrophobicity, in addition to
monochromatic surfaces of any color.
Figure 10: Setting surface transparency

2. Select the surface type and what you want to

include and exclude in the Advanced Molec-
ular Surfaces dialog box.
Figure 8: Generating a partial surface
You can also restrict the surface either by distance
Set surface type
from the selected group, or by flooding.

Use selected or
unselected atoms
for the surface.
Include/exclude hidden atoms
Include/exclude ligand

90 Displaying Models CambridgeSoft

Molecular Surface Displays
Figure 11: Restricted surface with ligand excluded Figure 3-16: van der Waals surfaces
Solvent accessible surface
van der Waals surface

Solvent probe

Connolly Molecular Surface

Solvent Accessible Surface
The Connolly surface, also called the molecular
The solvent accessible surface represents the surface, is similar to the solvent-accessible surface.
portion of the molecule that solvent molecules can Using a small spherical probe to simulate a solvent,
access. When viewed in the ball and stick it is defined as the surface made by the center of the
representation, a molecule may appear to have solvent sphere as it contacts the van der Waals
many nooks and crannies, but often these features surface. The volume enclosed by the Connolly
are too small to affect the overall behavior of the surface is called the solvent-excluded volume.
molecule. For example, in a ball-and-stick These surfaces are shown in the following
representation, it might appear that a water illustration.
molecule could fit through the big space in the
center of a benzene molecule. The solvent Figure 3-17: Connolly or solvent-excluded surface
accessible surface (which has no central hole) shows
that it cannot. The size and shape of the solvent
accessible surface depends on the particular
solvent, since a larger solvent molecule will
predictably enjoy less access to the crevices and
interstices of a solute molecule than a smaller one.

To determine the solvent-accessible surface, a small

probe sphere simulating the solvent molecule is
rolled over the surface of the molecule (van der
Waals surface). The solvent-accessible surface is
defined as the locus described by the center of the The Connolly Surface of icrn is shown in
probe sphere, as shown in the diagram below. Figure 3-18.

Chem & BioOffice 2006 /Chem3D Displaying Models 91

Molecular Surface Displays
 Figure 3-18: Conolly surface of icrn
Administrator
Total Charge Density
The Total Charge Density is the electron density in
the space surrounding the nuclei of a molecule, or
the probability of finding electrons in the space
around a molecule. The default isocharge value of
0.002 atomic units (a.u.) approximates the
molecules van der Waals radius and represents
about 95% of the entire three-dimensional space
occupied by the molecule.
The Total Charge Density surface is the best visible
representation of a molecules shape, as determined
by its electronic distribution. The Total Charge
Density surface is calculated from scratch for each
molecule. The Total Charge Density is generally
more accurate than the Space Filling display.
For Total Charge Density surfaces, the properties
available for mapping are Molecular Orbital, Spin
Density, Electrostatic Potential, and Partial
Charges. The color scale uses red for the highest
magnitude and blue for the lowest magnitude of the
property. Neutral is white.
You can choose the orbital to map onto the surface
with the Molecular Orbital tool on the Surfaces
menu. The orbital number appears in parentheses
in the HOMO/LUMO submenu.
92 Displaying Models
Total Spin Density
The total spin density surface describes the
difference in densities between spin-up and
spin-down electrons in any given region of a
molecules space. The larger the difference in a
given region, the more that region approximates an
unpaired electron. The relative predominance of
spin-up or spin-down electrons in regions of the
total spin density surface can be visualized by color
when total spin density is mapped onto another
surface (total charge density). Entirely spin-up
(positive value) electrons are red, entirely
spin-down (negative) blue, and paired electrons
(neutral) are white.
The total spin density surface is used to examine the
unpaired electrons of a molecule. The surface exists
only where unpaired electrons are present. Viewing
the total spin density surface requires that both Spin
Density and Molecular Surfaces are calculated by
MOPAC or Gaussian using an Open Shell
Wavefunction.
Molecular Electro-
static Potential
The molecular electrostatic potential (MEP)
represents the attraction or repulsion between a
molecule and a proton. Attraction is represented by
negative values and repulsion is indicated by
positive values. Experimental MEP values can be
obtained by X-ray diffraction or electron diffraction
techniques, and provide insight into which regions
of a molecule are more susceptible to electrophilic
or nucleophilic attack. You can visualize the relative
MEP values by color when MEP is mapped onto
another surface (total charge density). The most
positive MEP value is red, the most negative blue,
and neutral is white.
CambridgeSoft
Molecular Surface Displays
Molecular Orbitals
Molecular orbital (MO) surfaces visually represent
the various stable electron distributions of a
molecule. According to frontier orbital theory, the
shapes and symmetries of the highest-occupied and
lowest-unoccupied molecular orbitals (HOMO and
LUMO) are crucial in predicting the reactivity of a
species and the stereochemical and regiochemical
outcome of a chemical reaction.
To set the molecular orbital being displayed:
From the Surfaces menu, point to Molecular
Orbital to see the HOMO/LUMO options.
Select the orbital.
You can specify the isocontour value for any
computed MO surface using the Isocontour tool on
the Surfaces menu. The default isocontour value
for a newly computed surface is the value you last
Chem & BioOffice 2006 /Chem3D
specified for a previously computed surface. If you
have not specified an isocontour value, the default
value is 0.01.
NOTE: The default isocontour value for an MO surface
imported from a cube file is 0.01 regardless of any previously
set isocontour value.
Visualizing Surfaces
from Other Sources
You can use files from sources other than Chem3D
to visualize surfaces. From Windows sources, you
can open a Gaussian Formatted Checkpoint (.fchk)
or Cube (.cub) file.
From sources other than Windows, create a
Gaussian Cube file, which you can open in
Chem3D.
Displaying Models 93
Visualizing Surfaces from Other Sources
Administrator

94 Displaying Models CambridgeSoft

Visualizing Surfaces from Other Sources
Chapter 4: Building and Editing
Models
Overview Intelligent mode yields a chemically reasonable 3D
model as you build. Fast mode provides a quick way
Chem3D enables you to build or change a model by to generate a backbone structure. You can then turn
three principal methods: it into a chemically reasonable 3D model by using
the Structure menu Rectify and Clean Up tools.
Using the ChemDraw panel, which utilizes
ChemDraw to build and insert or copy and edit To change the Building mode:
models.
1. From the File menu, choose Model Settings.
Using Bond tools, which build using carbon
exclusively. The Model Settings dialog box appears.
Using the Build from Text tool (hereafter 2. Select the Model Building tab.
referred to as the Text tool), which allows you
Figure 4-1: The Model Building controls
to build or edit models using atom labels and
substructures.
Usually, a combination of methods yields the best
results. For example, you might build a carbon
skeleton of a model with ChemDraw or the bond
tools, then change some of the carbons into other
elements with the Text tool. Or you can build a
model exclusively using the Text tool.

In addition, you can use Structure tools to change

bond lengths and angles, or to change
stereochemistry.

Setting the Model

Building Controls
You control how you build by changing options in
the Building control panel in the Model Settings
dialog box. The default mode is all options selected.
You can choose to build in a faster mode, with less
built-in chemical intelligence, by turning off one 3. Select or deselect the appropriate radio
or more of the options. buttons.

Chem & BioOffice 2006 /Chem3D Building and Editing Models 95

Setting the Model Building Controls
 The following table describes the Model Build
controls
Control Description
Administrator
Correct Atom Determines whether atom types
Types are assigned to each atom as you
build. Atom types, such as C
Alkane specify the valence,
bond lengths, bond angles, and
geometry for the atom.
Rectify Determines whether the open
valences for an atom are filled,
usually with hydrogen atoms.
Apply Standard Determines whether the stan-
Measurements dard measurements associated
with an atom type are applied as
you build.
Fit Model to Determines whether the entire
Window model is resized and centered in
the model window after a
change to the model is made.
Detect Conju- When selected, all bonds in a
gated System conjugated system are set at a
bond order of 1.5. When unse-
lected, bonds are displayed as
drawn. Does not affect previ-
ously drawn structures.
Bond Proxi- Determines whether a bond is
mate Addition created between a selection of
(%) atoms. For more information
see Creating Bonds by Bond
Proximate Addition on page
106.
96 Building and Editing Models
NOTE: For more information about atom types, standard
measurements, and rectification, see Model Building
Basics on page 44.
Building with the Chem-
Draw Panel
Chem3D 10 makes it easier than ever to create or
edit models in ChemDraw. The ChemDraw panel is
activated from the View menu. Using ActiveX
technology, it puts the functionality of ChemDraw
Pro at your fingertips.
To add a new structure to Chem3D:
1. Open the ChemDraw Panel by selecting it from
the View menu.
The ChemDraw panel appears on the right of
the model window.
2. Click in the panel to activate it.
The Tools palette appears.
TIP: If you dont see the Tools palette, right-click in
the ChemDraw panel, and check the View menu to see
that it has been activated. There should be a check
mark next to Show Main Tools. While you are at it,
you might want to activate other toolbars. Activating the
General tools toolbar, for example, will give you access
to undo/redo commands.
3. Build the structure.
The model appears simultaneously in both the
ChemDraw and Chem3D model windows.
Unsynchronized Mode
By default, the ChemDraw panel works in
synchronized mode. In this mode, your model
appears simultaneously in the ChemDraw panel
and in Chem3D. Editing either model changes the
other automatically. This affords maximum editing
flexibility.
CambridgeSoft
Building with the ChemDraw Panel
To turn off synchronized mode:
Click the Synch button at the top left of the
ChemDraw panel. The button toggles synchro-
nization on and off.
To copy a model to Chem3D, click either the
Add or Replace icon.
Name=Struct
The ChemDraw panel has a Name=Struct window
that allows you to build models by entering a
chemical name or SMILES string. You can also
copy names or SMILES strings from other
documents and paste them, either into the
Name=Struct window, or directly into the Chem3D
model window.
TIP: You can also paste chemical formulas into the
Chem3D model window. Be aware, however, that a formula
may not represent a unique structure, and the results may not
be correct.
Building with Other 2D
Programs
You can use other 2D drawing packages, such as
ISIS/Draw to create chemical structures then copy
them into Chem3D for automatic conversion to a
3D model.
To build a model with 2D drawings:
1. In the source program, copy the structure to
the clipboard.
2. In Chem3D, from the Edit menu, choose
Paste.
The 2D structure is converted to a 3D model.
Chem & BioOffice 2006 /Chem3D
The standard measurements are applied to the
structure. For more information see
Appendix D: 2D to 3D Conversion.
NOTE: You cannot paste from ISIS/Draw into the
ChemDraw panel, only into the Chem3D model
window. You can, however use the synchronize control to
add the model to the ChemDraw panel.
You can also cut-and-paste, or drag-and-drop,
models to and from ChemDraw to Chem3D or the
ChemDraw panel. See Copying to Other
Applications on page 154 for more information on
pasting into other applications.
Non-bond or atom objects copied to the clipboard
(arrows, orbitals, curves) are ignored by Chem3D.
Superatoms in ISIS/Draw are expanded if
Chem3D finds a corresponding substructure. If a
corresponding structure is not found, you must
define a substructure. For more information see
Defining Substructures on page 212.
Building With the Bond
Tools
Use the bond tools to create the backbone structure
of simple models. Bond tools always create bonds
that terminate with carbon atoms. Hydrogens
display automatically by default. You can hide them
to reduce clutter. You can change the carbons or
hydrogens to other elements after you create the
generic model.
To create a model using a Bond tool:
1. Choose a bond tool. The Single Bond tool is
used in this example.
2. Point in the model window, and drag in the
direction you want the bond to be oriented.
3. Release the mouse button to complete the
bond.
Building and Editing Models 97
Building With the Bond Tools
 When Correct Atom Types and Rectify settings
are selected in the Building control panel, the
atom type is set according to the bond tool
used (C Alkane in this example) and the
Administrator
appropriate number of hydrogens are added.
To add bonds to the model:
4. Point to an atom and drag in the direction you
want to create another atom.
Figure 4-1: Adding bonds to a model
1. Click and hold the 2. Drag in any direction and
mouse button on an atom release the mouse button
When the Rectify option is set in the Building
control panel, the hydrogen is replaced by a
carbon.
Figure 4-2: Viewing a model with Rectify on
5. Repeat adding bonds until you have the model
you want.
After you have the backbone, you can change
the carbons to different heteroatoms.
Creating Uncoordinated
Bonds
Use the Uncoordinated Bond tool to create an
uncoordinated bond with a dummy atom (labeled
Du). Uncoordinated Bonds and dummy atoms are
98 Building and Editing Models
ignored in all computations. An uncoordinated
bond allows you to specify a connection between
two atoms without a strict definition of the type of
bond. This bond is often used in coordination
complexes for inorganic compounds, where
another element might be substituted.
Dummy atoms are also useful for positioning atoms
in a Z-matrix, perhaps for export to another
application for further analysis. This is a common
use when models become large and connectivities
are difficult to specify.
To add an uncoordinated bond and dummy atom:
1. Select the Uncoordinated Bond tool .
2. Point to an atom and drag from the atom.
An uncoordinated bond and a dummy atom
are added to the model. The atom created is
labeled Du, the Chem3D element symbol
for Dummy atoms.
Figure 4-3: Dummy atoms
Dummy atom
Removing Bonds and Atoms
When you remove bonds and atoms:
Click a bond to remove only that bond.
Click an atom to remove the atom and all
attached bonds.
To remove an atom or bond, do one of the
following:
CambridgeSoft
Building With the Bond Tools

Click the Eraser tool and click the atom
or bond.
Select the atom or bond, and from the Edit
menu, choose Clear.
Select the atom or bond and press Delete.
NOTE: If automatic rectification is on, you will not be able
to delete hydrogen atoms. Turn rectification off when editing
a model.
Building With The Text
Tool
The Text tool allows you to enter text that
represents elements, atom types (elements with
specific hybridization), substructures, formal
charges, and serial numbers. The text you enter
must be found in either the Elements, Atom Types,
or Substructures tables. The match must be exact,
including correct capitalization. These tables can be
found in the Parameter Tables list on the View
menu.
NOTE: For all discussions below, all the Building control
panel options in the Chem 3D Model Settings dialog box are
assumed to be turned on.
Some general rules about using the Text Tool are as
follows:
Text is case sensitive. For example, the correct
way to specify a chlorine atom is Cl. The
correct way to specify the phenyl group
substructure is to type Ph. PH or ph will not be
recognized.
Pressing the Enter key applies the text to the
model.
Typing a formal charge directly after an
element symbol will set the formal charge for
that atom. For example PhO- will create a
model of a phenoxide ion instead of phenol.
Chem & BioOffice 2006 /Chem3D
If you double click an atom, the contents of the
previous text box are applied to that atom. If
the atom is one of several selected atoms, then
the contents of the previous text box are
applied to all of the selected atoms.
If a tool other than the Text tool is selected,
double-clicking in the model window is equiv-
alent to clicking with the Text tool selected.
Triple-clicking in the model window is equiva-
lent to double-clicking with the Text tool
selected.
The interpretation of the text in a text box depends
on whether atoms are selected as follows:
If the model window is empty, a model is built
using the text.
If you have one or more atoms selected, the
text is added to the model at that selection if
possible. If the specifications for a selected
atom are violated, the connection cannot be
made.
If you have a model in the window, but do not
have anything selected, a second fragment is
added, but is not connected to the model.
When a text box is visible, you can modify the
selection by Shift+clicking or Shift-dragging
across atoms.
Using Labels
To use an element symbol in a text box:
1. Select the Text tool.
2. Click in the model window.
A text box appears.
3. Type C.
4. Press the Enter key.
A model of methane appears.
The atom type is automatically assigned as a
C Alkane, and the appropriate number of
hydrogens are automatically added.
Building and Editing Models 99
Building With The Text Tool
 To use the same text to add another methyl group:
1. Point to the atom you want to replace, in this
example a hydrogen, and click.
Administrator
The Table Editor
To use the Table Editor to enter text in a text box:
1. From the View menu, point to Parameter

The text box appears with the previous label. Tables, and choose Atom Types.
2. Press the Enter key.
2. Select the element or atom type in the table.
To add a different element: 3. From the Edit menu, choose Copy.

1. Click a hydrogen atom. 4. Double-click in the Chem3D Model Window.

A text box appears over the atom. 5. In Chem3D, from the Edit menu, choose
Paste.
2. Type N.
The copied text appears in the text box.
3. Press the Enter key.
A nitrogen is added to form ethylamine. Specifying Order of Attachment
To build ethylamine in one step: In both the simple and complex forms for using the
Text tool, you can specify the order of attachment
1. Click in the model window. and repeating units by numbers and parentheses.
A text box appears. For example:
2. Type CH3CH2NH.
Type (CH3)3CNH2 into a text box with no
3. Press the Enter key. atoms selected and press the Enter key.
A model of ethylamine appears. A model of tert-butylamine appears.

Changing atom types Using Substructures

You can use a text box to change the atom type and You can use pre-defined functional groups called
bonding characteristics. substructures to build models. Some advantages for
To change the atom type of some atoms: using substructures in your model building process
are as follows:
1. Click a carbon atom.
Substructures are energy minimized.
A text box appears.
Substructures have more than one attachment
2. Shift+click the other carbon atom. atom (bonding atom) pre-configured.
Both atoms are selected. For example, the substructure Ph for the
3. Type C Alkene. phenyl group has a single attachment point.
The substructure COO for the carboxyl group
4. Press the Enter key.
has attachment points at both the Carboxyl
The atom type and the bond order are changed carbon and the Alcohol Oxygen. These
to reflect the new model of ethyleneamine. You provide for insertion of this group within a
can point at the atoms and bonds to display this model. Similar multi-bonding sites are defined
new information. for all amino acid and other polymer units.

100 Building and Editing Models CambridgeSoft

Building With The Text Tool
 Amino Acid substructures come in both alpha
(indicated by the amino acid name alone) and
beta (indicated by a - preceding the name of
the amino acid) forms. The dihedral angles
have been preset for building alpha helix and
beta sheet forms.
You can use substructures alone or in combi-
nation with single elements or atom types.
Using a substructure automatically creates a
record in the Groups table that you can use for
easy selection of groups, or coloring by group.
Substructures are particularly useful for
building polymers.
You can define your own substructures and
add them to the substructures table, or create
additional tables. For more information, see
Defining Substructures on page 212.
The substructure appears in the model
window.
When you replace an atom or atoms with a
substructure, the atoms which were bonded to the
replaced atoms are bonded to the attachment
points of the substructure. The attachment points
left by the replaced atoms are also ordered by serial
number.
Example 1. Building Ethane with
Substructures
To build a model of ethane using a substructure:
1. Type Et or EtH into a text box with no atoms
selected.
2. Press the Enter key.

To view the available substructures: A model of ethane appears.

From the View menu, point to Parameter Figure 4-4: Ethane model
Tables, and choose Substructures.

Building with Substructures

You must know where the attachment points are
for each substructure to get meaningful structures
using this method. Pre-defined substructures have
attachment points as defined by standard chemistry
conventions. For more information see
Attachment point rules on page 211.
To use a substructure as an independent fragment,
make sure there are no atoms selected.
To insert a substructure into a model, select the
atoms which are bonded to the attachment points
of the substructure.
NOTE: When automatic rectification is on, the free valence
To build a model using a substructure: in the ethyl group is filled with a hydrogen. If automatic
1. Type the name of the substructure into a text
rectification is off, you need to type EtH to get the same result.
box (or copy and paste it from the For substructures with more than one atom with an open
Substructures table). valence, explicitly specify terminal atoms for each open
valence.
2. Press the Enter key.

Chem & BioOffice 2006 /Chem3D Building and Editing Models 101
Building With The Text Tool
 Example 2. Building a Model with a
Substructure and Several Other
Elements
Administrator
To build a model with substructures and other
elements:
1. Type PrNH2 into a text box with no atoms
selected.
2. Press the Enter key.
A model of propylamine appears.
The appropriate bonding site for the Pr
substructure is used for bonding to the
additional elements NH2.
Figure 4-5: Propylamine model
Example 3. Polypeptides
Use substructures for building polymers, such as
proteins:
1. Type HAlaGlyPheOH into a text box with no
atoms selected.
The additional H and OH cap the ends of the
polypeptide. If you dont cap the ends and
automatic rectification is on, Chem3D tries to
fill the open valences, possibly by closing a
ring.
2. Press the Enter key.
Ring closing bonds appear whenever the text in
a text box contains two or more open valences.
102 Building and Editing Models
The alpha form of the neutral polypeptide
chain composed of Alanine, Glycine, and
Phenylalanine appears.
NOTE: You can use the amino acid names preceded
with a to obtain the beta conformation, for example
HAlaGlyPheOH. To generate the
character, type Alt+0223 using the number pad
[Option+s.
The appropriate bonding and dihedral angles
for each amino acid are pre-configured in the
substructure.
Figure 4-6: HAlaGlyPheOH polypeptide model
TIP: To better view the alpha helix formation, use the
Trackball Tool to reorient the model to an end-on view. For
more information see Trackball Tool on page 120.
To change the polypeptide to a zwitterion:
1. Select the Text tool.
2. Click the terminal nitrogen.
A text box appears over the nitrogen atom.
3. Type + and press the Enter key.
The charge is applied to the nitrogen atom. Its
atom type changes and a hydrogen atom is
added.
4. Click the terminal oxygen.
A text box appears over the oxygen atom.
CambridgeSoft
Building With The Text Tool
 5. Type - in the text box and press the Enter key.
The charge is applied to the oxygen atom. Its
atom type changes and a hydrogen atom is
removed.
For amino acids that repeat, put parentheses around
the repeating unit plus a number rather than type
the amino acid repeatedly. For example, type
HAla(Pro)10GlyOH.
4. Press the Enter key.
The substructure replaces the selected atom.
For example, to change benzene to biphenyl:
1. Click the atom to replace.
A text box appears.
Figure 4-8: Changing a model with the text box

Example 4. Other Polymers

The formation of a PET (polyethylene
terephthalate) polymer with 4 units (a.k.a.: Dacron,
Terylene, Mylar) ia shown below:
Type OH(PET)4H into a text box with no atoms
selected and press the Enter key.
The H and OH are added to cap the ends of
the polymer.
Figure 4-7: PET model 2. Type Ph.
3. Press the Enter key.
Figure 4-9: Biphenyl model

Replacing an Atom with a

Substructure
The substructure you use must have the same
number of attachment points as the atom you are
replacing. For example, if you try to replace a
carbon in the middle of a chain with an Ethyl
substructure, an error occurs because the ethyl
group has only one open valence and the selected
carbon has two.
To replace an individual atom with a substructure:
Building From Tables
1. Click the Text tool.
Cartesian Coordinate tables and Z-Matrix tables
2. Click the atom to replace.
can be saved as text files or in Excel worksheets.
A text box appears. (See Z-matrix on page 48 and Cartesian
3. Type the name of the substructure to add Coordinates on page 49 for more information.)
(case-sensitive). Likewise, tables from text files or worksheets can be

Chem & BioOffice 2006 /Chem3D Building and Editing Models 103
Building From Tables
 copied into blank tables in Chem3D to create C-0.4956 0.57820.0037
models. Text tables can use spaces or tabs between
C0.4956 -0.57820.0037
columns.
H0.0552 1.55570.0037
For a Cartesian table, there must be four columns
Administrator

(not including the Serial Number column) or five H-1.1517 0.52520.9233

columns (if the Serial Number column is included.) H-1.1569 0.5248-0.9233
The relative order of the the X-Y-Z columns must
H-0.0552 -1.55570.0037
be preserved; otherwise column order is not
important. H1.1517 -0.52520.9233

For a Z-Matrix table, there must be seven columns H1.1569 -0.5248-

(not including Serial Number column) or eight 0.9233
columns (if the Serial Number column is included.) -----------------------
The column order must NOT be changed.
Example 3: ethenol Z-Matrix table (tab as
To copy a Cartesian or Z-Matrix table into separator)
Chem3D:
C
1. Select the table in the text or Excel file.
C1 1.33
2. Use Ctrl+C to transfer to the clipboard.
O2 1.321 119.73
3. Right-click in a blank table in Chem3D and
H3 0.9782 109 1 180
select Paste.
H2 0.991 119 3 180
Examples H1 0.9892 119.5 3 180
Example 1: chloroethane Cartesian table H1 0.9882 119 3 0
(space character as separator)

C 0 -0.464725 0.336544 0.003670

Changing an Atom to
C 0 0.458798 -0.874491 0.003670
Another Element
Cl 0 0.504272 1.818951 0.003670 To change an atom from one element to another:
H 0 -1.116930 0.311844 0.927304 1. Click the Text tool.
H 0 -1.122113 0.311648 -0.927304 2. Click the atom to change.

H 0 -0.146866 -1.818951 0.003670 A text box appears.

H 0 1.116883 -0.859095 0.923326
H 0 1.122113 -0.858973 -0.923295
-------------------------
Example 2: ethane Cartesian table (tab as separator)
3. Type the symbol for the element you want
(case-sensitive).
4. Press the Enter key.
As long as the Text tool is selected, you can double-
click other atoms to make the same change.

104 Building and Editing Models CambridgeSoft

Changing an Atom to Another Element
For example, to change benzene to pyridine: To change more than one atom:

1. Click the atom to replace and type NH2. 1. Use Shift+click to select the atoms to change.

Figure 4-10: Making multiple changes with the text 2. Type the name of the atom type (case sensi-
box tive).
3. Press the Enter key.
For many atom types that change bond order, you
must select all atoms attached to the bond so that
the correct bond forms.
For example, to change ethane to ethene:
1. Select both carbons.
2. Type C Alkene.
2. Press the Enter key. 3. Press the Enter key.

Figure 4-11: Pyridine model

Changing Bonds
To change the bond order of a bond you can use the
bond tools, commands, or the Text tool.
You can change the bond order in the following
ways:
One bond at a time.
Several bonds at once.
By changing the atoms types on the bond.

To change the bond order with the bond tool:

1. Select a bond tool (of a different order).

Changing an Atom to 2. Drag from one atom to another to change.

Another Atom Type To change the bond order using a command:

1. Select a bond.
To change a single atom:
2. From the context menu, point to Set Bond
1. Click the Text tool. Order, and choose a bond order.
2. Click the atom to change.
To change the bond order by changing the atom
A text box appears. type of the atoms on either end of the bond:
3. Type the name of the atom type (case sensi- 1. Click the Text tool.
tive).
2. Shift+click all the atoms that are attached to
4. Press the Enter key. bonds whose order you want to change.

Chem & BioOffice 2006 /Chem3D Building and Editing Models 105
Changing Bonds
 3. Type the atom type to which you want to
change the selected atoms.
4. Press the Enter key.
The bond orders of the bonds change to reflect
Administrator
the new atom types.
To change several bonds at once:
1. Open the ChemDraw panel and click in it to
activate the ChemDraw control.
2. Choose either selection tool, Lasso or
Marquee.
3. Click the first bond to be changed, then use
Shift+Click to select the others.
4. Right-click in the selected area, and choose the
bond type.
Figure 4-12: Using a context menu to change bonds
5. Click in the Chem3D window to complete the
action.
Creating Bonds by Bond
Proximate Addition
Atoms that are within a certain distance (the bond
proximate distance) from one another can be
automatically bonded.
Chem3D determines whether two atoms are
proximate based on their Cartesian coordinates and
the standard bond length measurement.
106 Building and Editing Models
Pairs of atoms whose distance from each other is
less than the standard bond length, plus a certain
percentage, are considered proximate. The lower
the percentage value, the closer the atoms have to
be to the standard bond length to be considered
proximate. Standard bond lengths are stored in the
Bond Stretching Parameters table.
To set the percentage value:
1. From the File menu, choose Model Settings.
The Chem 3D Model Settings dialog box
appears.
2. Select the Model Build tab.
3. Use the Bond Proximate Addition% arrows
to adjust the percentage added to the standard
bond length when Chem3D assesses the prox-
imity of atom pairs.
You can adjust the value from 0 to 100%. If the
value is zero, then two atoms are considered
proximate only if the distance between them is
no greater than the standard bond length of a
bond connecting them. For example, if the
value is 50, then two atoms are considered
proximate if the distance between them is no
greater than 50% more than the standard
length of a bond connecting them.
To create bonds between proximate atoms:
1. Select the atoms that you want tested for bond
proximity.
2. From the context menu, point to Bond(s) and
choose Proximate.
If they are proximate, a bond is created.
Adding Fragments
A model can be composed of several fragments.
If you are using bond tools, begin building in a
corner of the window.
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Adding Fragments
If you are using the Text tool:
1. Click in an empty area of the window.
A text box appears.
2. Type in the name of an element, atom type, or
substructure.
3. Press the Enter key.
The fragment appears.
For example, to add water molecules to a window
containing a model of formaldehyde:
1. Click the Text tool.
2. Click in the approximate location you want a
water molecule to appear.
A text box appears.
3. Type H2O.
4. Press the Enter key.
The fragment appears.
5. Double-click in a different location to add
another H2O molecule.
Figure 4-13: H2O model
View Focus
As models become large, keeping track of the
section you are working on becomes more difficult.
With version 9.0.1, Chem3D adds the notion of
view focus, defined as the set of atoms that the
user is interested in working on. By default, the view
focus includes all of the atoms in the model.
Chem & BioOffice 2006 /Chem3D
To change the view focus to include only those
atoms and bonds you are working on:
1. Select the fragment or set of atoms or bonds.
2. Click Set Focus to Selection on the View Focus
submenu of the View menu.
Once you have set the view focus, the following
things happen:
When building with the bond tools, Chem3D
will resize and reposition the view so that all of
the atoms in the view focus are visible.
As new atoms are added, they become part of
the view focus.
When rotating, or resizing the view manually,
the rotation or resize will be centered around
the view focus.
Setting Measurements
You can set the following measurements using the
Measurements submenu of the Structure menu:
Bond lengths
Bond angles
Dihedral angles
Close contacts
NOTE: When you choose Measurement from the Structure
menu, the display of the Set Measurement option will vary,
depending on what you have selected. The grayed-out option
says Set Measurement; when you select a bond, it says Set
Bond Length, etc.
When you use the Clean Up Structure command,
the bond length and bond angle values are
overridden by the standard measurements from the
Optimal column of the Measurement table. These
optimal values are the standard measurements in
the Bond Stretching and Angle Bending parameter
tables. For all other measurements, performing a
Building and Editing Models 107
Setting Measurements
 Clean Up Structure or MM2 computation alters
these values. To use values you set in these
computations, you must apply a constraint.
Setting Bond Lengths
Administrator
To set the length of a bond between two bonded
atoms:
1. Select two adjacent atoms.
2. From the Structure menu, point to Measure-
ment and choose Set Bond Length Measurement.
The Measurements table appears, displaying
distance between the two atoms. The Actual
value is highlighted.
3. Edit the highlighted text.
4. Press the Enter key.
Setting Bond Angles
To set a bond angle:
1. Select three contiguous atoms for a bond angle.
2. From the Structure menu, point to Measure-
ment and choose Set Bond Angle Measurement.
The Measurements table appears, displaying
the angle value. The Actual value is highlighted.
3. Edit the highlighted text.
4. Press the Enter key.
Setting Dihedral Angles
To set a dihedral angle:
1. Select four contiguous atoms.
2. From the Structure menu, point to Measure-
ment and choose Set Dihedral Measurement.
The Measurements table appears, displaying
the angle value. The Actual value is highlighted.
3. Edit the highlighted text.
4. Press the Enter key.
108 Building and Editing Models
Setting Non-Bonded
Distances (Atom Pairs)
To set the distance between two non-bonded atoms
(an atom pair):
1. Select two unbonded atoms.
2. From the Structure menu, point to Measure-
ment and choose Set Distance Measurement.
The Measurements table appears, displaying
the distance. The Actual value is highlighted.
3. Edit the highlighted text.
4. Press the Enter key.
Atom Movement When
Setting Measurements
When you change the value of a measurement, the
last atom selected moves. Chem3D determines
which other atoms in the same fragment also move
by repositioning the atoms that are attached to the
moving atom and excluding the atoms that are
attached to the other selected atoms.
If all of the atoms in a measurement are within a
ring, the set of moving atoms is generated as
follows:
Only one selected end atom that describes the
measurement moves while other atoms
describing the measurement remain in the
same position.
If you are setting a bond length or the distance
between two atoms, all atoms bonded to the
non-moving selected atom do not move. This
set of non-moving atoms is extended through
all bonds. From among the remaining atoms,
any atoms which are bonded to the moving
atom move; this set of moving atoms is also
extended through all bonds.
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Setting Measurements
 If the Automatically Rectify check box in the
Building control panel is selected, rectification
atoms that are positioned relative to an atom
that moves may also be repositioned.
For example, consider the structure in Figure 4-14:
Figure 4-14: Cyclopentylmethanol model
If you set the bond angle C(1)-C(2)-C(3) to 108
degrees, C(3) becomes the end moving atom. C(1)
and C(2) remain stationary. H(11) and H(12) move
because they are not part of the ring but are bonded
to the moving atom. If the Automatically Rectify
check box is selected, H(10) may move because it is
a rectification atom and is positioned relative to
C(3).
Setting Constraints
You can override the standard measurements which
Chem3D uses to position atoms by setting
constraints. Constraints can be used to set an
optimal value for a particular bond length, bond
angle, dihedral angle, or non-bonded distance,
which is then applied instead of the standard
measurement when you use Clean Up Structure or
perform a Docking, Overlay, or MM2 computation.
To set constraints:
Enter a new value for the constraint in the
Optimal field of the Measurements table.
Chem & BioOffice 2006 /Chem3D
In the case of dihedral angles and non-bonded
distances, a constraint will have the effect of
keeping that measurement constant (or nearly so)
while the remainder of the model is changed by the
computation. The constraint doesnt remove the
atoms from a computation.
Setting Charges
Atoms are assigned a formal charge based on the
atom type parameter for that atom and its bonding.
You can display the charge by pointing to the atom.
To set the formal charge of an atom:
1. Click the Text tool.
2. Select the atom or atoms to change.
3. Type + or - followed by the number of the
formal charge.
4. Press the Enter key.
To set the formal charge of an atom in a molecular
fragment as you build you can add the charge after
the element in the text as you build.
To add the charge:
1. Type PhO- into a text box with no atoms
selected.
2. Press the Enter key.
The phenoxide ion molecule appears.
To remove the formal charge from an atom:
1. Click the Text tool.
2. Select the atom or atoms whose formal charge
you want to remove.
3. Type +0.
4. Press the Enter key.
Setting Serial Numbers
Atoms are assigned serial numbers when they are
created. You can view the serial numbers in the
following ways:
Building and Editing Models 109
Setting Charges
 Point to the atom to display the pop-up infor-
mation.
From the Model Display submenu of the View
menu, choose Show Serial Numbers.
Administrator
In the Chem 3D Model Settings dialog box,
choose the Atom Labels tab, then check the
Show Serial Numbers checkbox.
Click the Serial Number toggle on the
Model Display Toolbar.
Serial numbers are initially assigned based on the
order in which you add atoms to your model.
To change the serial number of an atom:
1. If you are using the Model Explorer, select the
atoms you want to re-number, and select Hide
Atom Serial Number from the Atom Serial
Numbers submenu of the context menu.
Figure 4-15: Changing atom serial numbers with a
context menu
NOTE: The Model Explorer cannot update its
numbering to match the changes you are making on the
model when Serial Numbers are displayed. If you forget
this step, you will see different numbers on the tree
control and the model. If this happens, simply hide the
serial numbers momentarily and redisplay them.
2. Click the Text tool.
3. Click the atom to reserialize.
110 Building and Editing Models
A text box appears.
4. Type the serial number.
5. Press the Enter key.
If the serial numbers of any unselected atoms
conflict with the new serial numbers, then those
unselected atoms are renumbered also.
To reserialize another atom with the next sequential
number:
Double-click the next atom you want to reseri-
alize.
To reserialize several atoms at once:
1. Click the Text tool.
2. Hold down Shift and select several atoms.
3. Type the starting serial number.
4. Press the Enter key.
Normally, the selected atoms are reserialized in the
order of their current serial numbers. However, the
first four atoms selected are reserialized in the order
you selected them.
Changing Stereochem-
istry
You can alter the stereochemistry of your model by
inversion or reflection.
Inversion
The Invert command performs an inversion
symmetry operation about a selected chiral atom.
To perform an inversion:
1. Select the atom.
2. From the Structure menu, choose Invert.
The Invert command only repositions side
chains extending from an atom.
For example, if you choose Invert for the structure
in Figure 4-16 when C(1) is selected:
CambridgeSoft
Changing Stereochemistry
Figure 4-16: Cyclohexylmethylamine model
The structure in Figure 4-17 is created.
Figure 4-17: Inverted cyclohexylmethylamine model
To invert several dihedral angles (such as all of the
dihedral angles in a ring) simultaneously:
1. Select the dihedral angles to invert.
2. From the Structure menu, choose Invert stere-
ochemistry.
All of the dihedral angles that make up the ring
are negated. Atoms positioned axial to the ring
are repositioned equatorial. Atoms positioned
equatorial to the ring are repositioned axial.
Reflection
use the Reflect command to perform reflections on
your model through any of the specified planes.
When you choose the Reflect commands certain
Cartesian coordinates of each of the atoms are
negated. When you choose Reflect Through Y-Z
Plane, all of the X coordinates are negated. You can
choose Reflect Through X-Z Plane to negate all of the
Y coordinates. Likewise, you can choose Reflect
Through X-Y Plane to negate all of the Z coordinates.
You can choose Invert through Origin to negate all of
the Cartesian coordinates of the model.
Chem & BioOffice 2006 /Chem3D
If the model contains any chiral centers, each of
these commands change the model into its
enantiomer. If this is done, all of the Pro-R
positioned atoms become Pro-S and all of the Pro-S
positioned atoms become Pro-R. All dihedral
angles used to position atoms are negated.
NOTE: Pro-R and Pro-S within Chem3D are not
equivalent to the specifications R and S used in standard
chemistry terminology.
For example, for the structure in Figure 4-18, when
any atom is selected:
From the Structure menu, point to Reflect
Model and choose Through X-Z Plane.
Figure 4-18: Reflecting through a plane
Chem3D produces the enantiomer in Figure 4-19.
Figure 4-19: Enantiomer produced by reflection
Refining a Model
After building a 3D structure, you may need to
clean it up. For example, if your model was built
without automatic rectification, atom type
assignment, or standard measurements, you can
apply these as a refinement.
Building and Editing Models 111
Refining a Model
 Rectifying Atoms
To rectify the selected atoms in your model:
Administrator
From the Structure menu, choose Rectify.
Hydrogen atoms are added and deleted so that
each selected atom is bonded to the correct
number of atoms as specified by the geometry
for its atom type. This command also assigns
atom types before rectification.
The atom types of the selected atoms are
changed so that they are consistent with the
bound-to orders and bound-to types of
adjacent atoms.
112 Building and Editing Models
Cleaning Up a Model
Normally, Chem3D creates approximately correct
structures. However, it is possible to create
unrealistic structures, especially when you build
strained ring systems. To correct unrealistic bond
lengths and bond angles use the Clean Up Structure
command.
To clean up the selected atoms in a model:
From the Structure menu, choose Clean Up .
The selected atoms are repositioned to reduce
errors in bond lengths and bond angles. Planar
atoms are flattened and dihedral angles around
double bonds are rotated to 0 or 180 degrees.
CambridgeSoft
Refining a Model
Chapter 5: Manipulating Models
Overview Figure 5-1: The Model Explorer

Chem3D provides tools to manipulate the models

you create. You can show or hide atoms and select
groups to make them easier to manipulate.
Molecules can be rotated, aligned, and resized.

Selecting
Most operations require that the atoms and bonds
that are operated on be selected. Selected atoms and
bonds are highlighted in the model display. You can
change the default highlight color in the Model
Model Explorer tab
Settings dialog box.
Figure 1: The Model Settings dialog box
Colors and Fonts
tab

Set Highlight
Color

To select an atom using the Model Explorer:

Selecting Single Atoms and
Bonds
You can select atoms and bonds in the model
window or by using the Model Explorer. If the
Model Explorer is not active, open it from the View
menu.
1. Open the Model Explorer.
2. Select the atom in the Explorer.
The atom is selected in the model. Any
previously selected atoms or bonds are
deselected.
To select an atom or bond in the display window:
1. Click the Select tool .
2. Click the atom or bond.
Any previously selected atoms and bonds are
deselected. When you click a bond, both atoms
on the bond are selected.

Chem & BioOffice 2006 /Chem3D Manipulating Models 113

 Selecting Multiple Atoms
and Bonds
To select multiple individual atoms and bonds, do
Administrator
one of the following:
Shift+click atoms or bonds in the display
window to select them.
Ctrl+click atoms in the Model Explorer to
select them.
Shift+click atoms in the Model Explorer to
select all atoms between (and including) the
two selected.
NOTE: Selecting two adjacent atoms will also select
the bond between them.
To quickly select all atoms and bonds in a model:
From the Edit menu, choose Select All.
NOTE: If the last action performed was typing in a text
box, all of its text is selected instead of the atoms in the model.
Deselecting Atoms and
Bonds
When you deselect an atom, you deselect all
adjacent bonds. When you deselect a bond, you
deselect the atoms on either end if they are not also
connected to another selected bond.
To deselect a selected atom or bond, do one of the
following:
Shift+click the atoms or bonds in the display
window.
Ctrl+click the atom in the Model Explorer.
114 Manipulating Models
If Automatically Rectify is on when you deselect an
atom, adjacent rectification atoms and lone pairs are
also deselected.
NOTE: A rectification atom is an atom bonded to only one
other atom and whose atom type is the rectification type for
that atom.
To deselect all atoms and bonds:
Click in an empty area of the Model window.
With the Model Explorer, you can use different
selection highlight colors for different fragments or
groups. To change the highlight color in the Model
Explorer:
Right-click at any level and choose Select Color.
See Working With the Model Explorer on page
136 for information on other functions of the
Model Explorer.
Selecting Groups of Atoms
and Bonds
You can define groups of atoms (and fragments or
large models) and use the Model Explorer to select
the entire group. You can also select groups of
atoms without defining them as a group with the
selection rectangle.
Using the Selection Rectangle
To select several atoms and bonds using the
Selection Rectangle:
Drag diagonally across the atoms you want to
select.
Figure 5-2
CambridgeSoft
Any atoms that fall at least partially within the
Selection Rectangle are selected when you release
the mouse button. A bond is selected only if both
atoms connected by the bond are also selected.
To keep previously selected atoms selected:
Hold down the Shift key while you make
another selection.
If you hold down the Shift key and all of the
atoms within the Selection Rectangle are
already selected, then these atoms are
deselected.
Defining Groups
You can define a portion of your model as a group.
This provides a way to easily select and to highlight
part of a model (such as the active site of a protein)
for visual effect.
To define a group:
1. Select the atoms and bonds you want in the
group. Using the select tool, select the first
atom then use Shift+click to select the other
atoms and bonds.
Once colors are assigned in the Substructures table,
you can use them to apply color by group:
1. From the File menu, choose Model Settings.
2. Select the Model Display control panel.
3. Select the Group radio button in the Color by
section.
Each atom in your model appears in the color
specified for its group.
NOTE: Color by Group is only displayed when Ribbon or
Cartoon display mode is selected.
Selecting a Group or Fragment
There are several ways to select a group or
fragment. The simplest is to use the Model
Explorer, and select the fragment.
Figure 5-3: Using the Model Explorer to select a frag-
ment
selects the entire chain

2. While still pointing at one of the selected

atoms, right-click and choose New Group from
the context menu.
If the groups in your model are substructures
defined in the Substructures table
(substructures.xml), you can assign standard colors
to them.

To assign (or change) a color:
1. From the View menu, point to Parameter tables
and select Substructures.
2. Double click in a cell in the Color field.
The Color dialog box appears.
3. Select a color and click OK.
4. Close and Save the Substructures table.
You may also select a single atom or bond and use
the Select Fragment command on the Edit menu.
NOTE: If you want to select more than one fragment, you
must use the Model Explorer.
After you have selected a single atom or bond, each
successive double-click will select the next higher
level of hierarchy.

Chem & BioOffice 2006 /Chem3D Manipulating Models 115

 Figure 5-4: Selection hierarchy

Option Result
Administrator

Select Atoms Selects all atoms lying within

within Distance of the specified distance from
Selection any part of the current selec-
tion.

Select Groups Selects all groups that contain

within Distance of one or more atoms lying
Selection within the specified distance
from any part of the current
selection.

Selecting Atoms or Groups
by Distance
You can select atoms or groups based on the
distance or radius from a selected atom or group of
objects. This feature is useful, among other things,
for highlighting the binding site of a protein.
To select atoms or groups by distance:
1. Use the Model Explorer to select an atom or
fragment.
2. Right-click the selected object. From the
context menu point to Select and click the
appropriate option:
Select Atoms Selects all atoms lying within
within Radius of the specified distance of the
Selection Centroid centroid of the current selec-
tion.
Select Groups Selects all groups that contain
within Radius of one or more atoms lying
Selection Centroid within the specified distance
of the centroid of the current
selection.
NOTE: 1. Atoms or groups already selected are not
included.
2. The current selection will be un-selected unless
multiple selection is used. Hold the shift key down
to specify multiple selection.

Showing and Hiding

Atoms
You may want to view your models with different
atoms visible or not visible. You can temporarily
hide atoms using the Model Explorer. To hide
atoms or groups:

116 Manipulating Models CambridgeSoft

Showing and Hiding Atoms
 Right-click at any level, point to Visibility and
click Hide... (Atom Group, etc.).
Hidden atoms or groups are displayed in
parentheses in the tree control.
By default, all levels in the hierarchy are set to
inherit the settings of the level above, but you can
reset the default to hide a group but show individual
atoms in it. To show an atom belonging to a hidden
group:
Right-click on the atom in the tree control,
point to Visibility and choose Show.
Showing Hs and Lps
To show all hydrogen atoms and lone pairs in the
model:
From the Model Display submenu of the View
menu, choose Show H's and Lp's.
A check mark appears beside the command,
indicating that it has been selected.
When Show Hs and Lps is not selected, hydrogen
atoms and lone pairs are automatically hidden.
Showing All Atoms
If you are working with a large model, it may be
difficult to keep track of everything you have
hidden. To show all atoms or groups that are
hidden:
1. Select a level in the tree control above the
hidden atoms or groups, or Shift+click to
select the entire model.
2. From the context menu point to Select and
click Select All Children.
3. Right-click again, point to Show... and choose
Inherit Setting.
Chem & BioOffice 2006 /Chem3D
Hydrogen Bonding and
Polar Hydrogen Display
Chem3D can now detect and display hydrogen
bonds in a model. You can also selectively display
only the polar hydrogen atoms in a model. Chem3D
recognizes the following hydrogen bond donor and
acceptor groups:
Hydrogen Bond Donors:
*-N-H
*-O-H
Hydrogen Bond Acceptors:
All Oxygen atoms
Nitrogen atoms in delocalized systems
Chem3D uses a liberal set of criteria to judge
whether the geometry of the donor/acceptor pair
will form a hydrogen bond.
To display hydrogen bonds:
1. On the View menu, point to Model Display,
then Hydrogen Bonds.
Figure 5-5: Displaying hydrogen bonds
2. Select which bonds you want to view.
TIP: You can also set the Model Settings dialog box
to display hydrogen bonds.
Hydrogen bonds are represented as dashed lines
between the donor hydrogen and the acceptor
atom. Bonds with less than ideal geometry are
displayed with a blue tint. The intensity of the color
increases as the bond becomes less ideal.
Manipulating Models 117
Showing and Hiding Atoms
 Figure 5-6: Hydrogen bonds in MM2 optimized water
Moving Atoms or Models
Use the Move Objects tool to move atoms and
other objects to different locations. If the atom,
Administrator

group of atoms, bond, or group of bonds that you

want to move are already selected, then all of the
selected atoms move. Using the Move Objects tool
changes the view relative to the model coordinates.
The following examples use the visualization axes
to demonstrate the difference between different
types of moving. To move an atom to a different
location on the X-Y plane:
.i.Displaying: hydrogens and lone pairs; 1. Click both the Model Axis and View Axis tools
to visualize the axes.
Chem3D 10 gives you more control over the display
of hydrogen atoms and lone pairs. There are NOTE: The axes will only appear if there is a model
separate controls for hydrogen atoms and lone in the window.
pairs, and you can choose to display only polar
hydrogens (those bonded to oxygen or nitrogen). 2. Drag with the single bond tool to create a
As with displaying hydrogen bonds, you control the model of ethane.
setting either from the View menu or the Model 3. Point to an atom using the Move Objects Tool.
Settings dialog box.
4. Drag the atom to a new location.
Figure 5-7: Setting hydrogen and lone-pair display
Figure 5-8: Moving an atom
1

Display/Hide
Hydrogen atoms

Display/Hide
Lone pairs

By default, Show Polar is selected when a

macromolecular PDB or mmCIF file is loaded.
These display modes are global options, but their
effect can be overridden by explicitly changing the
display mode of a particular atom or group in the
Model Explorer.

118 Manipulating Models CambridgeSoft

Moving Atoms or Models
 Dragging moves atoms parallel to the X-Y Moving Models with the
plane, changing only their X- and
Y-coordinates.
Translate Tool
If Automatically Rectify is on, then the
Use the Translate tool to move a model in the
unselected rectification atoms that are adjacent
to selected atoms move with the selected view window. When you use the Translate tool, you
atoms. move both the focus view and the model
coordinates along with the model. Thus, the
To move a model: models position does not change relative to the
1. With the Move Objects tool, drag across the origin.
model select it.
Figure 5-10: Translating a model
2. Drag the model to the new location.
Figure 5-9: Moving a model
1

2
Rotating Models
Chem3D allows you to freely rotate the model
around axes. When you select the Trackball tool,
four pop-up rotation bars are displayed on the
periphery of the model window. You can use these
rotation bars to view your model from different
angles by rotating around different axes. You can
also open the Rotate dialog box where you can use
the rotate dial or type the number of degrees to
Note that the View axis has moved relative to the
rotate.
model coordinates.
To display the Rotation bars:

Select the Trackball tool from the Building

toolbar.

When you mouse over an edge of the model

window, the Rotation bars appear on the edges
of the Model window.

Chem & BioOffice 2006 /Chem3D Manipulating Models 119

Rotating Models
 Figure 5-11: Rotating a model
Internal Rotation Bar Z-Axis Rotation Bar
Administrator
Y-Axis Rotation Bar X-Axis Rotation Bar
X- Y- or Z-Axis Rotations
To perform a rotation about the X-, Y-, or Z-axis:
1. Point to the appropriate Rotation bar.
If Show Mouse Rotation Zones is selected on the
GUI tab of the Preferences dialog box, the
rotation bars will pop up. This is the default
setting.
NOTE: The rotation bars are active when the
Trackball tool is selected, even if they are hidden.
2. Drag the pointer along the Rotation bar.
The number of degrees of rotation appears in
the Status bar.
Rotating Fragments
If more than one model (fragment) is in the model
window, you can rotate a single fragment or rotate
all fragments in the model window.
120 Manipulating Models
To rotate only one fragment:
1. Select an atom in the fragment you want to
rotate.
2. Hold the Shift key while dragging a rotation
bar.
To rotate all fragments, drag a rotation bar.
Trackball Tool
Use the Trackball tool to freely rotate a model.
Starting anywhere in the model window, drag
the pointer in any direction
The Status bar displays the X and Y axis
rotation.
Internal Rotations
Internal rotations alter a dihedral angle and create
another conformation of your model. You can
rotate an internal angle using the dihedral rotators
on the Rotation Dial.
Using the Rotation Dial
The Rotation Dial offers a quick method of rotating
a model or dihedral a chosen number of degrees
with reasonable accuracy. For more precision, you
can enter exact numbers into the degree display
box. The Internal Rotation icons are only available
when atoms or bonds have been selected in the
model.
To perform internal rotations in a model, you must
select at least two atoms or one bond. You may then
either rotate the model around the bond axis, or
rotate either end.
CambridgeSoft
Rotating Models
Figure 5-12: The Rotation dial
degree display box
rotate around bond axis rotate fragment
NOTE: Using the Internal Rotation Bar (the one to the left
of the workspace) rotates the model around the selected bond
axis. Note that this is a change from earlier versions of
Chem3D, where the Internal Rotation Bar rotated the
dihedral.
Internal rotation is typically specified by a bond.
The fragment at one end of the bond is stationary
while the fragment attached to the other end
rotates. The order in which you select the atoms
determines which fragment rotates. (See the
following examples.)
For example, consider ethoxybenzene (phenetole):
Chem & BioOffice 2006 /Chem3D
Figure 5-13: Rotating around a bond
To perform a rotation about the C-O bond where
the phenyl group moves:
1. Click the arrow next to the Trackball tool, and
drag the Rotation Dial onto the workspace.
2. Hold down the S key, and select the O atom.
3. Hold down the Shift and S keys, and select the
C1 atom.
4. Click the left-hand dihedral rotator.
5. Drag the dial to rotate the phenyl group.
Figure 5-14: Selecting atoms for rotation around a
bond
1st selection 2nd selection
(Anchor)
faded fragment
is rotating
To perform a rotation about the C-O bond where
the ethyl group moves, do one of the following:
Click the right-hand dihedral rotator.
Reverse the order of selection: first select C1,
then O.
Manipulating Models 121
Rotating Models
 3. Drag the dial or enter a number in the text box.
TIP: To deselect the atoms, hold down the S key and
click anywhere in the model window. TIP: The keyboard shortcuts for dihedral rotation are
Shift+B and Shift+N.
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Rotating Around a Bond Figure 5-16: Rotating a dihedral angle

To rotate the model around a specific bond:

1. Select a bond.
2. Drag the pointer along the Internal Rotation
bar.

Rotating Around a Specific Axis

You can rotate your model around an axis you
specify by selecting any two atoms in your model.
You can add dummy atoms (see Creating
Uncoordinated Bonds on page 98) as fragments to
specify an axis around which to rotate. Figure 5-17: Using the Rotation dial

Figure 5-15: Rotating Around a Specific Axis

Dummy atom
Internal
Rotation

free rotation
bond
Axis of
Rotation
axis rotation
dihedral

To rotate the model around an axis: Changing Orientation

1. Select any two atoms. Chem3D allows you to change the orientation of
2. Drag the pointer along the Internal Rotation your model along a specific axis. However your
bar. model moves, the origin of the model (0, 0, 0) does
not change, and is always located in the center of
Rotating a Dihedral Angle the model window. To change the origin, see
Centering a Selection on page 124.
You can select a specific dihedral angle to rotate. To
rotate a dihedral:

1. Select four atoms that define the dihedral.

2. Select on of the dihedral rotators on the Rota-
tion Dial.

122 Manipulating Models CambridgeSoft

Changing Orientation
Aligning to an Axis
To position your model parallel to either the
X-, Y-, or Z-axis:
1. Select two atoms only.
2. From the View menu, point to View Position,
then click Align View (choose an axis) With
Selection.
The model rotates so that the two atoms you
select are parallel to the appropriate axis.
NOTE: This changes the view, not the coordinates of
the molecule. To change the model coordinates, use the
Model Position submenu of the Structure menu.
For example, to see an end-on view of ethanol:
1. Click the Select tool.
2. Shift+click C(1) and C(2).
Figure 5-18: Selecting atom for alignment
3. From the View menu, point to View Position,
then click Align View Z Axis With Selection.
Figure 5-19: Ethane aligned on the Z-axis
Chem & BioOffice 2006 /Chem3D
Aligning to a Plane
You can align a model to a plane when you select
three or more atoms. When you select three atoms,
those atoms define a unique plane. If you select
more than three atoms, a plane is computed that
minimizes the average distance between the
selected atoms and the plane.
To position a plane in your model parallel to a plane
of the Cartesian Coordinate system:
1. Select three or more atoms.
2. From the View menu, point to View Position,
then click Align View (choose a plane) With
Selection.
The entire model rotates so that the computed
plane is parallel to the X-Y, Y-Z, or X-Z plane.
The center of the model remains in the center
of the window.
To move three atoms to a plane and two of the
atoms onto an axis:
1. Select the two atoms.
2. From the View menu, point to View Position,
then click Align View (choose an axis) With
Selection.
3. Shift+click the third atom.
4. From the View menu, point to View Position,
then click Align View (choose a plane) With
Selection.
For example, to move a cyclohexane chair so that
three alternating atoms are on the X-Y Plane:
1. Select two non-adjacent carbon atoms in the
ring, as shown in Figure 5-20 A.
2. From the View menu, point to View Position,
then click Align View X Axis With Selection.
The model moves to the position shown in
Figure 5-20 B.
Manipulating Models 123
Changing Orientation
 Figure 5-20: Aligning to the XY plane
A B
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C just the active frame.
3. Select the third carbon atom such that no two
selected atoms in the ring are adjacent.
4. From the View menu, point to View Position,
then click Align View X-Y Plane With Selection.
The model moves to the position shown in
Figure 5-20 C.
Resizing Models
Chem3D provides the following ways to resize your
model:
Resizing Windows
Scaling a Model
Centering a Selection
When resizing a model, or before doing
computations, it is often useful to center the model.
Chem3D allows you to select an atom (or atoms) to
determine the center, or performs the calculation
on the entire model.
To center your model based on a particular
selection:
1. Select one or more atoms. (optional)
2. Choose Center Model from the Model Position
submenu of the Structure menu.
124 Manipulating Models
This command places the centroid of the selected
atoms at the coordinate origin. Chem3D calculates
the centroid of the selected atoms by averaging their
X, Y, and Z coordinates. If you do not select any
atoms, the command operates on the entire model.
NOTE: This command affects all frames of your model, not
Using the Zoom Control
You can reduce or enlarge a model using the Zoom
tool.
NOTE: The Zoom tool lets you resize the
model by dragging.This changes the view, not the
coordinates of the molecule.
Scaling a Model
You can scale a model to fit a window. If you have
created a movie of the model, you have a choice of
scaling individual frames or the whole movie.
To scale a model to the window size, do one of the
following:
From the View menu, point to View Position
and click Fit To Window.
From the View menu, point to View Position
and choose Fit All Frames To Window to scale an
entire movie.
The Model To Window command operates only on
the active frame of a movie. To scale more than one
frame, you must repeat the command for each
frame you want to scale.
NOTE: The Fit command only affect the scale of the model.
Atomic radii and interatomic distances do not change.
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Resizing Models
Changing the Z-matrix
The relative position of each atom in your model is
determined by a set of internal coordinates known
as a Z-matrix. The internal coordinates for any
particular atom consist of measurements (bond
lengths, bond angles, and dihedral angles) between
it and other atoms. All but three of the atoms in
your structure (the first three atoms in the Z-matrix
which describes your model) are positioned in
terms of three previously positioned atoms.
To view the current Z-matrix of a model:
From the View menu choose Z-Matrix Table.
The First Three Atoms in a
Z-matrix
The first three atoms in a Z-matrix are defined as
follows:
Origin atomThe first atom in a Z-matrix.
All other atoms in the model are positioned
(either directly or indirectly) in terms of this
atom.
First Positioned atomPositioned only in
terms of the Origin atom. Its position is speci-
fied by a distance from the Origin atom.
Usually, the First Positioned atom is bonded to
the Origin atom.
Second Positioned atomPositioned in
terms of the Origin atom and the First Posi-
tioned atom. There are two possible ways to
position the Second Positioned atom, as
described in Figure 5-21.
Chem & BioOffice 2006 /Chem3D
Figure 5-21: Atoms in a Z-matrix
In the left example, the Second Positioned atom is
a specified distance from the First Positioned atom.
In addition, the placement of the Second
Positioned atom is specified by the angle between
the Origin atom, the First Positioned atom, and the
Second Positioned atom.
In the right example, the Second Positioned atom is
a specified distance from the Origin atom. In
addition, the placement of the Second Positioned
atom is specified by the angle between the First
Positioned atom, the Origin atom, and the Second
Positioned atom.
Atoms Positioned by Three
Other Atoms
In the following set of illustrations, each atom D is
positioned relative to three previously positioned
atoms C, B, and A. Three measurements are needed
to position D: a distance, and two angles.
Atom C is the Distance-Defining atom; D is placed
a specified distance from C. Atom B is the First
Angle-Defining atom; D, C, and B describe an
angle.
Atom A is the Second Angle-Defining atom. It is
used to position D in one of two ways:
By a dihedral angle A-B-C-D
By a second angle A-C-D.
Manipulating Models 125
Changing the Z-matrix
 In Figure 5-22 A, atom D is positioned in terms of
a dihedral angle, thus the second angle is the
dihedral angle described by A-B-C-D. This dihedral
angle is the angle between the two planes defined by
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D-C-B and A-B-C.
In Figure 5-22 B, if you view down the C-B bond,
then the dihedral angle appears as the angle formed
by D-C-A. A clockwise rotation from atom D to
atom A when C is in front of B indicates a positive
dihedral angle.
Figure 5-22: Positioning with a dihedral
A B
When D is positioned using two angles, there are
two possible positions in space about C for D to
occupy: a Pro-R position and a Pro-S position.
Figure 5-23: Positioning with two angles
NOTE: The terms Pro-R and Pro-S used in Chem3D to
position atoms bear no relation to the Cahn-Ingold-Prelog
R/S specification of the absolute stereochemical configuration
of a chiral atom. Pro-R and Pro-S refer only to the
positioning of D and do not imply any stereochemistry for C.
C may be chiral, or achiral.
126 Manipulating Models
The most convenient way to visualize how the
Pro-R/Pro-S terms are used in Chem3D to
position D is described in the following examples:
To position Atom D in Pro-S Orientation (Figure
5-24 A) and Pro-R Orientation (Figure 5-24 B):
1. Orient the Distance-Defining atom, C, the
First Angle-Defining atom, B, and the Second
Angle-Defining atom, A, such that the plane
which they define is parallel to the X-Y plane.
2. Orient the First Angle-Defining atom, B, to be
directly above the Distance-Defining atom, C,
such that the bond joining B and C is parallel to
the Y-axis, and the Second Angle-Defining
atom, A, is somewhere to the left of C.
Figure 5-24: Pro-S and Pro-R orientation
A B
In this orientation, D is somewhere in front of the
plane defined by A, B and C if positioned Pro-R,
and somewhere behind the plane defined by A, B
and C if positioned Pro-S.
When you point to or click an atom, the
information box which appears can contain
information about how the atom is positioned.
Positioning Example
If H(14) is positioned by C(5)-C(1), C(13) Pro-R,
then the position of H(14) is a specified distance
from C(5) as described by the H(14)-C(5) bond
length. Two bond angles, H(14)-C(5)-C(1), and
H(14)-C(5)-C(13), are also used to position the
atom.
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Changing the Z-matrix
Because H(14) is positioned by two bond angles,
there are two possible positions in space about C(5)
for H(14) to occupy; the Pro-R designation
determines which of the two positions is used.
Figure 5-25: Positioning example
If an atom is positioned by a dihedral angle, the
three atoms listed in the information about an atom
would all be connected by dashes, such as
C(6)-C(3)-C(1), and there would be no Pro-R or
Pro-S designation.
The commands in the Set Z-Matrix submenu allow
you to change the Z-matrix for your model using
the concepts described previously.
Because current measurements are retained when
you choose any of the commands in the Set Z-
Matrix submenu, no visible changes in the model
window occur.
Positioning by Bond Angles
To position an atom relative to three previously
positioned atoms using a bond distance and two
bond angles:
1. With the Select tool, click the second
angle-defining atom.
2. Shift-click the first angle-defining atom.
3. Shift-click the distance-defining atom.
4. Shift-click the atom to position.
You should now have four atoms selected, with
the atom to be positioned selected last.
5. From the Structure menu, point to Set
Z-Matrix, then choose Position by Bond Angles.
Chem & BioOffice 2006 /Chem3D
For example, consider the structure in Figure 5-26.
Figure 5-26: Bicyclohexane model
To position atom C(7) by two bond angles, select
atoms in the following order: C(5), C(1), C(6), C(7),
then choose Position by Bond Angles.
Positioning by Dihedral Angle
To position an atom relative to three previously
positioned atoms using a bond distance, a bond
angle, and a dihedral angle:
1. With the Select tool, click the dihedral-angle
defining atom.
2. Shift-click the first angle-defining atom.
3. Shift-click the distance-defining atom.
4. Shift-click the atom to position.
You should now have four atoms selected, with
the atom to be positioned selected last.
5. From the Structure menu, point to Set
Z-Matrix, then choose Position by Dihedral.
For example, using the previous illustration, choose
atoms in the following order: C(7), C(6), C(1), C(10)
to position C(10) by a dihedral angle in a ring. Then
choose Position by Dihedral.
Setting Origin Atoms
To specify the origin atoms of the Z-matrix for a
model:
1. With the Select tool, click the first one, two, or
three atoms to start the Z-matrix.
2. From the Structure menu, point to Set
Z-Matrix, then choose Set Origin Atom or Set
Origin Atoms.
Manipulating Models 127
Changing the Z-matrix
 The selected atoms become the origin atoms
for the Z-matrix and all other atoms are
positioned relative to the new origin atoms.
Because current measurements are retained, no
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visible changes to the model occur.

128 Manipulating Models CambridgeSoft

Changing the Z-matrix
Chapter 6: Inspecting Models
Model Data Figure 6-1: Pop-up information

You can view information about an active model as

a pop-up or in measurement windows.

Pop-up Information
You can display information about atoms and
bonds by pointing to them so that pop-up
information appears. You specify what information
appears by using the Pop-up Info tab of the
Preferences dialog box.
You can display the following information about an
atom:
Cartesian coordinates
Atom type NOTE: Precise bond orders for delocalized pi systems
Internal coordinates (Z-matrix) are displayed if the MM2 Force Field has been
Measurements computed.
Bond Length The information about an atom or bond always
Bond Order begins with the name of that object, such as C(12)
Partial Charge for an atom or O(5)-P(3) for a bond.
Examples of pop-up information are shown in , To set what pop-up information appears:
Inspecting Models.
If you want to Then Select
display

The three numerical Cartesian Coordinates.

values indicating the
atoms position along
the X, Y, and Z axes

the atom type corre- Atom Type.

sponding to the first
column of a record in
the Atom Types table

Chem & BioOffice 2006 /Chem3D Inspecting Models 129

 If you want to Then Select If you want to Then Select
display display
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a list of the atoms used Z-matrix. the bond orders calcu- Bond Order.
to position the atom lated by Minimize
NOTE: The Z-matrix Energy, Steric Energy, Bond orders are usually
definition includes or Molecular 1.000, 1.500, 2.000, or
whether the second Dynamics 3.000 depending on
angle used to position whether the bond is a
the selected atom is a single, delocalized,
dihedral angle or a double, or triple bond.
second bond angle. Computed bond orders
can be fractional.
If atoms other than the
one at which you are the partial charge Partial Charge.
pointing are selected, according to the
the currently selected See Displaying Molec-
calculation ular Surfaces on page
measurement formed by all 85 for information on
the selected atoms appears. how to select a calcula-
tion.
information relative to Measurements
other selected atoms, Non-Bonded Distances
such as the distance
between two atoms, To display non-bonded atoms measurements:
the angle formed by
three atoms, or the Select two non-bonded atoms and point to one
dihedral angle formed of them.
by four atoms.
The interatomic non-bonded distance appears in
the last line of the pop-up window.
the distance between Bond Length.
the atoms attached by a For example, in the cyclohexane model in Figure 6-
bond in angstroms 2, when you select two non-bonded atoms and
point to one of them, the interatomic non-bonded
distance appears in the last line of the pop-up
window.

130 Inspecting Models CambridgeSoft

Figure 6-2: viewing the interatomic non-bonded
distance
Measurement Table
Another way to view information about your model
is to activate the Measurement Table. This table can
display internal measurements between atoms in
your model in various ways.
To display internal measurements:
1. From the View menu, click Measurement Table.
A blank table appears in the Tables window.
2. From the Structure menu, point to Measure-
ments and select a measurement to display.
Figure 6-3: The Measurements submenu
The measurement values appear in the table.
You can display several measurements sequentially
in the table. The following table shows the bond
lengths and angles for Ethene.
Chem & BioOffice 2006 /Chem3D
Figure 6-4: Measurements table
bond
lengths
{
bond
angles
{
Editing Measurements
If you select a measurement in the Measurements
table, the corresponding atoms are selected in the
model window. If you select atoms in your model,
any corresponding measurements are selected.
To change the value of a measurement:
1. Select the text in the Actual column.
2. Type a new measurement value in the selected
cell.
3. Press the Enter key
The model reflects the new measurement.
When atoms are deleted, any measurements that
refer to them are removed from the Measurements
table.
Optimal Measurements
Optimal values are used instead of the
corresponding standard measurements when a
measurement is required in an operation such as
Clean Up Structure. Optimal measurements are
only used when the Measurements table is visible.
When the Measurements table is not visible, the
standard measurements are taken from the
parameter tables.
Inspecting Models 131
Measurement Table
 To specify optimal values for particular
measurements, edit the value in the Optimal
column.
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Chem3D also uses the optimal values with the
Dock command. When you choose Dock from the
Structure menu, Chem3D reconciles the actual
distance between atoms in two fragments to their
optimal distances by rigidly moving one fragment
relative to the other.
Non-Bonded Distances in
Tables
To display non-bonded atom measurements:
1. Select the atoms.
2. From the Structure menu, point to Measure-
ments and choose Set Distance Measurement.
The measurement between the selected atoms
is added to the table.
Figure 6-5: Adding measurements to a table
non-bonded distance
Showing the Deviation from Plane
The Deviation from Plane command allows you to
compute the RMS Deviation from the least squares
plane fitted to the selected atoms in the model.
132 Inspecting Models
Example:
To examine the Deviation from Plane for five
atoms in a penicillin molecule:
1. Build a penicillin model, as in the previous
example.
2. Using the Select tool, click on the S (4) atom.
3. Shift+click the other atoms in the
five-membered penicillin ring.
The molecule should appear as follows:
Figure 6-6: Viewing Deviation from a Plane
4. From the Structure menu, choose Deviation
from Plane.
When the deviation from plane calculation is
complete, the value appears in the Output
window.
Figure 6-7: The Output window
The result indicates that the atoms in the five-
membered ring of penicillin are not totally coplanar;
there is a slight pucker to the ring.
Removing Measurements from a Table
You can remove information from the
Measurements table without affecting the model.
To remove measurements from a table:
CambridgeSoft
Measurement Table
 From the Structure menu, point to Measure- Figure 6-8: The Internal Coordinates table
ments and choose Clear.

Displaying the Coordinates

Tables
You can view the internal coordinates or the
Cartesian coordinates of your model by choosing
Cartesian Table or Z-Matrix Table from the View
menu.

Internal Coordinates
The Internal Coordinates table contains one entry
for each atom. The fields contain a description of
how each atom in the model is positioned relative to
the other atoms in the model.
The order of atoms in the Internal Coordinates
NOTE: The default condition is that all of the tables open
table is determined by the Z-matrix. The origin
in a tabbed window when you select any one.
atom is listed first, and the rest of the atoms are
listed in the order that they are positioned. For
more information see Scaling a Model on page When you select a record in the Internal
124. Coordinates table, the corresponding atom is
selected in the model. When you select atoms in the
To display the Internal Coordinates table: model, the corresponding records are selected in
the Internal Coordinates table.
1. From the View menu choose Z-Matrix Table.
The Internal Coordinates table appears. To edit measurements in the Z-matrix:

1. Type a new measurement in the selected cell.

2. Press the Enter key.

To change which atoms Chem3D uses to position

each atom use the commands in the Set Z-matrix
submenu in the Structure menu.

Cartesian Coordinates
The fields in the Cartesian Coordinates table
contain the atom name and the X-, Y- and Z-
coordinates for each atom. The order of atoms is
determined by their serial numbers. All of the atoms
in a fragment are listed in consecutive records.
Hydrogen, lone pair and dummy atoms are listed
after heavy atoms.

Chem & BioOffice 2006 /Chem3D Inspecting Models 133

Measurement Table
 To display the Cartesian Coordinates table, do one
of the following:
If the Tables window has been activated, click
the XYZ tab at the bottom of the window.
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If the Tables window has not been activated,
choose Cartesian Table from the View menu.
The Cartesian Coordinates table appears.
The Cartesian Coordinates table acts like the other
tables: you can select atoms or bonds either in the
table or in the model. Use the pin icon to collapse
the window to save space.
Figure 6-9: Collapsed table tabs
Collapsed table tabs
Mouse over a tab to display
the table. The most recently used
table displays the full name.
Comparing Models by
Overlay
The Overlay submenu on the Structure menu is
used to lay one fragment in a model window over a
second fragment. Each fragment remains rigid
during the overlay computation.
Common uses of Overlay include:
Comparing structural similarities between
models with different composition.
Comparing conformations of the same model.
134 Inspecting Models
Chem3D provides two overlay techniques.
Tutorial 6: Overlaying Models on page 63
describes the Fast Overlay method. This section
uses the same examplesuperimposing a molecule
of Methamphetamine on a molecule of
Epinephrine (Adrenalin) to demonstrate their
structural similaritiesto describe the
Minimization Method.
1. From the File menu, choose New Model.
2. Select the Text Building tool and click in the
model window.
A text box appears.
3. Type Epinephrine and press the Enter key.
A molecule of Epinephrine appears.
4. Click in the model window, below the Epineph-
rine molecule.
A text box appears.
5. Type Methamphetamine and press the Enter key.
A molecule of Methamphetamine appears
beneath the Epinephrine molecule.
6. From the Model Display submenu of the View
menu, deselect Show Hs and Lps.
The hydrogen atoms and lone pairs in the
molecule are hidden.
The two molecules should appear as shown in
the following illustration. You may need to
move or rotate the models to display them as
shown.
TIP: To move only one of the models, select an atom in
it before rotating.
CambridgeSoft
Comparing Models by Overlay
Figure 6-10: Overlaying models Your measurements table should look something
like this:
Figure 6-11: Adding optimal values for overlay to the
Measurements table

7. From the Model Display submenu of the View Now perform the overlay computation:
menu, select Show Atom Labels and Show Serial
Numbers. NOTE: To help see the two overlaid fragments, you
can color a fragment. For more information see
The atom labels and serial numbers appear for
Working With the Model Explorer on page 136
all the visible atoms.
To perform an overlay, you must first identify atom 1. From the Model Display submenu of the View
pairs by selecting an atom in each fragment, and menu, deselect Show Atom Labels and Show
then display the atom pairs in the Measurements Serial Numbers.
table.
2. From the Structure menu point to Overlay,
Atom Pair an atom in one fragment which has a and click Minimize.
distance specified to an atom in a second fragment. The Overlay dialog box appears.
1. Select C(9) in the Epinephrine molecule. Figure 6-12: The Overlay dialog box
2. Shift+click C(27) in the Methamphetamine
molecule.
3. From the Structure menu, point to Measure-
ments and choose Set Distance.
The Measurements table appears. The Actual
cell contains the current distance between the
two atoms listed in the Atom cell.
3. Type 0.100 for the Minimum RMS Error and
4. For an acceptable overlay, you must specify at 0.010 for the Minimum RMS Gradient.
least three atom pairs, although it can be done
The overlay computation will stop when either
with only two pairs. Repeat steps 1 to 3 to
the RMS Error becomes less than the
create at least three atom pairs.
Minimum RMS Error or the RMS Gradient
5. The optimal distances for overlaying two frag- becomes less than the Minimum RMS
ments are assumed to be zero for any atom pair Gradient value.
that appears in the Measurements table. For
4. Click Display Every Iteration.
each atom pair, type 0 into the Optimal column
and press the Enter key. 5. Click Start.

Chem & BioOffice 2006 /Chem3D Inspecting Models 135

Comparing Models by Overlay
 How the fragments are moved at each iteration The default setting for all properties is Inherit
of the overlay computation is displayed. Setting. This means that parents determine the
properties of children, until you choose to change
To save the iterations as a movie, click the Record
a property. By changing some property of a lower
Each Iteration check box.
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level object, you can better visualize the part of the

To stop the overlay computation before it reaches model you want to study.
the preset minima, click Stop Calculation on Use the Model Explorer to:
the toolbar.
Define objects.
The Overlay operation stops. Recording is also
Add objects to groups.
stopped.
Rename objects.
The following illustration shows the distances
Delete objects, with or without their contents.
between atom pairs at the completion of the overlay
computation. The distances in the Actual cells are The display properties of objects you can alter
quite close to zero. include:
Changing the display mode.
Figure 6-13: Measurements table after overlay
Showing or hiding.
Changing the color.
At the atom level, you can display or hide:
Atom spheres
Atom dots
Element symbols
Your results may not exactly match those described. Serial numbers
The relative position of the two fragments or
molecules at the start of the computation can affect Model Explorer Objects
the final results.
The Model Explorer objects are:
Working With the Model Fragments
Explorer Chains
Groups
The Model Explorer displays a hierarchical tree
Atoms
representation of the model. It provides an easy way
to explore the structure of any model, even Bonds
complex macromolecules, and alter display Solvents
properties at any level. Backbone
The Model Explorer defines the model in terms of The Fragment object represents the highest level
objects. Every object has a set of properties, segment (parent) of a model. Fragments
including a property that defines whether or not it represent separate parts of the model, that is, if you
belongs to another object (is a child of a higher start at an atom in one fragment, you cannot trace
level parent object.) through a series of bonds that connect to an atom

136 Inspecting Models CambridgeSoft

Working With the Model Explorer
in another fragment. If you create a bond between
two such atoms, Chem3D will collapse the
hierarchical structure to create one fragment.
Fragment objects typically consist of chains and
groups, but may also contain individual atoms and
bonds.
virtual children of the Backbone object. This allows
you to select display properties for the backbone
that override the display properties of the chains
and groups above them in the hierarchy.
To display the Model Explorer:

In Chem3D, chains and groups are functionally
identical. Chains are special groups found in PDB
files. If you rename a group as a chain, or vice versa,
the icon will change. This is also the reason that
only the work Group is used in the menus. All
Group commands also apply to chains.
From the View menu choose Model Explorer.
The Model Explorer window appears along the
left side of the model.
Figure 6-14: The Model Explorer

Group objects can consist of other groups, atoms

and bonds. Chem3D does not limit a group to
contiguous atoms and bonds, though this is the
logical definition.

Bond objects do not appear by default in the Model

Explorer. If you want to display bonds, select Show
Bonds in the GUI tab of the Chem3D Preferences
dialog box.

The Solvent object is a special group containing all

of the solvent molecules in the model. The
individual molecules appear as child groups
within the Solvent object. A Solvent object should
not be child of any other object.

NOTE: When importing PDB models, solvents will

sometimes show up in chains. While this is incorrect,
Chem3D preserves this structure in order to be able to save
the PDB file again.
The Backbone object is a display feature that allows
you to show the carbon-nitrogen backbone
structure of a protein. It appears in the Model
Explorer as a separate object with no children. The
atoms and bonds that make up the backbone
belong to other chains and groups, but are also
To view or change a property in a model:
1. Select the object (fragment, group, or atom)
you wish to change.
TIP: To select multiple objects, use Shift+click if they
are contiguous or Ctrl+click if they are not.
2. Right-click, select the appropriate submenu,
and choose a command.

Chem & BioOffice 2006 /Chem3D Inspecting Models 137

Working With the Model Explorer
 Figure 6-15: Model Explorer context menus
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When you change an object property, the object
icon changes to green. When you hide an object,
the icon changes to red. Objects with default
properties have a blue icon.
Figure 6-16: Icons in the Model Explorer
hidden
changed
Creating Groups
Some models, PDB proteins for example, have
group information incorporated in the file. For
other models you will need to define the groups. To
do this in the Model Explorer:
1. Holding down the Ctrl key, select the atoms in
the group.
2. Choose New Group from the context menu.
138 Inspecting Models
The group is created with the default name
selected.
3. Rename the group by typing a new name.
Adding to Groups
You can add lower level objects to an existing
group, or combine groups to form new groups.
To add to a group:
1. Select the objects you want to combine, using
either Shift+click (contiguous) or Ctrl+click
(non-contiguous).
2. Select Move Objects to Group from the context
menu.
3. Rename the group, if necessary.
NOTE: The order of selection is important. The group
or chain you are adding to should be the last object
selected.
Pasting Substructures
You can cut-and-paste or copy-paste any
substructure into another structure, either within or
between model windows. In addition to the usual
methodsusing the Cut, Copy, and Paste
commands on either the Edit or Context-Sensitive
menus, or Ctrl+X, Ctrl+C, and Ctrl+Vyou can use
the Text tool to paste substructures.
To paste a substructure with the Text tool:
1. Select a fragment, chain, or group.
2. Choose Replace with Text Tool from the context
menu.
The substructure appears in a Text tool in the
model window.
3. Click the Text tool on the atom that you want
to link to the substructure.
CambridgeSoft
Working With the Model Explorer
Deleting Groups Coloring Groups
When deleting groups, you have two options: Another means of visualization is by assigning
different colors to groups. Changing a group color
If you want to Then Select in the Model Explorer overrides the standard color
settings in the Elements table and the Substructures
remove the grouping, Delete Group table.
but leave the model To change a group color:
intact
1. Select a group or groups.
delete the group from Delete Group and 2. Choose Select Color on the context menu.
the model Contents
The Color Dialog box appears.
3. Choose a color and click OK.
Using the Display Mode The Apply Group Color command is
One means of bringing out a particular part of a automatically selected.
model is by changing the display mode. The usual
To revert to the default color:
limitations apply (see Model Types on page 76).
The submenu will only display available modes. 1. Select a group or groups.
Figure 6-17 shows the effect of changing the 2. Right-click, point to Apply Group Color on the
HEM155 group of PDB-101M from Wireframe context menu and select Inherit Group Color.
(the default) to Space Filling.
The default group color is displayed.
Figure 6-17: Changing display types in the Model
Explorer Resetting Defaults
To remove changes, use the Reset All Children
command.

Animations
You can animate iterations from computations by
saving frames in a movie.You control the creation
and playback of movies from the Movie menu or
toolbar.

Creating and Playing

Movies
To display the Movie toolbar:
From the View menu, point to Toolbars and
choose Movies.
The Movie toolbar appears.

Chem & BioOffice 2006 /Chem3D Inspecting Models 139

Animations
 To create a movie, select the Record Every Iteration Spin About Selected Axis
checkbox when you set up the calculation.
To spin the model around an axis specified by a
To stop recording click Stop Calculations on selection:
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the Calculation toolbar Movie, or let the calculation Choose Spin About... from the Movie menu.
terminate according to preset values.
The Spin About... command automatically
To view different frames of your movie: activates the Record command.

1. Click the arrow on the Position button of the To stop spinning:

Movie toolbar. On the Movie toolbar, click the Stop button.
The Movie Process tool appears. Spins are automatically recorded.
Figure 6-18:The Movie tool
To replay the spins:
Click Start.

Editing a Movie
You can change a movie by removing frames.

To remove a frame:

1. Position the movie to the frame you want to

delete.
TIP: You can tear the toolbar off by dragging the title
bar. 2. Click the Remove Frame button.

2. Drag the Slider knob to the frame you wish to Movie Control Panel
view.
You can control how a movie is created by changing
TIP: You can also use the Previous and Next buttons settings in the Movies control panel in the Model
to locate a frame in the movie. Settings dialog box. You can specify the number of
frames and at what increment they are captured.
To play back a movie you created:
To display the Movies control panel:
Click Start.
1. From the Movies menu, choose Properties.
To stop playback of a movie:
2. Take the appropriate actions:
Click Stop.

Spinning Models If you want to Then

You can spin models about a selected axis. The set the movie to loop Click the Loop or Back
number of frames created when you choose a Spin or repeat backwards and Forth radio button.
command is set using the Smoothness Slider in the and forwards
Movies control panel.

140 Inspecting Models CambridgeSoft

Animations
If you want to Then

specify the speed at Drag the Speed slider

which the movie is knob to the left to play
replayed your movie at a slower
speed (a smaller
number of degrees per
second). Drag the
Speed slider knob to the
right to play your movie
at a faster speed (a
larger number of
degrees per second).

specify the number of Drag the Smoothness

degrees of rotation that slider knob to the left to
is captured as a frame capture more frames (a
while recording. smaller number of
degrees of rotation
capture a frame). Drag
the Smoothness slider
knob to the right to
capture fewer frames (a
larger number of
degrees of rotation
capture a frame).

Chem & BioOffice 2006 /Chem3D Inspecting Models 141

Animations
Administrator

142 Inspecting Models CambridgeSoft

Animations
Chapter 7: Printing and Exporting
Models
Printing Models 2. Select the appropriate options:

You can print Chem3D models to PostScript and

If you want to Then select
non-PostScript printers. Before printing you can
specify options about the print job.
resize your model Scale To and type a scaling
Specifying Print Options according to a scaling value.
factor
To prepare your model for printing: Scaling factors are
measured in pixels per
1. From the File menu, choose Print Setup.
angstrom. A pixel is 1/72
The Print Setup dialog box appears. The of an inch, or approxi-
available options depend on the printer you mately 1/28 of a centi-
use. There are five options specific to meter. With a value of 28
Chem3D, which are described in the following pixels/ngstrom your
table. model is scaled so that a
Figure 7-1: The Print Setup dialog box distance of one ngstrom
in the model is 1 centi-
meter in the printed image.
If you specify a value of 72
pixels/angstrom, a
distance of one angstrom
in the model is scaled to 1
inch on the printed image.

Chem3D options scale your model so Scale To Full Page.

the printed image fills
the printed page

print with white back- Always Print with White

ground (default) Background

Chem & BioOffice 2006 /Chem3D Printing and Exporting Models 143
 If you want to Then select
File Format Name Extension
produce publication High Resolution Printing
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quality output. (this can also be set with Alchemy Alchemy .alc; .mol
the OpenGL Preferences
settings.) Cartesian Coordi- Cart Coords 1 .cc1
nate
print a footer at the Include Footer.
bottom left of the Cart Coords 2 .cc2
printed page
containing the name CCDB Cambridge Crys- .ccd
of the model and the tallographic
date and time Database
changes were last
made
Chem3D .c3xml; .c3d

Printing Chem3D .c3t

To print the contents of the active window: template
From the File menu, choose Print.
ChemDraw ChemDraw .cdx; .cdxml
The Print dialog box appears. The contents of
the dialog box depend upon the type of printer
you are using. Connection Table Conn Table .ct; .con

The picture of the model is scaled according to the

GAMESS Input GAMESS Input .inp
settings in the Page Setup dialog box.
To print a table, right-click in the table and select Gaussian Check- .fchk; .fch
Print. point
Exporting Models Using
Gaussian Cube .cub
Different File Formats
The following table shows all of the chemistry file Gaussian Input Gaussian Input .gjc; .gjf
formats supported by Chem3D. For more
information about file formats, see Appendix E: Internal Coordi- Int Coords .int
File Formats. nates

MacroModel MacroModel .mcm; .dat;

.out

144 Printing and Exporting Models CambridgeSoft

Exporting Models Using Different File Formats
 Publishing Formats
File Format Name Extension
The following file formats are used to import
Molecular Design MDL MolFile .mol and/or export models as pictures for desktop
Limited MolFile publishing and word processing software.

Image Format Features

MSI ChemNote MSI ChemNote .msm
Chem3D 10 gives you more options when saving
MOPAC input MOPAC .mop; .dat; graphic formats, and the options are easier to set
file .mpc; 2mt than ever.
Transparent OLE copy/paste
MOPAC graph .gpt
Save bitmap images up to 1200 DPI.
file
JPEG Quality (compression) can be adjusted
from 0 to 100%.
Protein Data Protein DB .pdb; .ent
Bank Movies can be saved in animated GIF, multi-
page TIFF, or AVI formats.
ROSDAL Rosdal .rdl The defaults are set in the new Pictures tab of the
Preferences dialog box.
Standard Molec- SMD File .smd The Save dialog box now displays the available
ular Data options, to make it easier to override defaults when
you save.
SYBYL MOL SYBYL .sml
Figure 8: Save as GIF dialog box

SYBYL MOL2 SYBYL2 .sm2; .ml2

Transparent background and
To save a model with a different format, name or animation support
location:
Set JPEG compression
1. From the File menu, choose Save As.
Set resolution
The Save File dialog box appears.
2. Specify the name of the file, the folder, and disk
where you want to save the file.
3. Select the file format in which you want to save
the model.
4. Click Save. Graphic file formatting uses CxImage, an open
When you save a file in another file format, only source toolset under the zlib license.1
information relevant to the file format is saved. For 1. CxImage: Copyright 2001 - 2004,
example, you will lose dot surfaces, color, and atom Davide Pizzolato
labels when saving a file as an MDL MolFile. http://www.xdp.it

Chem & BioOffice 2006 /Chem3D Printing and Exporting Models 145
Exporting Models Using Different File Formats
 WMF and EMF
Chem3D supports the Windows Metafile and
Enhanced Metafile file formats. These are the only
graphic formats (as opposed to chemistry modeling
Administrator
formats) that can be used for import. They may also
be used for export, EMF by using the Save As...
File menu command or the clipboard, and WMF by
using the clipboard (only). See Exporting With the
Clipboard on page 154 for more information.
EMF files are exported with transparent
backgrounds, when this is supported by the
operating system (Windows 2000 and
Windows XP). The WMF and EMF file formats are
supported by applications such as Microsoft Word
for Windows.
NOTE: Chem3D no longer embeds structural information
in models exported as EMF files. If you have EMF files
produced with previous versions of Chem3D, you can still
open them in Chem3D and work with the structure.
However, EMF files saved from Chem3D 8.0 contain
graphic information only and cannot be opened in Chem3D
10.
BMP
The Bitmap file format saves the bitmapped
representation of a Chem3D picture. The Bitmap
file format enables you to transfer
Chem3D pictures to other applications, such as
Microsoft Word for Windows, that support
bitmaps.
EPS
The PostScript file format saves models as
encapsulated postscript file (EPS). EPS files are
ASCII text files containing the scaleable PostScript
representation of a Chem3D picture. You can open
EPS files using other applications such as
PageMaker. You can transfer EPS files among
platforms, including Macintosh, Windows, and
UNIX.
146 Printing and Exporting Models
TIF
The Tagged Image File Format (TIFF) contains
binary data describing a bitmap image of the model.
TIFF is a high resolution format commonly used
for saving graphics for cross-platform importing
into desktop publishing applications. TIFF images
can be saved using a variety of resolution, color, and
compression options. As TIFF images can get large,
choosing appropriate options is important.
When you save a file as TIF, an option button
appears in the Save As dialog box.
To specify the save options:
1. Click Options:
The TIFF Options dialog box appears.
Figure 7-2: The TIFF Options dialog box
2. Choose a resolution. The size of the file
increases as the square of the resolution.
3. Choose a color option.
If you want to Then choose
force objects to black Monochrome.
and white.
store colors using RGB Indexed.
computer monitor
style of color
encoding.
CambridgeSoft
Exporting Models Using Different File Formats
 the world wide web. Each of these formats uses a
If you want to Then choose compression algorithm to reduce the size of the file.
Applications that can import GIF, PNG, and JPG
use printing press CMYK Contiguous. files include Netscape Communicator and
style of color Stores colors non-sequen- Microsoft Internet Explorer.
encoding. tially. For example: The model window background color is used as the
CMYKCMYK. The Pack-
transparent color in the GIF format graphic.
Bits compression type
provides no compression
for this type of file. NOTE: The size of the image in Chem3D when you save
the file will be the size of the image as it appears in your web
page. If you turn on the Fit Model to Window building
NOTE: If objects in your document are black and white preference in Chem3D, you can resize the Chem3D window
they are saved as black and white regardless of which Color (in Chem3D) to resize the model to the desired size then
options you set. If you import drawings from other save.
applications and want them to print Black and White you
must set the Color option to Monochrome.
3DM
4. Choose a compression option: The QuickDraw 3D MetaFile (3DM) file format
contains 3-dimensional object data describing the
If you want to Then choose model. You can import 3DM files into many 3D
modeling applications. You can transfer 3DM files
between Macintosh and Windows platforms.
reduce file size by encoding PackBits.
repeating bytes of informa-
tion as output. For
AVI
example, for a line of color Use this file format to save a movie you have
information such as: created for the active model. You can import the
CCCCC- resulting movie file into any application that
MMMMMYYYYYKKKK supports the AVI file format.
K, the compression yields
a smaller file by repre- Formats for Chemistry
senting the information as
C5M5Y5K5.
Modeling Applications
The following file formats are used to export
fax transmissions of CCITT Group 3 or models to chemistry modeling application other
images CCITT Group 4. than Chem3D. Most of the formats also support
import.

GIF and PNG and JPG Alchemy

Use the Graphics Interchange Format (GIF), Use the ALC file format to interface with
Portable Network Graphics (PNG) file format, or TRIPOS applications such as Alchemy. This is
the JPEG format to publish a Chem3D model on supported only for input.

Chem & BioOffice 2006 /Chem3D Printing and Exporting Models 147
Exporting Models Using Different File Formats
 Cartesian Coordinates
Use Cartesian Coordinates 1 (.CC1) or 2 (.CC2) to
import or export the X, Y, and Z Cartesian
coordinates for your model.
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When you save a file as Cartesian Coordinates, an
option button appears in the Save As dialog box.
To specify the save options:
1. Click Options:
The Cartesian Coordinates Options dialog
box appears.
Figure 7-3: The Cartesian Coordinates Options dialog
box
2. Select the appropriate options:
If you want the file to Then click
contain a connection table for By Serial Number.
each atom with serial numbers
contain a connection table for By Position.
each atom that describes adja-
cent atoms by their positions
in the file
not contain a connection table Missing.
contain serial numbers Include Serial
Numbers.
contain atom type numbers Include Atom Type
Text Numbers.
148 Printing and Exporting Models
If you want the file to Then click
contain internal coordinates Save All Frames.
for each view of the model
Connection Table
Chem3D uses the atom symbols and bond orders
of connection table files to guess the atom symbols
and bond orders of the atom types. There are two
connection table file formats, CT and CON. The
CON format is supported only for import.
When you save a file as a Connection Table, an
Options button appears in the Save As dialog box.
To specify the save options:
1. Click Options.
The Connection Table Options dialog box
appears.
Figure 7-4: The Connection Table Options dialog box
2. Select the appropriate options:
If you want to add Then click
a blank line to the top of 1 Blank Line.
the file
two blank lines to the top 2 Blank Lines.
of the file
three blank lines to the top 3 Blank Lines.
of the file
CambridgeSoft
Exporting Models Using Different File Formats
Gaussian Input
Use the Gaussian Input (GJC, GJF) file format to
interface with models submitted for Gaussian
calculations. Either file format may be used to
import a model. Only the Molecule Specification
section of the input file is saved. For atoms not
otherwise specified in Chem3D, the charge by
default is written as 0, and the spin multiplicity is
written as 1. You can edit Gaussian Input files using
a text editor with the addition of keywords and
changing optimization flags for running the file
using the Run Gaussian Input file within Chem3D,
or using Gaussian directly.
Gaussian Checkpoint
A Gaussian Checkpoint file (FCHK; FCH) stores
the results of Gaussian Calculations. It contains the
final geometry, electronic structure (including
energy levels) and other properties of the molecule.
Checkpoint files are supported for import only.
Chem3D displays atomic orbitals and energy levels
stored in Checkpoint files. If Cubegen is installed,
molecular surfaces are calculated from the
Checkpoint file.
Gaussian Cube
A Gaussian Cube file (CUB) results from running
Cubegen on a Gaussian Checkpoint file. It contains
information related to grid data and model
coordinates. Gaussian Cube files are supported for
import only.
Chem3D displays the surface the file describes. If
more than one surface is stored in the file, only the
first is displayed. You can display additional surfaces
using the Surfaces menu.
Internal Coordinates
Internal Coordinates (.INT) files are text files that
describe a single molecule by the internal
coordinates used to position each atom. The serial
Chem & BioOffice 2006 /Chem3D
numbers are determined by the order of the atoms
in the file. The first atom has a serial number of 1,
the second is number 2, and so on. Internal
Coordinates files may be both imported and
exported.
You cannot use a Z-matrix to position an atom in
terms of a later-positioned or higher serialized
atom. If you choose the second or third options in
the Internal Coordinates Options dialog box, the
nature of the serialization of your model determines
whether a consistent Z-matrix can be constructed.
If the serial numbers in the Z-matrix which is about
to be created are not consecutive, a message
appears. You are warned if the atoms in the model
must be reserialized to create a consistent Z-matrix.
When you click Options in the Save As dialog box,
the following dialog box appears:
Figure 7-5: The Internal Coordinates Options dialog
box
Select the appropriate options:
If you want to Then click
save your model using Use Current Z-matrix.
the Z-matrix described
in the Internal Coordi-
nates table of the model
Printing and Exporting Models 149
Exporting Models Using Different File Formats
 in the Journal of Chemical Information and
If you want to Then click Computer Science, Volume 32, Number 3, 1992,
pages
build a Z-matrix in Only Serial Numbers; 244255.
Administrator

which the current serial Bond and Dihedral

number ordering of the Angles. Use this format to interface with MDLs ISIS
atoms in the model is applications and other chemistry-related
Pro-R/Pro-S and applications. Both import and export are
preserved in the Z- Dihedral angles are
matrix supported.
used to position
atoms.
MSI ChemNote
build a Z-matrix in Only Serial Numbers; Use the MSI ChemNote (.MSM) file format to
which the current serial Dihedral Angles Only. interface with Molecular Simulations applications
number ordering of the such as ChemNote. The file format is defined in the
atoms in the model is The Pro-R and Pro-S ChemNote documentation. Both import and
preserved in the Z- stereochemical desig- export are supported.
matrix nations are not used
in constructing the MOPAC Files
Z-matrix from a
model. All atoms are MOPAC data may be stored in MOP, DAT, MPC,
positioned by dihe- or 2MT file formats. Chem3D can import any of
dral angles only. these file formats, and can export MOP files. You
can edit MOPAC files using a text editor, adding
MacroModel Files keywords and changing optimization flags, and run
the file using the Run MOPAC Input file command
The MacroModel1 (MCM; DAT; OUT) file formats within Chem3D.
are defined in the MacroModel Structure Files
When you click Options in the Save As dialog box,
version 2.0 documentation. Chem3D supports
the MOPAC Options dialog box appears:
import of all three file types, and can export MCM
Figure 7-6: The MOPAC options dialog box
Molecular Design Limited MolFile
(.MOL)
The MDL Molfile format saves files by MDL
applications such as ISIS/Draw, ISIS/Base,
MAACS and REACCS. The file format is defined in
the article, Description of Several Chemical
Structure File Formats Used by Computer
Programs Developed at Molecular Design Limited Click the Save All Frames check box to create a
1. MacroModel is produced within the MOPAC Data file in which the internal coordinates
Department of Chemistry at Columbia for each view of the model are included. The initial
University, New York, N.Y. frame of the model contains the first 3 lines of the

150 Printing and Exporting Models CambridgeSoft

Exporting Models Using Different File Formats
usual MOPAC output file (see the example file
below). Each subsequent frame contains only lines
describing the Z-matrix for the atoms in that frame.
NOTE: For data file specifications, see page 13 of the
online MOPAC manual.
Chem & BioOffice 2006 /Chem3D
To edit a file to run using the Run MOPAC Input
File command:
1. Open the MOPAC output file in a text editor.
The output file below shows only the first four
atom record lines. The first line and column of the
example output file shown below are for purposes
of description only and are not part of the output
file.
Printing and Exporting Models 151
Exporting Models Using Different File Formats
 Col. 1 Col. 2 C3 Col. 4 C5 Col. 6 Col. 7 Col. 8
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Line 1

Line 2: Cyclohexanol

Line 3:

Line 4: C 0 0 0 0 0 0 0 0 0

Line 5: C 1.54152 1 0 0 0 0 1 0 0

Line 6: C 1.53523 1 111.7747 1 0 0 2 1 0

L7..Ln C 1.53973 1 109.7114 1 -55.6959 1 1 2 3

Ln+1

2. In Line 1, type the keywords for the computa-
tions you want MOPAC to perform (blank in
the example above).
Line 2 is where enter the name that you want to
assign to the window for the resulting model.
However, Chem3D ignores this line.
3. Leave Line 3 blank.
4. Line 4 through Ln (were n is the last atom
record) include the internal coordinates, opti-
mization flags, and connectivity information
for the model.
Column 1 is the atom specification.
Column 2 is the bond distance (for the
connectivity specified in Column 8).
Column 3 is the optimization flag for the
bond distance specified in Column 2.
Column 4 is the bond angle (for the
connectivity specified in Column 8).
Column 5 is the optimization flag for the
bond angle specified in Column 4.
Column 6 is the dihedral angle (for the
connectivity specified in Column 8).
Column 7 is the optimization flag for the
dihedral angle specified in Column 6.
5. To specify particular coordinates to optimize,
change the optimization flags in Column 3,
Column 5 and Column 7 for the respective
internal coordinate. The available flags in
MOPAC are:
1 Optimize this internal coordinate
0 Do not optimize this internal
-1 Reaction coordinate or grid index
T Monitor turning points in DRC
6. Add additional information in line Ln+1. For
example, symmetry information used in a
SADDLE computation.

152 Printing and Exporting Models CambridgeSoft

Exporting Models Using Different File Formats
 7. Leave the last line in the data file blank to indi-
cate file termination.
8. Save the file in a text only format.
MOPAC Graph Files
A MOPAC Graph (GPT) file stores the results of
MOPAC calculations that include the GRAPH
keyword. It contains the final geometry, electronic
structure, and other properties of the molecule.
Chem3D supports the MOPAC Graph file format
for import only.
Protein Data Bank Files
Brookhaven Protein Data Bank files (PDB; ENT)
are used to store protein data and are typically large
in size. Chem3D can import both file types, and
exports PDB. The PDB file format is taken from
the Protein Data Bank Atomic Coordinate and
Bibliographic Entry Format Description.
ROSDAL Files (RDL)
The ROSDAL Structure Language1 (RDL) file
format is defined in Appendix C: ROSDAL Syntax
of the MOLKICK Users Manual, and in this
manual in Appendix E, File Formats. on
page 242. The ROSDAL format is primarily used
for query searching in the Beilstein Online
Database. Chem3D supports the ROSDAL file
format for export only.
1. ROSDAL is a product of Softron, Inc.
Chem & BioOffice 2006 /Chem3D
Standard Molecular Data (SMD)
Use the Standard Molecular Data (.SMD) file
format for interfacing with the STN Express
application for online chemical database searching.
Both import and export are supported.
SYBYL Files
Use the SYBYL (SML, SM2, ML2) file formats to
interface with Triposs SYBYL applications. The
SML and SM2 formats can be used for both import
and export; the ML2 format is supported for
import only.
Job Description File Formats
You can use Job description files to save
customized default settings for calculations. You
can save customized calculations as a Job
Description file (.JDF) or Job Description
Stationery (.JDT). Saving either format in a
Chem3D job folder adds it to the appropriate
Chem3D menu.
JDF Files
The JDF file format is a file format for saving job
descriptions. When you open a JDF file, you can
edit CSBR and save the settings.
JDT Files
The JDT file format is a template format for saving
settings that can be applied to future calculations.
You can edit the settings of a template file, however
you cannot save your changes.
Printing and Exporting Models 153
Exporting Models Using Different File Formats
 Exporting With the Clip-
board
You can export a Chem3D model to other
Administrator
applications as a picture or in chemical notation.
Two graphic formats are available: bitmap and
EMF, and three notation formats: ChemDraw
structure, SMILES, and InChI1.
NOTE: Chemical notation formats are mostly suitable for
exporting smaller models. You should be aware of the
limitations of the format before using it.
You can also export an Embedded Object that uses
the Chem3D ActiveX Control to manipulate the
object.
When exporting in a graphic format, the size of the
file that you copy to the clipboard from Chem3D is
determined by the size of the Chem3D model
window. If you want the size of a copied molecule
to be smaller or larger, resize the model window
accordingly before you copy it. If the model
windows for several models are the same size, and
Fit Model to Window is on, then the models should
copy as the same size.
Copying to ChemDraw
You can transfer information to ChemDraw as a
picture or as a 2D model.
To transfer a model as a 3D picture:
1. Select the model.
2. From the Edit menu, point to Copy As, then
choose Bitmap or Enhanced Metafile.
1. InChI is a trademark of the Interna-
tional Union of Pure and Applied
Chemistry. InChI Material in Chem-
Draw is IUPAC 2005.
154 Printing and Exporting Models
3. In ChemDraw, select Paste from the Edit
menu.
NOTE: The model is imported as a bitmap or EMF
graphic and contains no structural information.
To transfer a model as a 2D structure:
1. Select the model.
2. From the Edit menu, point to Copy As, then
choose ChemDraw Structure.
3. Open ChemDraw.
4. From the Edit menu, choose Paste.
The model is pasted into ChemDraw.
TIP: To have the ChemDraw model look like the
Chem3D model, select or deselect the ChemDraw
Show Labels on Terminal Carbons and Hide
Implicit Hydrogens options on the Atom Labels tab
of the Document Settings dialog box to match the
settings in Chem3D.
Copying to Other Applica-
tions
To copy and paste a model into a word processing,
desktop publishing, presentation or drawing
application, such as Microsoft Word or PowerPoint:
1. Select the model.
2. From the Edit menu, point to Copy As, then
choose Bitmap or Enhanced Metafile.
3. Paste the model into the target application
document.
TIP: If you are pasting into MS Word or PowerPoint,
select Paste Special and choose the type of graphic you
wish to import: bitmap, WMF, or EMF. The EMF
option will copy with a transparent background.
Alternatively, you could use Save As Bitmap or
EMF to create a file to insert into or link to the
target application document.
CambridgeSoft
Exporting With the Clipboard
To copy the model as a SMILES or InChI string, Figure 9: Chem3D model embedded in FrontPage
select the model and chose the SMILES or InChI
option from the Copy As submenu.

Embedding Models in Other

Applications
The improved Chem3D ActiveX control allows
you to embed animated models in PowerPoint
presentations, Word documents, or HTML-based
documents.
To embed a model:
1. Use the Ctrl+A key combination to select the
entire model, or drag a rectangle with the Select
tool.
NOTE: Modifying the embedded image in HTML is
2. Point to Copy As on the Edit menu, and click
Embedded Object.
beyond the scope of this document. If you are a programmer
developing 3D modeling HTML pages, see
3. Paste the object in the target document using ReadMeC3DP.htm in the Chem3D application folder.
Edit>Paste or Ctrl+V.

NOTE: Use the normal Paste command, not Paste
Special.
When you embed a model in a PowerPoint
presentation, you can modify the display properties.
To display the Properties dialog box, select
Properties from the context (right-click) menu.
Figure 10: Changing Chem3D display properties

Chem & BioOffice 2006 /Chem3D Printing and Exporting Models 155
Exporting With the Clipboard
 Table 1lists the properties you can change in an Table 1: Embedded Chem3D object display
properties
embedded object.
Table 1: Embedded Chem3D object display Property Data
properties
Administrator

Property Data ShowRota- Shows/hides the Rotation toolbar.

tionBar
DataURL Normally left blank. You can
reference a file rather than using ShowToolbar Determines placement of the
cut-paste, but the slide presenta- Toolbar (left, right, top, bottom)
tion may not have access to that or hides the toolbar.
file later.
Top Defines the top of the object
EncodeData Cannot be changed. window., measured from the top
of the slide.
Fullscreen Cannot be changed.
Visible Shows/hides the object window.
Height Defines the height of the object
window. Width Defines the width of the object
window.
Left Defines the placement of the left
edge of the object window. Background Effects and Images
Chem3D 10 has nearly two dozen background
Modified Cannot be changed. effects for presentation images. You can also insert
an image into the background, to display your
Rotation Specifies the model rotation. companys logo or for visual effect. Figure 11shows
Enter data in the following format: the Sea and Sky background with an embedded
axis speed (angle) logo GIF file.
Angle can be X, Y, or Z or a
Figure 11: Background with logo
combination, for example: XY.
Speed may be 0-5, but the default
setting of 1 generally gives best
results. Specifying an angle means
that the model will rock rather
than spin. For example, x 1 45 will
rock the model on the X axis at
speed 1 through an angle of 45.

ShowContext- Shows/hides right-click menus in

Menu the object window.

156 Printing and Exporting Models CambridgeSoft

Exporting With the Clipboard
Chapter 8: MM2 and MM3 Computa-
tions
MM2 Overview 1. Build the model for which you want to
minimize the energy.
The Chem3D MM2 menu provides computations
using the MM2 force field. 2. To impose constraints on model measure-
ments, set Optimal column measurements in
The MM2 procedures described assume that you the Measurements table.
understand how the potential energy surface relates
to conformations of your model. If you are not 3. From the Calculations menu, point to MM2,
familiar with these concepts, see Computation and choose Minimize Energy.
Concepts
The Minimize Energy dialog box appears.
As discussed in Appendix G: Computation
Figure 8-1: The Minimize Energy dialog box
Concepts, the energy minimization routine
performs a local minimization only. Therefore, the
results of minimization may vary depending on the
starting conformation in a model.

Minimize Energy
To minimize the energy of the molecule based on
MM2 Force Field:
Minimum RMS Gradient
NOTE: You cannot minimize models containing phosphate
groups drawn with double bonds. For information on how to
create a model with phosphate groups you can minimize, see
the Chem3D Drawing FAQ at:
http://www.cambridgesoft.com/services/faqs.cfm

Chem & BioOffice 2006 /Chem3D MM2 and MM3 Computations 157
Minimize Energy
 4. Set the convergence criteria using the following
options:.

If you want to Then

Administrator

specify the convergence Enter a value for Minimum RMS Gradient.

criteria for the gradient of
the potential energy surface If the slope of the potential energy surface becomes too small, then the mini-
mization has probably reached a local minimum on the potential energy
surface and the minimization terminates.

The default value of 0.100 is a reasonable compromise between accuracy and

speed.
Reducing the value means that the calculation continues longer as it tries to
get even closer to a minimum.
Increasing the value shortens the calculation, but leaves you farther from a
minimum. Increase the value if you want a better optimization of a
conformation that you know is not a minimum, but you want to isolate for
computing comparative data.

watch the minimization Select Display Every Iteration.

process live at each itera-
tion in the calculation NOTE: Displaying or recording each iteration adds significantly to the time
required to minimize the structure.

store each iteration as a Select Record Every Iteration.

frame in a movie for replay
later

view the value of each Select Copy Measurements to Output.

measurement in the Output
window

restrict movement of a Select Move Only Selected Atoms.

selected part of a model
during the minimization Constraint is not imposed on any term in the calculation and the values of
any results are not affected.

158 MM2 and MM3 Computations CambridgeSoft

Minimize Energy

NOTE: If you are planning to make changes to any of the
MM2 constants, such as cutoff values or other parameters
used in the MM2 force field, please make a backup copy of
the parameter tables before making any changes. This will
assure that you can get back the values that are shipped with
Chem3D, in case you need them
NOTE: Chem3D guesses parameters if you try to
minimize a structure containing atom types not supported by
MM2. Examples include inorganic complexes where known
parameters are limited. You can view all parameters used in
the analysis using the Show Used Parameters command. See
Showing Used Parameters on page 169.
Running a Minimization
To begin the minimization of a model, click Run.
TIP: In all of the following minimization examples,
you can use the MM2 icon on the Calculation toolbar
instead of the Calculations menu.
The Output window appears when the
minimization begins if it was not already
opened. The data is updated for every iteration
of the computation, showing the iteration
number, the steric energy value at that iteration,
and the RMS gradient. If you have not selected
the Copy Measurements to Output option, only
the last iteration is displayed.
After the RMS gradient is reduced below the
requested value, the minimization ends, and the
final steric energy components and total appear
in the Output window.
Intermediate status messages may appear in the
Output window. A message appears if the
minimization terminates abnormally, usually
due to a poor starting conformation.
To interrupt a minimization that is in progress:
Click Stop in the Computing dialog box.
Chem & BioOffice 2006 /Chem3D
The minimization and recording stops.
Queuing Minimizations
You can start to minimize several models without
waiting for each model to finish minimizing. If a
computation is in progress when you begin
minimizing a second model, the minimization of
the second model is delayed until the first
minimization stops.
If you are using other applications, you can run
minimization with Chem3D in the background.
You can perform any action in Chem3D that does
not change the position of an atom or add or delete
any part of the model. For example, you can move
windows around during minimization, change
settings, or scale your model.
Example: Minimizing Ethane
Ethane is a particularly straightforward example of
minimization, because it has only one
minimum-energy (staggered) and one
maximum-energy (eclipsed) conformation.
To minimize energy in ethane:
1. From the File menu, choose New.
An empty model window appears.
2. Draw a model of Ethane.
3. Choose Show Serial Numbers on the Model
Display submenu of the View menu.
You might also want to set the Model Display
Mode to Ball and Stick or Cylindrical Bonds.
4. On the Calculations menu, point to MM2 and
choose Minimize Energy.
5. Click Run on the Minimize Energy dialog
box.
The calculation is performed. Messages appear
in the Output Window.
To view all the messages:
Scroll in the Output Window.
MM2 and MM3 Computations 159
Minimize Energy
 You can also tear off the window and Figure 8-2: Dihedral measurement for Ethane
enlarge it to make it easier to view.
Figure 8-2: Output for Ethane minimization
Administrator

The 60 degree dihedral represents the lowest

energy conformation for the ethane model.

Select the Trackball tool:

1. Reorient the model by dragging the X- and Y-

axis rotation bars until you have an end-on
view.
Figure 8-3: Ethane model, end-on view
The Total Steric Energy for the conformation is
0.8181 kcal/mol. The 1,4 VDW term of 0.6764
dominates the steric energy. This term is due to the
H-H repulsion contribution.

NOTE: The values of the energy terms shown are

approximate and can vary slightly based on the type of
processor used to calculate them.
To view the value of one of the dihedral angles that
contributes to the 1,4 VDW contribution:
1. Select the atoms making up the dihedral angle
as shown in Figure 8-1 by Shift+clicking H(7),
C(2), C(1), and H(4) in that order.
Figure 8-1: Selecting dihedral atoms
To force a minimization to converge on the
transition conformation, set the barrier to rotation:
1. In the Measurements table, type 0 in the
Optimal column for the selected dihedral angle
and press the Enter key.
2. On the MM2 submenu of the Calculations
menu, choose Minimize.
The Minimize Energy dialog box appears.
3. Click Run.
The model conforms to the structure in Figure
8-4.
Figure 8-4: Minimized Ethane, end-on view

2. From the Structure menu, point to Measure-

ment, and select Set Dihedral Measurement.

The following measurement appears.

160 MM2 and MM3 Computations CambridgeSoft

Minimize Energy
Entering a value in the Optimal column imposes a
constraint on the minimization routine. You are
increasing the force constant for the torsional term
in the steric energy calculation so that you can
optimize to the transition state.
When the minimization is complete, the reported
energy values shown in Figure 8-5. The energy for
this eclipsed conformation is higher relative to the
staggered form. The majority of the energy
contribution is from the torsional energy and the
1,4 VDW interactions.
NOTE: The values of the energy terms shown here are
approximate and can vary slightly based on the type of
processor used to calculate them.
Figure 8-5: Output for eclipsed Ethane model
The dihedral angle in the Actual column becomes 0,
corresponding to the imposed constraint.
The difference in energy between the global
minimum (Total, previous calculation) and the
transition state (Total, this calculation) is 2.73
kcal/mole, which is in agreement with literature
values.
To further illustrate points about minimization:
Chem & BioOffice 2006 /Chem3D
Delete the value from the Optimal column for
the dihedral angle and click the MM2 icon on
the Calculation toolbar.
After the minimization is complete, you are still at 0
degrees. This is an important consideration for
working with the MM2 minimizer. It uses first
derivatives of energy to determine the next logical
move to lower the energy. However, for saddle
points (transition states), the region is fairly flat and
the minimizer is satisfied that a minimum is
reached. If you suspect your starting point is not a
minimum, try setting the dihedral angle off by
about 2 degrees and minimize again.
Example: Comparing Two Stable
Conformations of Cyclohexane
In the following example you compare the
cyclohexane twist-boat conformation and the chair
global minimum.
To build a model of cyclohexane:
1. From the File menu, choose New.
An empty model window appears.
2. Select the Text Building tool.
3. Click in the model window.
A text box appears.
4. Type CH2(CH2)5 and press the Enter key.
CAUTION
While there are other, perhaps easier, methods of creating
a cyclohexane model, you should use the method described
to follow this example.
Before minimizing, it is wise to use the Clean Up
Structure command to refine the model. This
generally improves the ability of the Minimize
Energy command to reach a minimum point.
MM2 and MM3 Computations 161
Minimize Energy
 1. From the Edit menu, choose Select All.
2. From the Structure menu, choose Clean Up.
NOTE: The Clean Up command is very similar to the
Administrator
minimize energy command in that it is a preset, short
minimization of the structure.
To perform the minimization:
From the MM2 submenu of the Calculations
menu, choose Minimize Energy, and click Run.
When the minimization is complete, reorient
the model so it appears as in Figure 8-6.
Figure 8-6: Minimized cyclohexane model
The conformation you converged to is not the
well-known chair conformation, which is the global
minimum. Instead, the model has converged on a
local minimum, the twisted-boat conformation.
This is the closest low-energy conformation to your
starting conformation.
Had you built this structure using substructures
that are already energy minimized, or the
ChemDraw panel, you would be close to the chair
conformation. The minimizer does not surmount
the saddle point to locate the global minimum, and
the closest minimum is sought.
The energy values in the Output window should be
approximately as follows:
162 MM2 and MM3 Computations
Figure 8-7: Energy values for twisted boat conforma-
tion
The major contributions are from the 1,4 VDW and
Torsional aspects of the model.
For cyclohexane, there are six equivalent local
minima (twisted-boat), two equivalent global
minima (chair), and many transition states (one of
which is the boat conformation).
Locating the Global Minimum
Finding the global minimum is extremely
challenging for all but the most simple molecules. It
requires a starting conformation which is already in
the valley of the global minimum, not in a local
minimum valley. The case of cyclohexane is
straightforward because you already know that the
global minimum is either of the two possible chair
conformations. To obtain the new starting
conformation, change the dihedrals of the twisted
conformation so that they represent the potential
energy valley of the chair conformation.
The most precise way to alter a dihedral angle is to
change its Actual value in the Measurements table
when dihedral angles are displayed. An easier way to
alter an angle, especially when dealing with a ring, is
to move the atoms by dragging then cleaning up the
resulting conformation.
To change a dihedral angle:
1. Drag C1 below the plane of the ring.
The cursor appears as a box with a hand.
2. Drag C4 above the plane of the ring.
CambridgeSoft
Minimize Energy
Figure 8-8: Changing a dihedral angle 4. When the minimization is complete, reorient
1a 2a the model using the Rotation bars to see the
final chair conformation.

NOTE: The values of the energy terms shown here are

2b approximate and can vary slightly based on the type of
1b
processor used to calculate them.

Figure 8-10: Chair conformation of cyclohexane with

energy values

During dragging, the bond lengths and angles were

deformed. To return them to the optimal values
before minimizing, select the model by dragging a
box around it with the Select tool, and run Clean
Up.
Figure 8-9: Clean Up command on the Structure menu
This conformation is about 5.5 kcal/mole more
stable than the twisted-boat conformation.

For molecules more complicated than cyclohexane,

where you dont already know what the global
minimum is, some other method is necessary for
locating likely starting geometries for minimization.
One way of accessing this conformational space of
a molecule with large energy barriers is to perform
molecular dynamics simulations. This, in effect,
heats the molecule, thereby increasing the kinetic
energy enough to cross the energetically disfavored
Now run the minimization: transition states.
3. Click the MM2 tool on the Computation
toolbar. Molecular Dynamics
Molecular Dynamics uses Newtonian mechanics to
simulate motion of atoms, adding or subtracting
kinetic energy as the models temperature increases
or decreases.

Molecular Dynamics allows you to access the

conformational space available to a model by
storing iterations of the molecular dynamics run
and later examining each frame.

Chem & BioOffice 2006 /Chem3D MM2 and MM3 Computations 163
Molecular Dynamics
 Performing a Molecular
Dynamics Computation
To perform a molecular dynamics simulation:
Administrator
1. Build the model (or fragments) that you want
to include in the computation.
NOTE: The model display type you use affects the
speed of the molecular dynamics computation. Model
display will decrease the speed in the following order:
Wire Frame< Sticks < Ball and Sticks< Cylindrical
Bonds < Ribbons< Space Fill and VDW dot surfaces
< Molecular Surfaces.
2. Minimize the energy of the model (or frag-
ments), using MM2 or MOPAC.
3. To track a particular measurement during the
simulation, choose one of the following:
Select the appropriate atoms, and choose Set
Bond Angle or Set Bond Length on the
Measurement submenu of the Structure
menu.
4. Choose Molecular Dynamics on the MM2
submenu of the Calculations menu.
The Molecular Dynamics dialog box appears
with the default values.
Figure 8-11: The Molecular Dynamics dialog box.
164 MM2 and MM3 Computations
5. Enter the appropriate values.
6. Click Run.
Dynamics Settings
Use the Dynamics tab to enter parameter values for
the parameters that define the molecular dynamics
calculations:
Step Intervaldetermines the time between
molecular dynamics steps. The step interval
must be less than ~5% of the vibration period
for the highest frequency normal mode, (10 fs
for a 3336 cm-1 HX stretching vibration).
Normally a step interval of 1 or 2 fs yields
reasonable results. Larger step intervals may
cause the integration method to break down,
because higher order moments of the position
are neglected in the Beeman algorithm.
Frame Intervaldetermines the interval at
which frames and statistics are collected. A
frame interval of 10 or 20 fs gives a fairly
smooth sequence of frames, and a frame
interval of 100 fs or more can be used to obtain
samples of conformational space over a longer
computation.
Terminate Aftercauses the molecular
dynamics run to stop after the specified
number of steps. The total time of the run is
the Step Interval times the number of steps.
Heating/Cooling Ratedictates whether
temperature adjustments are made. If the
Heating/Cooling Rate check box is checked,
the Heating/Cooling Rate slider determines
the rate at which energy is added to or removed
from the model when it is far from the target
temperature.
A heating/cooling rate of approximately 1.0
kcal/atom/picosecond results in small
corrections which minimally disturb the
trajectory. A much higher rate quickly heats up
CambridgeSoft
Molecular Dynamics
 the model, but an equilibration or stabilization Select the appropriate options:
period is required to yield statistically
meaningful results. If you want to Then Click
To compute an isoenthalpic trajectory
(constant total energy), deselect Heating/ record each iteration Record Every Iteration.
Cooling Rate.
as a frame in a movie
Target Temperaturethe final temperature for later replay
to which the calculation will run. Energy is
added to or removed from the model when the track a particular Copy Measurements to
computed temperature varies more than 3% measurement Output.
from the target temperature.
The computed temperature used for this
restrict movement of Move Only Selected
purpose is an exponentially weighted average
a selected part of a Atoms.
temperature with a memory half-life of about
model during the
20 steps.
minimization
Job Type Settings
save a file containing Click Save Step Data In
Use the Job Type tab to set options for the the Time (in picosec- and browse to choose a
computation. onds), Total Energy, location for storing this
Figure 8-12: The Job Type tab Potential Energy, and file.
Temperature data for
each step. The word heating or
cooling appears for
each step in which
heating or cooling was
performed. A summary
of this data appears in the
Message window each
time a new frame is
created.

To begin the computation:

Click Run.
The computation begins. Messages for each
iteration and any measurements you are
tracking appear in the Output window.
If you have chosen to Record each iteration,
the Movie menu commands (and Movie
toolbar icons) will be active at the end of the
computation.

Chem & BioOffice 2006 /Chem3D MM2 and MM3 Computations 165
Molecular Dynamics
 The simulation ends when the number of steps To replay the movie:
specified is taken.
Click Start on the Movie menu.
To stop the computation prematurely:
The frames computed during the molecular
Administrator

Click Stop in the Computation dialog box.

dynamics calculation are played as a movie.
Example: Computing the Molecular To review the results:
Dynamics Trajectory for a Short
Segment of Polytetrafluoroethylene 1. View the Output window to examine the
(PTFE) measurement data included in the molecular
dynamics step data.
To build the model:
2. Drag the Movie slider knob to the left until the
1. From the File menu, choose New. first step appears.
2. Select the Text Building tool.
Figure 8-13: C(2) - C(33) distance before calculation
3. Click in the model window.
A text box appears.
4. Type F(C2F4)6F and press the Enter key.
A polymer segment consisting of six repeat
units of tetrafluoroethylene appears in the
model window. Selected

To perform the computation: The C(2)-C(33) distance for the molecule

before the molecular dynamics calculation
1. Select C(2), the leftmost terminal carbon, then
began is approximately 9.4.
Shift+click C(33), the rightmost terminal
carbon. 3. Scroll down to the bottom of the Output
2. Choose Set Distance from the Measurement window and examine the C(2)-C(33) distance
submenu of the Structure menu. for the molecule at 0.190 picoseconds (which
corresponds to frame 20 in the Movie slider of
A measurement for the overall length of the the model window).
molecule appears in the Measurements table.
Figure 8-14: C(2) - C(33) distance after calculation
3. Choose Molecular Dynamics from the MM2
submenu of the Calculations menu.
4. Click the Job Type tab and click the checkbox
for Copy Measurements to Output. If you want
to save the calculation as a movie, select Record
Every Iteration checkbox.
5. Click Run.
The C(2)-C(33) distance is approximately
When the calculation begins, the Output Window 13.7, 42% greater than the initial C(2)-C(33)
appears. distance.

166 MM2 and MM3 Computations CambridgeSoft

Molecular Dynamics
Compute Properties
Compute Properties represents a single point
energy computation that reports the total steric
energy for the current conformation of a model
(the active frame, if more than one exists).
NOTE: The Steric Energy is computed at the end of an
MM2 Energy minimization.
A comparison of the steric energy of various
conformations of a molecule gives you information
on the relative stability of those conformations.
NOTE: In cases where parameters are not available
because the atom types in your model are not among the
MM2 atom types supported, Chem3D will attempt an
educated guess. You can view the guessed parameters by using
the Show Used Parameters command after the analysis is
completed.
Compare the steric energies of cis- and trans-2-
butene.
To build trans-2-butene and compute properties:
1. From the File menu, choose New.
2. Select the Text Building tool.
3. Click in the model window.
A text box appears.
4. Type trans-2-butene and press the Enter key.
A molecule of trans-2-butene appears in the
model window.
5. From the MM2 submenu of the Calculations
menu, choose Compute Properties.
The Compute Properties dialog box appears.
Chem & BioOffice 2006 /Chem3D
Figure 8-15: The Compute Properties dialog box
6. Click Run.
The Output window appears. When the steric
energy calculation is complete, the individual
steric energy terms and the total steric energy
appear.
Use the Output window scroll bar to view all of the
output. The units are kcal/mole for all terms. At the
beginning of the computation the first message
indicates that the parameters are of Quality=4
meaning that they are experimentally
determined/verified parameters.
NOTE: The values of the energy terms shown here are
approximate and can vary slightly based on the type of
processor used to calculate them.
The following values are displayed:
The Stretch term represents the energy associ-
ated with distorting bonds from their optimal
length.
The second steric energy term is the Bend
term. This term represents the energy associ-
ated with deforming bond angles from their
optimal values.
MM2 and MM3 Computations 167
Compute Properties
 The Stretch-Bend term represents the energy The steric energy terms for cis-2-butene
required to stretch the two bonds involved in a appears in the Output window.
bond angle when that bond angle is severely
Below is a comparison of the steric energy
compressed.
components for cis-2-butene and trans-2-butene.
Administrator

The Torsion term represents the energy associ-

ated with deforming torsional angles in the
molecule from their ideal values. NOTE: The values of the energy terms shown here are
approximate and can vary slightly based on the type of
The Non-1,4 van der Waals term represents the
processor used to calculate them.
energy for the through-space interaction
between pairs of atoms that are separated by
more than three atoms.
For example, in trans-2-butene, the Non-1,4 van der Energy Term trans-2- cis-2-
Waals energy term includes the energy for the butene butene
interaction of a hydrogen atom bonded to C(1) with
a hydrogen atom bonded to C(4). Stretch: 0.0627 0.0839
The 1,4 van der Waals term represents the energy
for the through-space interaction of atoms Bend: 0.2638 1.3235
separated by two atoms.
For example, in trans-2-butene, the 1,4 van der Stretch-Bend: 0.0163 0.0435
Waals energy term includes the energy for the
interaction of a hydrogen atom bonded to C(1) with Torsion: -1.4369 -1.5366
a hydrogen atom bonded to C(2).
The dipole/dipole steric energy represents the Non-1,4 van der Waals: -0.0193 0.3794
energy associated with the interaction of bond
dipoles. 1,4 van der Waals: 1.1742 1.1621
For example, in trans-2-butene, the Dipole/Dipole
term includes the energy for the interaction of the Dipole/Dipole: 0.0767 0.1032
two C Alkane/C Alkene bond dipoles.
To build a cis-2-butene and compute properties: Total: 0.137 1.5512

1. From the Edit menu, choose Clear to delete

the model.
2. Double-click in the model window.
A text box appears.
3. Type cis-2-butene and press the Enter key.
A molecule of cis-2-butene appears in the
model window.
4. From the MM2 submenu of the Calculations
menu, choose Compute Properties.
The significant differences between the steric
energy terms for cis and trans-2-butene are in the
Bend and Non-1,4 van der Waals steric energy
terms. The Bend term is much higher in cis-2-
butene because the C(1)-C(2)-C(3) and the C(2)-
C(3)-C(4) bond angles had to be deformed from
their optimal value of 122.0 to 127.4 to relieve
some of the steric crowding from the interaction of
hydrogens on C(1) and C(4). The interaction of
hydrogens on C(1) and C(4) of trans-2-butene is

168 MM2 and MM3 Computations CambridgeSoft

Compute Properties
much less intense, thus the C(1)-C(2)-C(3) and the
C(2)-C(3)-C(4) bond angles have values of 123.9,
much closer to the optimal value of 122.0. The
Bend and Non-1,4 van der Waals terms for trans-2-
butene are smaller, therefore trans-2-butene has a
lower steric energy than cis-2-butene.
Showing Used Parame-
ters
You can display all parameters used in an MM2
calculation in the Output window. The list includes
a quality assessment of each parameter. Highest
quality empirically-derived parameters are rated as 4
while a lowest quality rating of 1 indicates that a
parameter is a best guess value.
To show the used Parameters:
From the MM2 submenu of the Calculations
menu, choose Show Used Parameters.
The parameters appear in the Output window.
Chem & BioOffice 2006 /Chem3D
Repeating an MM2 Compu-
tation
After you perform an MM2 computation, you can
repeat the job as follows:
1. Choose Repeat MM2 Job from the MM2
submenu of the Calculations menu,
The appropriate dialog box appears.
2. Change parameters if desired and click Run.
The computation proceeds.
Using JDF Files
The job type and settings are saved in a JDF file if
you click the Save As button on the dialog box
before running a computation. You can then run
these computations in a later work session.
To run a previously created MM2 job:
1. Choose Run MM2 Job from the MM2 submenu
of the Calculations menu.
2. Choose the file and click Open.
The dialog box for the appropriate
computation appears.
3. Change parameters if desired and click Run.
MM2 and MM3 Computations 169
Showing Used Parameters
Administrator

170 MM2 and MM3 Computations CambridgeSoft

Showing Used Parameters
Chapter 9: MOPAC Computations
Overview
MOPAC is a molecular computation application
developed by Dr. James Stewart and supported by
Fujitsu Corporation that features a number of
widely-used, semi-empirical methods. It is available
in two versions, Professional and Ultra.
MOPAC Pro allows you to compute properties
and perform simple (and some advanced) energy
minimizations, optimize to transition states, and
compute properties. The CS MOPAC Pro
implementation supports MOPAC sparkles, has an
improved user interface, and provides faster
calculations. It is included in some versions of
Chem3D, or may be purchased as an optional
addin. See
http://www.cambridgesoft.com/products/family.cfm?
FID=3 for details.
MOPAC Ultra is the full MOPAC implementation,
and is only available as an optional addin. The CS
MOPAC Ultra implementation provides support
for previously unavailable features such as
MOZYME and PM5 methods.
For both versions you need a separate installer to
install the MOPAC application, and Chem3D must
be installed first. Either version of MOPAC will
work with either version of Chem3D.
CS MOPAC provides a graphical user interface that
allows you to perform MOPAC computations
directly on the model in the Chem3D model
window. As a computation progresses, the model
changes appearance to reflect the computed result.
In this section:
Minimizing Energy
Chem & BioOffice 2006 /Chem3D
Optimizing Geometry
Optimizing to a Transition State
Computing Properties
Examples
Example: Locating the Eclipsed Transition
State of Ethane
Example 1: The Dipole Moment of
Formaldehyde
Example 2: Comparing Cation Stabilities in
a Homologous Series of Molecules
Example 3: Analyzing Charge Distribution
in a Series Of Mono-substituted Phenoxy
Ions
Example 4: Calculating the Dipole
Moment of meta-Nitrotoluene
Example 5: Comparing the Stability of
Glycine Zwitterion in Water and Gas
Phase
Example 6: Hyperfine Coupling Constants
for the Ethyl Radical
Example 8: RHF Spin Density for the
Ethyl Radical
Using MOPAC Properties
Using MOPAC files
The procedures assume you have a basic
understanding of the computational concepts and
terminology of semi-empirical methods, and the
concepts involved in geometry optimization
(minimization) and single-point computations.
For help with MOPAC, see the online MOPAC
manual at:
http://www.cachesoftware.com/mopac/Mopac2002
manual/
MOPAC Computations 171
 Minimizing Energy Option Function
Minimizing energy is generally the first molecular
computation performed on a model. Optimizer Selects a geometry mini-
Administrator

From the Calculations menu, point to mizer. See Optimizing

MOPAC Interface and choose Minimize Energy. Geometry on page 173 for
more information.
The MOPAC Interface dialog box appears,
with Minimize as the default Job Type.
Solvent Selects a solvent. For more
Figure 9-16: The MOPAC Interface dialog box
information on solvent
effects, see the online
MOPAC manual.

Move Which Allows you to minimize

part of a model by selecting
it.

Minimum RMS Specifies the convergence

criteria for the gradient of
the potential energy surface.
(See also Gradient Norm
on page 177.)

Use MOZYME Ultra For very large

models, alters the way the
SCF is generated, cutting
You may use the defaults, or set your own memory requirements and
parameters. running much faster.

Option Function Display Every Itera- Displays the minimization

tion process live at each itera-
tion in the calculation.
Job Type Sets defaults for different
types of computations. NOTE: Adds significantly
to the time required to
minimize the structure.
Method Selects a method.

Show Output in Sends the output to a text

Wave Function Selects close or open shell.
Notepad file.
See Specifying the Elec-
tronic Configuration on
page 296 for more details.

172 MOPAC Computations CambridgeSoft

Minimizing Energy

Option Function
Send Back Output Displays the value of each
measurement in the Output
window.
NOTE: Adds significantly
to the time required to
minimize the structure.
Notes
RMSThe default value of 0.100 is a reasonable
compromise between accuracy and speed.
Reducing the value means that the calculation
continues longer as it tries to get even closer to a
minimum. Increasing the value shortens the
calculation, but leaves you farther from a minimum.
Increase the value if you want a better optimization
of a conformation that you know is not a minimum,
but you want to isolate it for computing
comparative data.
NOTE: If you want to use a value <0.01, you must specify
LET in the keywords section (General Tab).
Wave FunctionSelecting a wave function from
the drop down menu involves deciding whether to
use RHF or UHF computations.
RHF is the default Hartree-Fock method used
for closed shell systems. To use RHF select the
Close Shell (Restricted) wave function.
UHF is an alternative form of the HF method
used for open shell systems. To use UHF select
the Open Shell (Unrestricted) wave function. If
Chem & BioOffice 2006 /Chem3D
you wish to calculate Hyperfine Coupling
Constants, you must select the UHF wave
function.
NOTE: UHF computations take at least twice as
long as RHF. This may be the deciding consideration of
method when large molecules are being studied.
Optimizing Geometry
Chem3D uses the Eigenvector Following (EF)
routine as the default geometry optimization
routine for minimization calculations. EF is
generally superior to the other minimizers, and is
the default used by MOPAC 2002. (Earlier versions
of MOPAC used BFGS as the default.) The other
alternatives are described below.
TS
The TS optimizer is used to optimize a transition
state. It is inserted automatically when you select
Optimize to Transition State from the MOPAC
Interface submenu.
BFGS
For large models (over about 500-1,000 atoms) the
suggested optimizer is the Broyden-Fletcher-
Goldfarb-Shanno procedure. By specifying BFGS,
this procedure will be used instead of EF.
LBFGS
For very large systems, the LBFGS optimizer is
often the only method that can be used. It is based
on the BFGS optimizer, but calculates the inverse
Hessian as needed rather than storing it. Because it
uses little memory, it is preferred for optimizing
very large systems. It is, however, not as efficient as
the other optimizers.
MOPAC Computations 173
Minimizing Energy
 Adding Keywords
Click the General tab to specify additional MOPAC
keywords. This will tailor a calculation to more
Administrator
exacting requirements. For example, you might use
additional keywords to control convergence criteria,
Figure 9-18: Optimizing to a transition state
to optimize to an excited state instead of the ground
state, or to calculate additional properties.
NOTE: Other properties that you might specify through the
keywords section of the dialog box may affect the outcome. For
more information see Using Keywords on page 294.
Figure 9-17: The General tab
Optimize to Transition State
To optimize your model to a transition state, use a
conformation that is as close to the transition state
as possible. Do not use a local or global minimum,
because the algorithm cannot effectively move the
geometry from that starting point.
174 MOPAC Computations
To optimize a transition state:
1. Choose Optimize to Transition State from the
MOPAC Interface submenu of the
Calculations menu.
The MOPAC Interface dialog box appears.
2. On the Job and Theory tab select a Method and
Wave Function.
NOTE: Unless you are an experienced MOPAC
user, use the Transition State defaults.
3. On the Properties tab, select the properties you
wish to calculate from the final optimized
conformation.
4. On the General tab, type any additional
keywords that you want to use to modify the
optimization.
5. Click Run.
The information about the model and the
keywords are sent to MOPAC. If you have
selected Send Back Output, the Output window
appears.
CambridgeSoft
Minimizing Energy
The Output window displays intermediate
messages about the status of the minimization. A
message appears if the minimization terminates
abnormally, usually due to a poor starting
conformation.
The following contains keywords automatically sent
to MOPAC and some additional keywords you can
use to affect convergence.
Keyword Description
EF Automatically sent to MOPAC
to specify the use of the Eigen-
vector Following minimizer.
GEO-OK Automatically sent to MOPAC
to override checking of the
Z-matrix.
MMOK Automatically sent to MOPAC
to specify Molecular Mechanics
correction for amide bonds.
Use the additional keyword
NOMM to turn this keyword
off.
RMAX=n.nn The maximum for the ratio of
calculated/predicted energy
change. The default is 4.0.
RMIN=n.nn The minimum for the ratio of
calculated/predicted energy
change. The default value is
0.000.
PRECISE Runs the SCF calculations
using a higher precision so that
values do not fluctuate from
run to run.
Chem & BioOffice 2006 /Chem3D
Keyword Description
LET Overrides safety checks to
make the job run faster (or
further).
RECALC=5 Use this keyword if the optimi-
zation has trouble converging
to a transition state.
For descriptions of error messages reported by
MOPAC see Chapter 11, pages 325331, in the
MOPAC manual.
To interrupt a minimization that is in progress:
Click Stop in the Movie Controller.
Example: Locating the Eclipsed Transi-
tion State of Ethane
Build a model of ethane:
1. From the File menu, choose New Model
2. Double-click in the model window.
A text box appears.
3. Type CH3CH3 and press the Enter key.
A model of ethane appears.
4. Select the Rotation tool.
5. Click the arrow next to the Rotation tool, and
drag down the Rotation dial.
Figure 9-19: The Rotation dial
click here to open the
Rotation dial
dihedral rotators
MOPAC Computations 175
Minimizing Energy
 6. Hold down the S key and select the bond
between the C(1) and C(2) atoms.
NOTE: Holding down the S key temporarily
Administrator
activates the Select tool.
7. Select one of the dihedral rotators, then enter
57 in the text box and press the Enter key.
A nearly eclipsed conformation of ethane is
displayed.
TIP: To view this better, rotate the model on the Y
axis until the carbon atoms are aligned.
Use Mopac to create the precise eclipsed transition
state:
8. Holding down the S and shift keys, click on any
two nearly eclipsed hydrogen atoms, such as
H(4) and H(7), to identify the dihedral to track.
You should have a nearly coplanar four-atom
chain, such as H(4)-C(1)-C(2)-H(7), selected.
9. From the Structure menu, point to Measure-
ments, and choose Dihedral Angle.
The Measurements table appears and displays
an actual value for the selected dihedral angle
of about 3 degrees (this will vary slightly
between experiments).
Figure 9-20: Eclipsed transition state with measure-
ments
dihedral = 2.9224
dihedral = 3.1551
176 MOPAC Computations
10.From the MOPAC Interface submenu of the
Calculations menu, choose Optimize to Transi-
tion State.
11.Click the Copy Measurements to Messages box
on the Job Type tab.
12.Click Run.
The ethane model minimizes so that the
dihedral is 0 degrees, corresponding to the
eclipsed conformation of ethane, a known
transition state between the staggered minima
conformations.
To see the Newman projection of the eclipsed
ethane model:
1. Select both carbon atoms.
2. From View Position submenu of the View
menu, click Align View Z-Axis With Selection.
NOTE: If you perform an Energy Minimization
from the same starting dihedral, your model would
optimize to the staggered conformation of ethane where
the dihedral is 60 degrees, instead of optimizing to the
transition state.
Computing Properties
To perform a single point calculation on the current
conformation of a model:
1. From the MOPAC Interface submenu of the
Calculations menu, choose Compute
Properties.
The Compute Properties dialog box appears.
2. On the Theory tab, choose a potential energy
function to use for performing the calculation.
3. On the Properties tab, select the properties to
calculate.
CambridgeSoft
Computing Properties
Figure 9-21: The Properties tab The heat of formation is composed of the
following terms:

=
f
e+
l
en+

c
u +
ic
s
o
lal
tom

Where:
Eelec is calculated from the SCF calculation.

Enucl is the core-core repulsion based on the

4. On the Properties tab, set the charges.
5. On the General tab, type any additional
keywords, if necessary.
6. Click Run.
MOPAC Properties
The following section describes the properties that
you can calculate for a given conformation of your
model, either as a single point energy computation
using the Compute Properties command, or after a
minimization using either the Minimize Energy or
Optimize to Transition State commands.
Heat of Formation, Hf
This energy value represents the heat of formation
for a models current conformation. It is useful for
comparing the stability of conformations of the
same model.
NOTE: The heat of formation values include the zero point
energies. To obtain the zero point energy for a conformation
run a force operation using the keyword FORCE. The zero-
point energy is found at the bottom of the *.out file.
nuclei in the molecule.
Eisol and Eatoms are parameters supplied by the
potential function for the elements within your
molecule.
NOTE: You can use the keyword ENPART and open the
*.out file at the end of a run to view the energy components
making up the heat of formation and SCF calculations. See
the MOPAC online manual reference page 137, for more
information.
Gradient Norm
This is the value of the scalar of the vector of
derivatives with respect to the geometric variables
flagged for optimization. This property (called
GNORM in the MOPAC manual) is automatically
selected for a minimization, which calculates the
GNORM and compares it to the selected minimum
gradient. When the selected minimum is reached,
the minimization terminates.
Selecting this property for a Compute Properties
operation (where a minimization is not being
performed) will give you an idea of how close to
optimum geometry the model is for the particular
calculation.

NOTE: The GNORM property is not the same as the

The heat of formation in MOPAC is the gas-phase MOPAC keyword GNORM. For more information see the
heat of formation at 298K of one mole of a MOPAC manual, pages 31 and 180.
compound from its elements in their standard state.

Chem & BioOffice 2006 /Chem3D MOPAC Computations 177

Computing Properties
 Dipole Moment
The dipole moment is the first derivative of the
energy with respect to an applied electric field. It
Administrator
measures the asymmetry in the molecular charge
distribution and is reported as a vector in three
dimensions.
The dipole value will differ when you choose
Mulliken Charges, Wang-Ford Charges or
Electrostatic Potential, as a different density matrix
is used in each computation.
NOTE: For more information see the MOPAC manual,
page 119.
The following table contains the keywords
automatically sent to MOPAC.
Keyword Description
GEO-OK Automatically sent to MOPAC to
override checking of the Z-matrix.
MMOK
Automatically sent to MOPAC to
specify Molecular Mechanics
correction for amide bonds. Use the
additional keyword NOMM to turn
this keyword off.
Charges
The property, Charges, determines the atomic
charges using a variety of techniques discussed in
the following sections. In this example the charges
are the electrostatic potential derived charges from
Wang-Ford, because Wang-Ford charges give useful
information about chemical stability (reactivity).
178 MOPAC Computations
Mulliken Charges
This property provides a set of charges on an atom
basis derived by reworking the density matrix from
the SCF calculation. Unlike the Wang-Ford charges
utilized in the previous example, Mulliken charges
give a quick survey of charge distribution in a
molecule.
NOTE: For more information, see the MOPAC online
manual, page 41 and 121.
The following table contains the keywords
automatically sent to MOPAC.
Keyword Description
MULLIK Automatically sent to MOPAC to
generate the Mulliken Population
Analysis.
GEO-OK Automatically sent to MOPAC to
override checking of the Z-matrix.
MMOK Automatically sent to MOPAC to
specify Molecular Mechanics
correction for amide bonds. Use
the additional keyword NOMM to
turn this keyword off.
Charges From an Electrostatic Potential
The charges derived from an electrostatic potential
computation give useful information about
chemical reactivity.
The electrostatic potential is computed by creating
an electrostatic potential grid. Chem3D reports the
point charges derived from such a grid.
In general, these atomic point charges give a better
indication of likely sites of attack when compared to
atomic charges derived from the Coulson density
CambridgeSoft
Computing Properties
matrix (Charges) or Mulliken population analysis
(Mulliken Charges). The uses for electrostatic
potential derived charges are generally the same as
for atomic charges. For examples, see Charges on
page 178.
There are two properties available for calculating
atomic point charges: Wang-Ford Charges and
Electrostatic Potential.
Wang-Ford Charges
This computation of point charges can be used with
the AM1 potential function only.
Electrostatic Potential
Use the electrostatic potential property when the
element coverage of the AM1 potential function
does not apply to the molecule of interest. For more
information see the MOPAC online manual, page
223.
The following table contains the keywords
automatically sent to MOPAC and those you can
use to affect this property.
Keyword Description

NOTE: For elements not covered by the AM1 potential ESP Automatically sent to MOPAC to
function, use the Electrostatic Potential property to get specify the Electrostatic Potential
similar information on elements outside this properties range. routine.

Below are the keywords automatically sent to POTWRT Add this keyword if you want to
MOPAC. print out the ESP map values.

GEO-OK Automatically sent to MOPAC to

Keyword Description override checking of the Z-matrix.

PMEP Automatically sent to MOPAC to MMOK Automatically sent to MOPAC to

specify the generation of Point
Charges from PMEP.
QPMEP Automatically sent to MOPAC to
specify the Wang/Ford electro-
static Potential routine.
GEO-OK Automatically sent to MOPAC to
override checking of the Z-matrix.
MMOK Automatically sent to MOPAC to
specify Molecular Mechanics
correction for amide bonds. Use
the additional keyword NOMM to
turn this keyword off.
specify Molecular Mechanics
correction for amide bonds. Use
the additional keyword NOMM to
turn this keyword off.
Molecular Surfaces
Molecular surfaces calculate the data necessary to
render the Total Charge Density, Molecular
Electrostatic Potential, Spin Density, and Molecular
Orbitals surfaces.
Polarizability
The polarizability (and hyperpolarizability)
property provides information about the
distribution of electrons based on presence of an

Chem & BioOffice 2006 /Chem3D MOPAC Computations 179

Computing Properties
 applied electric field. In general, molecules with
more delocalized electrons have higher values for
this property.
Polarizability data is often used in other equations
Administrator
Hyperfine interaction of the unpaired electron with
the central proton and other equivalent protons
cause complex splitting patterns in ESR spectra.
ESR spectroscopy measures the absorption of

microwave radiation by an unpaired electron when

for evaluation of optical properties of molecules.
For more information see the MOPAC online
manual, page 214.
The polarizability and hyperpolarizability values
reported are the first order (alpha) tensors (xx, yy,
zz, xz, yz, xy), second order (beta) tensors and third
order (gamma) tensors.
it is placed under a strong magnetic field.
Hyperfine Coupling Constants (HFCs) are related
to the line spacing within the hyperfine pattern of
an ESR spectra and the distance between peaks.
Species that contain unpaired electrons are as
follows:

NOTE: Polarizabilities cannot be calculated using the Free radicals

MINDO/3 potential function.
Odd electron molecules

Transition metal complexes

COSMO Solvation in Water
The COSMO method is useful for determining the Rare-earth ions
stability of various species in a solvent. The default Triplet-state molecules
solvent is water. For more information, see the
MOPAC online manual. For more information see the MOPAC online
manual, page 34.
To run the COSMO method, make the following
selections in the MOPAC Interface: The following table contains the keywords
On the Job & Theory tab, select COSMO in automatically sent to MOPAC and those you can
the Solvent field. use to affect this property.
On the Properties tab, check the COSMO Area
and/or COSMO Volume properties. You must Keyword Description
check each property you want to see in the
results. UHF Automatically sent to MOPAC if
you choose Open Shell (Unre-
NOTE: You can also use the Miertus-Scirocco-Tomasi stricted) wave functions to specify
solvation model, which is available using the H2O keyword. the use of the Unrestricted
This method is recommended only for water as the solvent. A Hartree-Fock methods.
discussion of this method can be found in the MOPAC
online documentation. Hyperfine Automatically sent to MOPAC to
specify the hyperfine computation.
Hyperfine Coupling Constants
GEO-OK Automatically sent to MOPAC to
Hyperfine Coupling Constants are useful for override checking of the Z-matrix.
simulating Electron Spin Resonance (ESR) spectra.

180 MOPAC Computations CambridgeSoft

Computing Properties
Keyword Description
MMOK Automatically sent to MOPAC to
specify Molecular Mechanics
correction for amide bonds. Use
the additional keyword NOMM to
turn this keyword off.
Spin Density
Spin density arises in molecules where there is an
unpaired electron. Spin density data provides
relative amounts of alpha spin electrons for a
particular state.
Spin density is a useful property for accessing sites
of reactivity and for simulating ESR spectra.
Two methods of calculating spin density of
molecules with unpaired electrons are available:
RHF Spin Density and UHF Spin Density.
UHF Spin Density
The UHF Spin Density removes the closed shell
restriction. In doing so, separate wave functions for
alpha and beta spin electrons are computed. For
more information see the MOPAC online manual,
page 152.
The following table contains the keywords
automatically sent to MOPAC and those you can
use to affect this property.
Keyword Description
UHF Automatically sent to MOPAC if
you choose Open Shell (Unre-
stricted) wave functions to specify
the use of the Unrestricted
Hartree-Fock methods.
Chem & BioOffice 2006 /Chem3D
Keyword Description
GEO-OK Automatically sent to MOPAC to
override checking of the Z-matrix.
MMOK Automatically sent to MOPAC to
specify Molecular Mechanics
correction for amide bonds. Use
the additional keyword NOMM to
turn this keyword off.
SPIN You can add this keyword to print
the spin density matrix in the *.out
file.
RHF Spin Density
RHF Spin Density uses the 1/2 electron correction
and a single configuration interaction calculation to
isolate the alpha spin density in a molecule. This
method is particularly useful when the UHF Spin
Density computation becomes too resource
intensive for large molecules. For more information
see the MOPAC online manual, page 28.
The following table contains the keywords
automatically sent to MOPAC and those you can
use to affect this property.
Keyword Description
ESR Automatically sent to MOPAC to
specify RHF spin density calcula-
tion.
GEO-OK Automatically sent to MOPAC to
override checking of the Z-matrix.
MOPAC Computations 181
Computing Properties

Keyword Description
MMOK Automatically sent to MOPAC to
Administrator
specify Molecular Mechanics
correction for amide bonds. Use
the additional keyword NOMM to
turn this keyword off.
Example 1: The Dipole Moment of
Formaldehyde
To calculate the dipole moment of formaldehyde:
1. From the File menu, choose New Model.
2. Click the Text Building tool.
3. Click in the model window.
A text box appears.
4. Type H2CO and press the Enter key.
A model of formaldehyde appears.
Figure 9-22: Formaldehyde model
5. From the MOPAC Interface submenu of the
Calculations menu, choose Minimize Energy.
6. On the Theory tab, choose AM1.
7. On the Properties tab, select Dipole.
8. Click Run.
182 MOPAC Computations
The results shown in the Messages window indicate
the electron distribution is skewed in the direction
of the oxygen atom.
X Y Z Total
Dipole -2.317 0.000 -0.000 2.317
(vector
Debye)
If you rotate your model, the X,Y, and Z
components of the dipole differ. However, the total
dipole does not. In this example, the model is
oriented so that the significant component of the
dipole lies along the X-axis.
Example 2: Comparing Cation Stabili-
ties in a Homologous Series of Mole-
cules
To build the model:
1. From the File menu, choose New Model.
2. Click the Text Building tool.
3. Click in the model window.
A text box appears.
4. For tri-chloro, type CCl3 and press the Enter
key.
5. Repeat step 1 through step 4 for the other
cations: type CHCl2 for di-chloro; type CH2Cl
for mono-chloro and CH3 for methyl cation.
NOTE: The cations in this example are even electron
closed shell systems and are assumed to have Singlet
ground state. No modifications through additional
keywords are necessary. The default RHF computation
is used.
6. For each model, click the central carbon, type
+ and press the Enter key.
The model changes to a cation and insures that
the charge is sent to MOPAC.
CambridgeSoft
Computing Properties
To perform the computation: 5. Click Run.

1. From the MOPAC Interface submenu of the
Calculations menu, choose Minimize Energy.
2. On the Theory tab, choose AM1.
3. On the Properties tab, select Charges in the
Properties list.
The results for the model appear in the
Message window when the computation is
complete.
The molecules are now planar, reflecting sp2
hybridization of the central carbon.

4. Select Wang-Ford from the Charges list. The following table shows the results:

tri-chloro cation di-chloro cation mono-chloro cation methyl cation

C(1) 0.03660 C(1) 0.11255 C(1) 0.32463 C(1) 0.72465
Cl(2) 0.31828 Cl(2) 0.33189 Cl(2) 0.35852 H(2) 0.08722
Cl(3) 0.32260 Cl(3) 0.33171 H(3) 0.15844 H(3) 0.09406
Cl(4) 0.32253 H(4) 0.22384 H(4) 0.15841 H(4) 0.09406

From these simple computations, you can reason Figure 9-23: Phenoxide ion model
that the charge of the cation is not localized to the
central carbon, but is rather distributed to different
extents by the other atoms attached to the charged
carbon. The general trend for this group of cations
is that the more chlorine atoms attached to the
charged carbon, the more stable the cation (the
decreasing order of stability is tri-chloro >di-chloro
> mono-chloro > methyl).

Example 3: Analyzing Charge Distribu-

tion in a Series Of Mono-substituted
Phenoxy Ions
1. From the File menu, choose New Model.
2. Click the Text Building tool.
3. Click in the model window.
A text box appears.
4. Type PhO- and press the Enter key.
A phenoxide ion model appears.
NOTE: All the monosubstituted phenols under
examination are even electron closed shell systems and are
assumed to have Singlet ground state. No modifications by
additional keywords are necessary. The default RHF
computation is used.
5. From the MOPAC Interface submenu of the
Calculations menu, choose Minimize Energy.
6. On the Theory tab, choose PM3. This automat-
ically selects Mulliken from the Charges list.
7. On the Property tab, select Charges.
8. Click Run.

Chem & BioOffice 2006 /Chem3D MOPAC Computations 183

Computing Properties
 To build para-nitrophenoxide ion:
Phenoxide p-Nitro m- Nitro o-Nitro
1. Click the Text Building tool.
H9 0.12069 H9 0.17553 N9 1.31296 H9 0.16911
2. Click H10, type NO2, then press the Enter key.
Administrator

H10 0.15700 N10 1.38043 H10 0.19979 H10 0.17281

Para nitrophenoxide ion is formed.
H11 0.12067 H11 0.17561 H11 0.14096 H11 0.13932
Perform minimization as in the last step.
H12 0.16946 H12 0.18715 H12 0.17948 H12 0.18090
For the last two monosubstituted nitro
phenols, first, select the nitro group using the O13 -0.70347 O13 -0.65265 O13 -0.71656

Select Tool and press the Delete key. Add the

O14 -0.70345 O14 -0.64406 O14 -0.65424
nitro group at the meta (H9) or ortho (H8) posi-
tion and repeat the analysis.
Example 4: Calculating the Dipole
The data from this series of analyses are shown Moment of meta-Nitrotoluene
below. The substitution of a nitro group at para,
meta and ortho positions shows a decrease in Create a model of m-nitrotoluene:
negative charge at the phenoxy oxygen in the order
1. From the File menu, choose New Model.
meta>para>ortho, where ortho substitution shows
the greatest reduction of negative charge on the 2. Click the Text Building tool.
phenoxy oxygen. You can reason from this data that 3. Click in the model window.
the phenoxy ion is stabilized by nitro substitution at
A text box appears.
the ortho position.
4. Type PhCH3 and press the Enter key.
Phenoxide p-Nitro m- Nitro o-Nitro A model of toluene appears. Reorient the
model using the Trackball tool until it is
C1 0.39572 C1 0.41546 C1 0.38077 C1 0.45789 oriented like the model shown in step 8.
C2 -0.46113 C2 -0.44929 C2 -0.36594 C2 -0.75764 5. From the Edit menu, choose Select All.

6. Select Show Serial Numbers from the Model

C3 -0.09388 C3 -0.00519 C3 -0.33658 C3 0.00316
Display submenu of the View menu.
C4 -0.44560 C4 -0.71261 C4 -0.35950 C4 -0.41505
NOTE: Show Serial Numbers is a toggle. When it is
C5 -0.09385 C5 -0.00521 C5 -0.10939 C5 -0.09544 selected, the number 1 displays in a frame.

C6 -0.46109 C6 -0.44926 C6 -0.41451 C6 -0.38967 7. With the Text Building tool, click H(11), then
type NO2 in the text box that appears.
O7 -0.57746 O7 -0.49291 O7 -0.54186 O7 -0.48265
8. Press the Enter key.
H8 0.16946 H8 0.18718 H8 0.21051 N8 1.38805
A model of m-nitrotoluene appears.

184 MOPAC Computations CambridgeSoft

Computing Properties
Figure 9-24: m-nitrotoluene model The following table contains the keywords
automatically sent to MOPAC and those you can
use to affect this property.

Keyword Description

POLAR Automatically sent to MOPAC

(E=(n1, n2, n3)) to specify the polarizablity
routine. n is the starting voltage
Use MOPAC to find the dipole moment: in eV. The default value is
E = 1.0.
1. From the MOPAC Interface submenu of the
Calculations menu, choose Minimize Energy.
You can reenter the keyword
2. On the Theory tab, choose AM1.
and another value for n to
3. On the Property tab, select Polarizabilities. change the starting voltage.
4. Click Run.
The following table is a subset of the results GEO-OK Automatically sent to MOPAC
showing the effect of an applied electric field on the to override checking of the
first order polarizability for m-nitrotoluene. Z-matrix.

MMOK Automatically sent to MOPAC

Applied to specify Molecular Mechanics
field (eV) alpha xx alpha yy alpha zz correction for amide bonds. Use
the additional keyword NOMM
0.000000 108.23400 97.70127 18.82380 to turn this keyword off.

0.250000 108.40480 97.82726 18.83561 Example 5: Comparing the Stability of

Glycine Zwitterion in Water and Gas
0.500000 108.91847 98.20891 18.86943 Phase
To compare stabilities:

1. From the File menu, choose New Model.

2. Click the Text Building tool.

3. Click in the model window.

A text box appears.

4. Type HGlyOH and press the Enter key.

A model of glycine appears.

Chem & BioOffice 2006 /Chem3D MOPAC Computations 185

Computing Properties
 Figure 9-25: Glycine model 4. Perform a minimization with and without the
COSMO solvation property selected as
performed for the glycine model.
The following table summarizes the results of the
Administrator

four analyses.

Form of H Solvent
glycine (kcal/mole) Accessible
5. From the MOPAC Interface submenu of the Surface 2
Calculations menu, choose Minimize Energy.
neutral (H2O) -108.32861 52.36067
6. On the Theory tab, choose PM3.
zwitterion (H2O) -126.93974 52.37133
7. On the Property tab, Ctrl+click Heat of Forma-
tion and COSMO Solvation. neutral (gas) -92.75386
8. Click Run.
zwitterion (gas) -57.83940
The results appear in the Messages window.
9. From the MOPAC Interface submenu of the
From this data you can reason that the glycine
Calculations menu, choose Minimize Energy. zwitterion is the more favored conformation in
water and the neutral form is more favored in gas
10. On the Property tab, deselect COSMO phase.
Solvation.
11. Click Run. Example 6: Hyperfine Coupling
Constants for the Ethyl Radical
The results appear in the Messages window.
To build the model:
To create the zwitterionic form:
1. From the File menu, choose New Model.
1. Click the Text Building tool.
2. Click the Text Building tool.
2. Click the nitrogen, type +, then press the
3. Click in the model window.
Enter key.
A text box appears.
3. Click the oxygen atom, type -, then press the
Enter key. 4. Type EtH and press the Enter key.

The glycine zwitterion is formed. 5. Click the Select tool.

6. Select H(8).
Figure 9-26: Glycine zwitterion
7. Press the Backspace key.
If you have automatic rectification on, a message
appears asking to turn it off to perform this
operation.
8. Click Turn Off Automatic Rectification.
The Ethyl Radical is displayed.

186 MOPAC Computations CambridgeSoft

Computing Properties
Figure 9-27: Ethyl radical model
Hyperfine Coupling Constants

H7 0.05479

Example 7: UHF Spin Density for the

Ethyl Radical
To calculate the UHF spin density:
To perform the HFC computation:
1. From the MOPAC Interface submenu of the
Calculations menu, choose Minimize Energy.
2. On the Theory tab, choose the PM3 potential
function and the Open Shell (Unrestricted) wave
function.
3. On the Properties tab, choose Hyperfine
Coupling Constants.
4. Click Run.
1. Create the ethyl radical as described in Spin
Density on page 181.
2. From the MOPAC Interface submenu of the
Calculations menu, choose Minimize Energy.
3. On the Theory tab, select PM3.
4. On the Properties tab, select Open Shell (Unre-
stricted) and Spin Density.
The Message window displays a list of atomic
orbital spin densities.
The atomic orbitals are not labeled for each
value, however, the general rule is shown in the
table below (MOPAC only uses s, px, py and pz
orbitals).

The unpaired electron in the ethyl radical is Atomic Orbital Spin Density A.O.
delocalized. Otherwise, there would be no coupling
0.07127 C1 s
constants.
0.06739 C1 px
Hyperfine Coupling Constants
0.08375 C1 py

C1 0.02376 0.94768 C1 pz

C2 -0.00504 -0.01511 C2 S

-0.06345 C2 px
H3 -0.02632
-0.01844 C2 py
H4 -0.02605
-0.03463 C2 pz
H5 0.00350
-0.07896 H3 s

H6 0.05672 0.07815 H4 s

Chem & BioOffice 2006 /Chem3D MOPAC Computations 187

Computing Properties
 Atomic Orbital Spin Density A.O. Total Spin Density

0.01046 H5 s 0.04395 H6
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0.05488 H6 s 0.04216 H7

0.05329 H7 s
You can reason from the result shown below that
the unpaired electron in the ethyl radical is more
localized at pz orbital on C1. Generally, this is a
good indication of the reactive site
Example 8: RHF Spin Density for the
Ethyl Radical
To calculate the RHF spin density:
1. Create the ethyl radical as described in Spin
Density on page 181.
2. From the MOPAC Interface submenu of the
Calculations menu, choose Minimize Energy.
3. On the Theory tab, choose PM3 and Closed
Shell (Restricted).
4. On the Properties tab, choose Spin Density.
The Message window displays the total spin
densities for each atom (spin densities for all
orbitals are totaled for each atom).
NOTE: You can look in the *.out file for a breakdown of
the spin densities for each atomic orbital.
Total Spin Density
0.90744 C1
0.00644 C2
You can reason from this result that the unpaired
electron in the ethyl radical is more localized on C1.
Generally, this is a good indication of the reactive
site.
MOPAC Files
CS MOPAC can use standard MOPAC text files for
input, and creates standard MOPAC output files.
These are especially useful when running repeat
computations.
Using the *.out file
In addition to the Messages window, MOPAC
creates two text files that contain information about
the computations.
Each computation performed using MOPAC
creates a *.out file containing all information
concerning the computation. A summary *.arax file
is also created, (where x increments from a to z after
each run). The *.out file is overwritten for each run,
but a new summary *.arax, file is created after each
computation (*.araa, *.arab, and so on.)
The OUT and AAX files are saved by default to the
\Mopac Interface subfolder in your My Documents
folder. You may specify a different location from
the General tab of the MOPAC Interface dialog
box.The following information is found in the
summary file for each run:
Electronic Energy (Eelectronic)

0.00000 H3 Core-Core Repulsion Energy (Enuclear)

Symmetry
0.00000 H4
Ionization Potential
0.00001 H5
HOMO/LUMO energies

188 MOPAC Computations CambridgeSoft

MOPAC Files
The *.out file contains the following information by
default.
Starting atomic coordinates
Starting Z-matrix
Molecular orbital energies (eigenvalues)
Ending atomic coordinates
The workings of many of the calculations can also
be printed in the *.out file by specifying the
appropriate keywords before running the
calculation. For example, specifying MECI as an
additional keyword will show the derivation of
microstates used in an RHF 1/2 electron
approximation calculation. For more information
see Using Keywords on page 294.
NOTE: Close the *.out file while performing MOPAC
computations or the MOPAC application stops functioning.
Creating an Input File
A MOPAC input file (.MOP) is associated with a
model and its dialog box settings.
To create a MOPAC input file:
1. From the MOPAC Interface submenu of the
Calculations menu, choose Create Input File.
Figure 9-28: Creating an input file
Chem & BioOffice 2006 /Chem3D
2. Select the appropriate settings and click Create.
Running Input Files
Chem3D allows you to run previously created
MOPAC input files.
To run an input file:
1. From the MOPAC Interface submenu of the
Calculations menu, click Run Input File.
The Run MOPAC Input File dialog box
appears.
Figure 9-29: The Run MOPAC Input File dialog box
2. Type the full path of the MOPAC file or
Browse to the file location.
3. Select the appropriate options. For more infor-
mation about the options see Specifying the
Electronic Configuration on page 296.
4. Click Run.
A new model window appears displaying the
initial model. The MOPAC job runs and the
results appear.
MOPAC Computations 189
MOPAC Files
 All properties requested for the job appear in
the *.out file. Only iteration messages appear
for these jobs.
Administrator
NOTE: If you are opening a MOPAC file where a model
has an open valence, such as a radical, you can avoid having
the coordinates readjusted by Chem3D by turning off
Automatically Rectify in the Building control panel.
NOTE: MOPAC input files that containing multiple
instances of the Z-matrix under examination will not be
correctly displayed in Chem3D. This type of MOPAC input
files includes calculations that use the SADDLE keyword,
or model reaction coordinate geometries.
Running MOPAC Jobs
Chem3D enables you to select a previously created
MOPAC job description file (JDF). The JDF file
can be thought of as a set of Settings that apply to a
particular dialog box. For more information about
JDF files see JDF Files on page 153.
To create a JDF file:
1. From the MOPAC Interface submenu of the
Calculations menu, choose a calculation.
2. After all settings for the calculation are speci-
fied, click Save As.
To run a MOPAC job from a JDF file:
1. From the MOPAC Interface submenu of the
Calculations menu, click Run MOPAC Job.
The Open dialog box appears.
190 MOPAC Computations
2. Select the JDF file to run.
The dialog box corresponding to the type of
job saved within the file appears.
3. Click Run.
Repeating MOPAC Jobs
After you perform a MOPAC calculation, you can
repeat the job as follows:
4. From the MOPAC Interface submenu of the
Calculations menu, choose Repeat [name of
computation].
The appropriate dialog box appears.
5. Change parameters if desired and click Run.
The computation proceeds.
Creating Structures From
ARC Files
When you perform a MOPAC calculation, the
results are stored in an ARC file in the \Mopac
Interface subfolder in your My Documents folder.
You can create a structure from the ARC file as
follows:
1. Open the ARC file in a text editor.
2. Delete the text above the keywords section of
the file as shown in the following illustration.
3. Save the file with a MOP extension.
4. Open the MOP file.
CambridgeSoft
MOPAC Files
 Delete text through
this line

Keywords
section

Chem & BioOffice 2006 /Chem3D MOPAC Computations 191

MOPAC Files
Administrator

192 MOPAC Computations CambridgeSoft

MOPAC Files
Chapter 10: Gaussian
Overview Predicting Spectra
Gaussian 2003 is a powerful, command-line driven, To run predictions, select the spectrum from the
computational chemistry application including Gaussian Interface submenu of the Calculations
both ab initio and semi empirical methods. It is not menu.
included with Chem3D, but can be purchased
Figure 10-30: Running a Spectrum
directly from CambridgeSoft. You can use the
Online menu command Browse ChemStore.com to
link directly to the website.

Chem3D 10 provides an all-new interface for

Gaussian 2003. The model in the Chem3D window
transparently provides the data for creating
Gaussian jobs or running Gaussian computations.
The new interface supports all Gaussian 2003
calculations, offering the following features not
previously available in Chem3D:

13
C and 1H NMR spectra predictions Predict spectra

IR and Raman spectra predictions

Multi-step Jobs
Partial Optimizations
Support for DFT Methods
Advanced Mode
For information on how to use Gaussian, see the NOTE: Depending on your computers speed and memory,
documentation supplied with the Gaussian Gaussian calculations can be slow. You should only run
application. spectrum predictions on models of small molecules.

New Gaussian Interface

The new Gaussian interface is more stable and
offers more Gaussian features, including prediction
of NMR, UV, IR, and Raman spectra. It makes use
of COEA, CambridgeSofts new extension
architecture. Some of the new features supported
are described in the following sections.
TIP: Run a minimization before predicting spectra. MM2
is faster than Gaussian minimization, and is usually
adequate. Gaussian may fail to produce a spectrum if the
model is not at a minimum energy state.
To view the predicted spectra, select the Spectrum
Viewer on the View menu.

Chem & BioOffice 2006 /Chem3D Gaussian 193

New Gaussian Interface
 Figure 10-31: Selecting the Spectrum Viewer
Administrator

For each prediction that you run on a given

compound, a new tab will open in the Spectrum
Viewer.

Figure 10-32: Predicted spectra for chlorobenzene

Multi-step Jobs
You can link jobs and run them with a single
command. There is no technical limit to the
number of jobs that can be linked. To run multiple
jobs:

194 Gaussian CambridgeSoft

New Gaussian Interface
 1. Select your first job (usually Minimization) Figure 12: Setting up a partial optimization
from the Gaussian Interface submenu of the
Calculations menu.
Figure 11: Gaussian Interface

Internal
coordinates

Input Template
The General tab of the Gaussian Interface dialog
2. Click the + button, and use the Job Type
box contains the input template.
drop-down menu to add a new job to the
queue. Figure 13: Input template
3. If you want to remove a job from the queue,
select the Link tab and click the - button.
4. Run the job queue. If you wish to terminate the
runs at any time, use the stop button on the
Calculations toolbar.

Partial Optimizations
To perform a partial optimization:
1. Select a portion of the model. You may
optimize either the selected or unselected
portion, whichever is more convenient.
2. Select optimization from the Gaussian Inter-
face submenu. In the Gaussian Interface
dialog box, click the Internal Coordinates radio
button.
3. In the Move Which text window, indicate
whether the selected or unselected atoms are to You can set output parameters with the checkboxes
be optimized. and edit keywords in the run file.

Chem & BioOffice 2006 /Chem3D Gaussian 195

New Gaussian Interface
 Advanced Mode Figure 15: DFT methods

If you are an expert user, you can go directly to a

text entry window similar to the input template. Just
click Use Advanced Mode on the Gaussian
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Interface submenu.
Figure 14: Advanced Mode

When you have chosen a method, the complete

DFT method information is displayed, and a
button appears next to the Method text box to allow
you to edit your input.

Figure 16: DFT display

Note the Gaussian 2003 Keywords link under the

text window. If you need help, clicking the link
opens your web browser to the keywords page of
the Gaussian website.

Support for DFT Methods

Selecting DFT for Method opens a dialog box
where you can choose which DFT method you
wish to use.
Minimizing Energy
Minimizing energy is generally the first molecular
computation performed on a model. You may
minimize all or part of a model. If you are
minimizing part of a model, you should make your
selection of what to include or exclude before
continuing. See Other Options on page 198.

1. From the Calculations menu, point to

Gaussian Interface and choose Minimize
(Energy/Geometry).

The Gaussian Interface dialog box appears,

with Minimize as the default Job Type.

196 Gaussian CambridgeSoft

Minimizing Energy
Figure 10-1Gaussian menu
2. You may use the defaults on the Jobs tab, or set
your own parameters.
Option Function
Job Type Sets defaults for different
types of computations.
Method Selects a method.
Basis Set Specifies the basis set. Most
methods require a basis set
be specified. See the Gaus-
sian Help file for excep-
tions.
Wave Function Selects closed or open shell.
See Specifying the Elec-
tronic Configuration on
page 296 for more details.
Chem & BioOffice 2006 /Chem3D
Option Function
Polarization Specifies a polarization
function for heavy atoms (P,
S, or heavier).
H If you selected a Polariza-
tion function, you should
also choose an H function.
Diffuse Adds a diffuse function to
the basis set. If you use a
diffuse function, you should
also specify Tight Conver-
gence on the Advanced tab.
See the Gaussian manual
for details.
The Advanced tab displays parameters that are
adjusted less often. Only those parameters that
apply to the job type you have selected are active.
For minimizations, they are:
Option Function
Solvation Model Selects a solvation model.
See the SCRF keyword in
the Gaussian manual for
information on methods.
Solvent If you select a solvation
model, you may select a
solvent. The default solvent
for all models is water.
Gaussian 197
Minimizing Energy
 Selecting the Internal Coordinate radio button allows
Option Function you to minimize only part of the model by choosing
either Selected Atoms or Unselected Atoms.
Force Constants Options are:
3. On the General Tab, set the parameters that
Administrator

No calculation control the output:

Initial force constants

Option Function
(CalcFC)

Calculate at each point Display Every Itera- Displays the minimization

(CalcAll) tion process live at each itera-
tion in the calculation.
Population Analysis Options are: NOTE: Adds significantly
None
to the time required to
minimize the structure.
Fullsame as Regular,
but for all orbitals Show Output in Sends the output to a text
Notepad file.
Minimumoutputs
the total atomic
Send Back Output Displays the value of each
charges and orbital
measurement in the Output
energies
window.
Regular outputs five
NOTE: Adds significantly
highest occupied and
to the time required to
five lowest virtual
minimize the structure.
orbitals, with density
matrices and full
Mulliken population Optimize to Transition State
analysis
To optimize your model to a transition state, use a
Other Options conformation that is as close to the transition state
as possible. Do not use a local or global minimum,
By default, Gaussian uses modest convergence because the algorithm cannot effectively move the
geometry from that starting point.
criteria to speed up calculations. The Use Tight
Convergence checkbox adds the keyword tight to To optimize a transition state:
the input template to specify full convergence. You
may also add a charge by first deselecting the default 1. From the Calculations menu, point to
Use Formal Charge checkbox, or change the Spin Gaussian Interface, and choose Optimize to
Transition State.
Multiplicity. Spins can be positive integers. Charges
may be plus or minus. The Gaussian Interface dialog box appears.

198 Gaussian CambridgeSoft

Minimizing Energy
Figure 10-2: Optimizing to a transition state
2. You may use the defaults, or set your own
parameters.
NOTE: Unless you are an experienced Gaussian
user, use the Transition State defaults.
3. On the Properties tab, select the properties you
wish to calculate from the final optimized
conformation.
4. On the General tab, type any additional
keywords that you want to use to modify the
optimization.
5. Click Run.
Computing Properties
To specify the parameters for computations to
predict properties of a model:
1. From the Calculations menu, point to
Gaussian and choose Compute Properties.
The Gaussian Interface dialog box appears,
with the Properties tab selected.
Chem & BioOffice 2006 /Chem3D
Figure 10-3: The Properties tab
2. Select the properties to estimate.
3. Click the Run button.
Job Description File
Formats
Job description files are like Preferences files; they
store the settings of the dialog box. You may save
the file as either a JDF or a JDT type. You modify
and save JDF files more easily than JDT files.
JDT Format
The JDT format is a template format intended to
serve as a foundation from which other job types
may be derived. The Minimize Energy and
Compute Properties job types supplied with
Chem3D are examples of these. To discourage
modification of these files, the Save button is
deactivated in the dialog box of a template file.
JDF Format
The JDF format is a file format for saving job
descriptions. Clicking Save within the dialog box
saves modifications without the appearance of a
warning or confirmation dialog box.
Gaussian 199
Computing Properties
 Saving either format within the Gaussian Job folder 4. Click Run.
adds it to the Gaussian submenu for convenient
access. The Gaussian job runs. At a certain point, a
new tab opens and the model appears in the
Job description files are like Preferences files; they Model Window.
Administrator

store the settings of the dialog box. You may save

the file as either a JDF or a JDT type. You modify
and save JDF files more easily than JDT files.
Running a Gaussian Input
File
If you have a previously created GJF Gaussian
input file, you can run the file from within Chem3D.
To run a Gaussian input file:
1. From the Calculations menu, point to
Gaussian Interface and choose Run Input File.
The Run Gaussian Input File dialog box
appears.
Figure 10-4: The Run Gaussian Input file dialog box
Running a Gaussian Job
Chem3D enables you to select a previously created
Gaussian job description file (JDF). The JDF file
can be thought of as a set of Settings that apply to a
particular dialog box.
You can create a JDF file from the dialog box of any
of the Gaussian calculations (Minimize Energy,
Optimize to Transition State) by clicking Save As
after all Settings for the calculation have been set.
For more information about JDF files see Job
Description File Formats on page 153.
To run a Gaussian job:
1. From the Gaussian submenu, choose Run
Gaussian Job.

The Open dialog box appears.

2. Select the file to run.

The dialog box corresponding to the type of

2. Type the full path of the Gaussian file or job (Minimize Energy, Compute Properties,
Browse to location. and so on.) saved within the file appears.
3. Select the appropriate options. 3. Click Run.

If you want to Then click Chem3D enables you to select a previously created
Gaussian job description file (JDF). The JDF file
can be thought of as a set of Settings that apply to a
Automatically Parse Results
particular dialog box.

save the output to a Show Output in Notepad You can create a JDF file from the dialog box of any
file. of the Gaussian calculations (Minimize Energy,
Optimize to Transition State) by clicking Save As
display the results in Send Back Output after all Settings for the calculation have been set.
the Output window For more information about JDF files see Job
Description File Formats on page 153.

200 Gaussian CambridgeSoft

Job Description File Formats
To run a Gaussian job:
1. From the Gaussian submenu, choose Run
Gaussian Job.
The Open dialog box appears.
2. Select the file to run.
The dialog box corresponding to the type of
job (Minimize Energy, Compute Properties,
and so on.) saved within the file appears.
3. Click Run.
Chem & BioOffice 2006 /Chem3D
Repeating a Gaussian Job
After you perform a Gaussian calculation, you can
repeat the job as follows:
1. From the Gaussian submenu, choose Repeat
[name of computation].
The appropriate dialog box appears.
2. Change parameters if desired and click Run.
The computation proceeds.
Gaussian 201
Job Description File Formats
Administrator

202 Gaussian CambridgeSoft

Job Description File Formats
Chapter 11 :
tions
GAMESS Overview
The General Atomic and Molecular Electronic
Structure System (GAMESS) is a general ab initio
quantum chemistry package maintained by the
Gordon research group at Iowa State University. It
computes wavefunctions using RHF, ROHF, UHF,
GVB, and MCSCF. CI and MP2 energy corrections
are available for some of these.
GAMESS is a command-line application, which
requires a user to type text-based commands and
data. Chem3D serves as a front-end graphical user
interface (GUI), allowing you create and run
GAMESS jobs from within Chem3D.
New in version 10, the GAMESS application is
installed automatically with Chem3D. You must,
however, accept a license agreement and register
the software before you can use it. This is done
automatically by Chem3D the first time you use the
GAMESS computation option. You can download
the GAMESS documentation from the following
web site:
http://www.msg.ameslab.gov/GAMESS/
GAMESS.html
The computation options on the GAMESS
interface menu are:
Minimize Energy
Chem & BioOffice 2006 /Chem3D
GAMESS Computa-
Optimize to Transition State
Compute Properties
Run Frequency
Predict IR/Raman Spectra
Predict NMR Spectra
When you choose one of these options, The
GAMESS Interface dialog box appears, with the
recommended default parameters for that
computation chosen. You may change parameters
on any of the tabbed pages of the dialog box before
running the computation. Thus, the options are a
convenience in that they insert defaults. If you
know what parameter settings you want to use, you
can run any computation using any of the options
as a starting point. If you are familiar with the
GAMESS keywords, you can choose Use Advanced
Mode and get a GUI version of the command line
interface.
Minimize Energy
To perform a GAMESS Minimize Energy
computation on a model:
1. From the Calculations menu, point to
GAMESS and choose Minimize Energy.
The Minimize Energy dialog box appears
with the Job & Theory tab displayed.
GAMESS Computations 203
Minimize Energy
 Figure 11-5: GAMESS minimizing energy 5. Set the Polarization functions.

If you select a function for Heavy Atom, also

select an H option.
Administrator

6. Select a Spin Multiplicity value between 1 and

10.

The General Tab

Use the General tab to set options for display and
recording results of calculations.

To set the job type options:

1. In the Minimize Energy dialog box, click the

Job Type tab.
2. Use the tabs to customize your computation.
2. Select the appropriate options:
See the following sections for details.
3. Click Run.
If you want to Then click

The Job & Theory Tab

watch the minimiza- Display Every Iteration
Use the Job & Theory tab to specify the combination tion process live at
of basis set and particular electronic structure each iteration in the NOTE: Displaying or
calculation recording each iteration
theory. By default, this tab is optimized for setting
adds significantly to the
up ab initio computations.
time required to
For more detailed information, see the $BASIS minimize the structure.
section of the GAMESS documentation.
record each iteration Record Every Iteration
To specify the calculation settings: as a frame in a movie
for later replay
1. From the Method list, choose a method.
2. From the Wave Function list, choose a function. view the value of Copy Measurements to
3. From the Basis Set list, choose the basis set. each measurement in Output
the Measurement
NOTE: To use a Method or Basis Set that is not on table
the list, type it in the Additional Keywords section on
the General tab. For more information, see Specifying calculate using the Use Tight Convergence
the General Settings on page 205. equivalent to the Criteria
Gamess keyword
4. From the Diffuse list, select the diffuse function Opt=Tight
to add to the basis set.

204 GAMESS Computations CambridgeSoft

Minimize Energy
Specifying Properties to
Compute
Use the Properties tab to specify which properties
are computed. The default Population Analysis type
is Mulliken.
To specify properties:
1. In the Minimize Energy dialog box, click
Properties.
Figure 11-6: The Properties tab
2. On the Properties tab, set the following options:
Select the properties to calculate
Select the Population Analysis type
Specifying the General
Settings
Use the General tab to customize the calculation to
the model.
Chem & BioOffice 2006 /Chem3D
To set the General settings:
1. In the Minimize Energy dialog box, click
General.
Figure 11-7: The General tab
2. On the General tab, set the following options:
Select the Solvation model.
Type the dielectric constant for the solvent.
The box does not appear for gas-phase
computations.
In the Results In box, type or browse to the
path to the directory where results are
stored.
If desired, add GAMESS keywords to the
Additional Keywords dialog box.
Saving Customized Job
Descriptions
After you customize a job description, you can save
it as a Job Description file to use for future
calculations.
For more information, see Job Description File
Formats on page 153.
GAMESS Computations 205
Saving Customized Job Descriptions
 To save a GAMESS job: To run the job file:

1. On the General tab, type the name of the file in 1. From the Calculations menu, point to
the Menu Item Name text box. GAMESS and choose Run a Job.
The Open dialog box appears.
Administrator

The name you choose will appear in the

GAMESS menu. 2. Type the full path of the GAMESS file or
Browse to location.
2. Click Save As.
3. Click Open.
The Save dialog box appears. The appropriate dialog box appears.
3. Open the folder 4. Change settings on the tabs if desired.
\Chem3D\C3D Extensions\GAMESS Job.
5. Click Run
NOTE: You must save the file in the GAMESS Job 6. Repeating a GAMESS Job
folder for it to appear in the menu. After a GAMESS computation has been
performed, you can repeat it using the GAMESS
4. Select the .jdf or .jdt file type. menu.
5. Click Save. To repeat a GAMESS job:
Your custom job description appears in the 7. From the Calculations menu, point to
GAMESS menu. GAMESS and choose Repeat [name of computa-
tion].
Running a GAMESS Job The appropriate dialog box appears.
If you have a previously created an INP GAMESS 8. Change parameters if desired and click Run.
job file, you can run the file in Chem3D. The computation is run.

206 GAMESS Computations CambridgeSoft

Running a GAMESS Job
Chapter 12: Jaguar
Overview 1. From the Calculations menu, point to Jaguar
Interface and choose Minimize
SCHRDINGER Jaguar is a high-performance (Energy/Geometry).
ab initio package for both gas and solution phase The Jaguar Interface dialog box appears, with
simulations, with particular strength in treating Minimize as the default Job Type.
metal containing systems. It is a practical quantum Figure 12-8: Jaguar minimization dialog box
mechanical tool for solving real-world problems.
The new Chem3D interface is the only Windows
platform GUI for Jaguar. The model in the
Chem3D window transparently provides the data
for creating Jaguar input files or running Jaguar
computations. The new interface offers the
following features:
Minimizing Energy/Geometry
Optimize to Transition State
Predict IR and Raman Spectra
Computing Properties
Advanced Mode
Jaguar must be purchased as a separate addin.
Academic customers may purchase Jaguar from
Cambridgesoft, see http://www.chem3d.com for
details. Commercial customers should go to
2. You may use the defaults on the Jobs tab, or set
http://www.schrodinger.com for information. For
your own parameters.
information on how to use Jaguar, see the
documentation supplied with the Jaguar
application. Option Function

Minimizing Energy Job Type Sets defaults for different

types of computations.
Minimizing energy is generally the first molecular
computation performed on a model. You may Method Selects a method.
minimize all or part of a model. If you are
minimizing part of a model, you should make your
selection of what to include or exclude before
continuing.

Chem & BioOffice 2006 /Chem3D Jaguar 207

Minimizing Energy
 Option Function
Basis Set Specifies the basis set. Most
Administrator
methods require a basis set
be specified. See the Jaguar
Help file for exceptions.
Wave Function Selects closed or open shell.
See Specifying the Elec-
tronic Configuration on
page 296 for more details.
Polarization Specifies a polarization
function for heavy atoms (P,
S, or heavier).
Diffuse Adds a diffuse function to
the basis set. If you use a
diffuse function, you should
also specify Tight Conver-
gence on the Advanced tab.
See the Jaguar manual for
details.
Move Which Used for partial minimiza-
tion. You may optimize the
selected or unselected
portion of the model,
whichever is more conve-
nient
Coord. System Select Cartesian or Internal
Coordinate radio button.
208 Jaguar
Option Function
Max Iterations Maximum iterations, if
minimum is not reached
sooner. Default is 100.
Pressure Default is 1 atm.
Temperature Default is 0C (298.15K).
Spin Multiplicity A positive integer. Default
is 1.
Net Charge You may set a positive or
negative charge by dese-
lecting the Use Formal
Charge checkbox and
entering a value.
Optimize to Transition
State
To optimize your model to a transition state, use a
conformation that is as close to the transition state
as possible. Do not use a local or global minimum,
because the algorithm cannot effectively move the
geometry from that starting point.
To optimize a transition state:
1. From the Calculations menu, point to Jaguar
Interface, and choose Optimize to Transition
State.
The Jaguar Interface dialog box appears.
CambridgeSoft
Optimize to Transition State
Figure 12-9: Jaguar optimize to transition state dialog 1. Run a minimization. If you have not run the
box Jaguar minimization routine on the model, the
MM2 tool on the Calculation toolbar is faster
and usually adequate.
2. Point to Jaguar Interface on the Calculations
menu, and select Predict IR Spectrum.
3. Click the Run button.
The predicted spectrum appears in the
Spectrum Viewer.

Computing Properties
To specify the parameters for computations to
predict properties of a model:
1. From the Calculations menu, point to Jaguar
and choose Compute Properties.
The Jaguar Interface dialog box appears, with
the Properties tab selected.
Figure 12-10: Computing Jaguar properties

2. You may use the defaults, or set your own

parameters.

NOTE: Unless you are an experienced Jaguar user,

use the Transition State defaults.

3. On the Properties tab, select the properties you

wish to calculate from the final optimized
conformation.

4. On the General tab, type any additional

keywords that you want to use to modify the
optimization.

5. Click Run.

Predicting Spectra
2. Select the properties to estimate.
To predict an IR spectrum: 3. Click the Run button.

Chem & BioOffice 2006 /Chem3D Jaguar 209

Predicting Spectra
 Advanced Mode Figure 12-11: Advanced Mode

If you are an expert user, you can go directly to a

text entry window similar to the input template. Just
Administrator

click Use Advanced Mode on the Jaguar Interface

submenu.

Note the Online Jaguar Keywords link under the

text window. If you need help, clicking the link
opens your web browser to the keywords page of
the Schrdinger website.

210 Jaguar CambridgeSoft

Advanced Mode
Appendix A: Substructures
Overview
You can define substructures and add them to a
substructures table. When you define a
substructure, the attachment points (where
unselected atoms are bonded to selected atoms) are
stored with the substructure.
If a substructure contains more than one
attachment point (such as Ala), the atom with the
lowest serial number normally becomes the first
attachment point. The atom with the second lowest
serial number becomes the second attachment
point, and so on. However, there are situations
where this general rule is not valid.
Attachment point rules
The following rules cover all possible situations for
multiple attachment points in substructures; Rule 3
is the normal situation described above:
1. If an atom has an open valence and is not
attached to an atom that is unselected, it goes
after any atom that is attached to an unselected
atom.
2. If an atom is attached only to rectification
atoms, it goes after any atom that is attached to
non-rectification atoms.
3. If two atoms are the same according to the
above criteria, the atom with the lowest serial
number goes first.
4. If two atoms are the same according to the
above criteria, then the one which is attached to
the atom with the lowest serial number goes
first.
Chem & BioOffice 2006 /Chem3D
Angles and measurements
In addition to the attachment points, the
measurements between the selected atoms and
nearby unselected atoms are saved with the
substructure to position the substructure relative to
other atoms when the substructure is used to
convert labels into atoms and bonds.
For example, Chem3D stores with the substructure
a dihedral angle formed by two atoms in the
substructure and two unselected atoms. If more
than one dihedral angle can be composed from
selected (substructure) and unselected
(non-substructure) atoms, the dihedral angle that is
saved with the substructure consists of the atoms
with the lowest serial numbers.
Consider the following model to define a
substructure for alanine:
Figure A-12: Alanine substructure
Since polypeptides are specified beginning with the
N-terminal amino acid, N(4) should have a lower
serial number than the Carboxyl C(6). To ensure
that a chain of alanine substructures is formed
correctly, C(1) should have a lower serial number
than O(3) so that the C-C-N-C dihedral angle is
used to position adjacent substructures within a
label.
Substructures 211
 Defining Substructures
To define a substructure:
Administrator
1. Build a model of the substructure. You can use
Chem3D tools, or build it in the ChemDraw
panel.
2. Select the atoms to define.
3. From the Edit menu, choose Copy.
To save the substructure definition:
1. Open Substructures.xml. From the
2. View menu, point to Parameter Tables and
choose Substructures.
3. Right-click in the Substructures table and
choose Append Row.
A new row is added to the table.
4. Select the cell in the Model column.
5. Right-click in the cell and choose Paste from
the context menu.
The structure is pasted into the table cell. Note
that it will be not be visible until you move to
another cell.
6. Select the cell in the Name column.
7. Type a name for the substructure.
8. Close and save the Substructures table.
For example, consider an ester substructure,
R1COOR2. You can build this substructure as part
of the following model:
Figure A-13: Ethoxypropanol model
212 Substructures
Select atoms 3-5 (the two oxygens and the carbon
between them) and using the instructions above,
create a new record in the Substructures Table.
If you want to append an ester onto the end of the
chain as a carboxylic acid, you can simply
double-click a hydrogen to replace it with the ester
(as long as the name of the substructure is in the
text box). Replacing H(8) (of the original structure)
would produce the following structure:
Figure A-14: Extended ethoxypropanol model
Notice that the carbon atom in the ester has
replaced the hydrogen. This is because, when the
ester was defined, the carbon atom had a lower
serial number (3) than the oxygen atom that formed
the other attachment point in the substructure (5).
NOTE: When defining substructures with multiple
attachment points, it is critical to note the serial numbers of
the atoms in the substructure so that you can correctly orient
the substructure when it is inserted in the model. See the rules
for multiple attachment points discussed at the beginning of
this section.
CambridgeSoft
Defining Substructures
Appendix B: Keyboard Modifiers
The following tables list the keyboard modifiers that allow you to manipulate your view of the model without
changing tools.

Rotation

Key Drag Shift+Drag

ALT Trackball rotate view Trackball rotate model selection

Shift+B Rotate 1/2 of fragment around bond

Shift+N which fragment rotates depends on the order in
which the atoms were selected.

V Rotate view about selected bond Rotate model selection about axis

X Rotate view about view X axis Rotate model about view X axis

Y Rotate view about view Y axis Rotate model about view Y axis

Z Rotate view about view Z axis Rotate model about view Z axis

In addition to the keyboard shortcuts, you can rotate a model by dragging with the mouse while holding down
both the middle mouse button or scroll wheel and the left mouse button. Tip: The order is important; press the middle
button first.

Zoom and Translate

Key Drag Shift+Drag

CTRL Translate view Translate model selection

A Zoom to center

Chem & BioOffice 2006 /Chem3D Keyboard Modifiers 213

 Key Drag Shift+Drag

Q Zoom to rotation center

Administrator

W Zoom to selection center

If you have a wheel mouse, you may also use the scroll wheel to zoom. Dragging with the middle button or
scroll wheel translates the view.

Selection
Standard Selection

Key Click Shift+Click Drag Shift+Drag

S Select atom/bond Multiple select atom/bond Box select atoms Multiple box select
/bonds atoms /bonds

Notes: Double-clicking a selected fragment selects the

next higher fragment; that is, each double-click
Clicking a bond selects the bond and the two moves you up one in the hierarchy until you
atoms connected to it. have selected the entire model.
Double-clicking an atom or bond selects the
fragment that atom or bond belongs to. Radial Selection
Radial selection is selection of an object or group of objects based on the distance or radius from a selected
object or group of objects. This feature is particularly useful for highlighting the binding site of a protein. Radial
selection is accessed through the Select submenu of the context menu in the Model Explorer or 3D display.

214 Keyboard Modifiers CambridgeSoft

Selection
In all cases, multiple selection is specified by holding the shift key down while making the selections.

Submenu option Effect

Select Atoms within Distance of Selects all atoms (except for those already selected) lying within the speci-
Selection fied distance from any part of the current selection. The current selection
will be un-selected unless multiple selection is used.

Select Groups within Distance Selects all groups (except for those already selected) that contain one or
of Selection more atoms lying within the specified distance from any part of the current
selection. The current selection will be un-selected unless multiple selec-
tion is used.

Select Atoms within Radius of Selects all atoms (except for those already selected) lying within the speci-
Selection Centroid fied distance of the centroid of the current selection. The current selection
will be un-selected unless multiple selection is used.

Select Groups within Radius of Selects all groups (except for those already selected) that contain one or
Selection Centroid more atoms lying within the specified distance of the centroid of the
current selection. The current selection will be un-selected unless multiple
selection is used.

Chem & BioOffice 2006 /Chem3D Keyboard Modifiers 215

Selection
Administrator

216 Keyboard Modifiers CambridgeSoft

Selection
Appendix C: Atom Types
Overview
Chem3D assigns atom types when you build with
Automatically Correct Atom Types turned on. You
can also create your own atom types.
Assigning Atom Types
When you replace atoms, Chem3D attempts to
assign the best atom type to each atom by
comparing the information about the atom (such as
its symbol and the number of bonds to the atom) to
each atom type record in the Atom Type table.
When you have selected the Automatically Correct
Atom Types check box in the Building control
panel, atom types are corrected when you delete
atoms or bonds, or when you add atoms or bonds.
In addition, if this check box is selected, then the
atom types of pre-existing atoms may change when
you replace other atoms with other atoms of a
different type.
If the wrong atom type is assigned to an atom, you
can specify the correct atom type by selecting the
Text Building Tool, clicking the atom, typing the
name of the atom type into the text box, and
pressing the Enter key.
Atom Type Characteristics
The characteristics of an atom must match the
following atom type characteristics for Chem3D to
assign the atom type to the atom.
The symbol.
The bound-to type (if specified for the atom
type).
The bound-to order (if the bound-to type is
specified).
Chem & BioOffice 2006 /Chem3D
The number of double, triple and delocalized
bonds.
NOTE: For comparing bond orders, an atom type that
contains one double bond may be assigned to an atom that
contains two delocalized bonds. For example, all six carbons
in benzene are C Alkene.
If the maximum ring size field of an atom type is
specified, then the atom must be in a ring of that
size or smaller to be assigned the corresponding
atom type.
If an atom is bound to fewer ligands than are
specified by an atom type geometry but the
rectification type is specified, then the atom can be
assigned to that atom type. Chem3D fills the open
valences with rectification atoms.
For example, consider the atom types for the
following structure:
Figure C-15: Ethanoic acid model
O(3) matches the criteria specified for the atom
type O Carbonyl. Specifically, it is labeled O, it is
bound to a C Carbonyl by a double bond and it is
attached to exactly one double bond and no triple
bonds.
Atom Types 217
 If an atom can be assigned to more than one atom
type, atom types are assigned to atoms in the
following order:
1. Atom types whose bound-to types are
Administrator
specified and are not the same as their
rectification types.
2. Atom types whose bound-to types are speci-
fied and are the same as their rectification
types.
3. Atom types whose bound-to types are not
specified.
For example, in the model depicted above, O(4)
could be one of several atom types. First, it could be
an O Ether atom for which the bound-to type is
unspecified (priority number 3, above).
Alternatively, it could be an O Alcohol for which
the bound-to type is the same as the rectification
type, H Alcohol (priority number 2, above). A third
possibility is O Carboxyl, for which the bound-to
type is C Carbonyl and the rectification type is H
Carboxyl (priority number 1). Because the
characteristic of a specified bound-to type which is
not the same as the rectification type (number 1 in
218 Atom Types
the priority list above) is given precedence over the
other two possibilities, the O Carboxyl atom type is
assigned to the oxygen atom.
Defining Atom Types
If you need to define atom types, whether to add to
the atom types table for building or to add to a file
format interpreter for importing, here is the general
procedure:
To add or edit an atom type to the Atom Types
table:
1. From the View menu, point to Parameter
Tables and choose Atom Types.
The Atom Types table opens in a window.
2. To edit an atom type, click in the cell that you
want to change and type new information.
3. Enter the appropriate data in each field of the
table. Be sure that the name for the parameter
is not duplicated elsewhere in the table.
4. Close and Save the table.
You now can use the newly defined atom type.
CambridgeSoft
Appendix D: 2D to 3D Conversion
Overview indicate the opposite: the atom at the wide end of a
wedged hashed bond is behind the atom at the
This section discusses how Chem3D performs the other end of the bond.
conversion from two to three dimensions when
opening a ChemDraw or ISIS/Draw document, Example 1
when pasting a ChemDraw or ISIS/Draw structure
Figure D-17: Trans phenyl rings
from the Clipboard, or when opening a ChemDraw
connection table file. While Chem3D can read in
and assimilate any ChemDraw structure, you can
assist Chem3D in the two- to three-dimensional
conversion of your models by following the
suggestions in this Appendix.

Chem3D uses the atom labels and bonds drawn in
ChemDraw to form the structure of your model.
For every bond drawn in ChemDraw, a
corresponding bond is created in Chem3D. Every
atom label is converted into at least one atom.
Dative bonds are converted to single bonds with a
positive formal charge added to one atom (the atom
at the tail of the dative bond) and a negative formal
charge added to the other (the head of the dative
bond).
Figure D-16: Dative bond
+ -
S O
Stereochemical Relation-
ships
Chem3D uses the stereo bonds and H-Dot and
H-Dash atom labels in a ChemDraw structure to
define the stereochemical relationships in the
corresponding model. Wedged bonds in
ChemDraw indicate a bond where the atom at the
wide end of the bond is in front of the atom at the
narrow end of the bond. Wedged hashed bonds
In Example 1, the two phenyl rings are trans about
the cyclopentane ring. The phenyl ring on the left is
attached by a wedged hashed bond; the phenyl ring
on the right is attached by a wedged bond.
You can also use dashed, hashed, and bold bonds.
However, you should be aware of potential
ambiguity where these non-directional bonds are
used. A dashed, hashed, or bold bond must be
between one atom that has at least three
attachments and one atom that has no more than
two attachments, including the dashed, hashed, or
bold bond.
Example 2
Figure D-18: Nitrogen behind the ring
NH2
In Example 2, the nitrogen atom is placed behind
the ring system and the two methyl groups are
placed in front of the ring system. Each of these

Chem & BioOffice 2006 /Chem3D 2D to 3D Conversion 219

 three atoms is bonded to only one other atom, so
they are presumed to be at the wide ends of the
stereo bonds.
Administrator
Example 3
Figure D-19: Ambiguous bond
H Chem3D uses standard bond lengths and angles as
In Example 3, however, the hashed bond is
ambiguous because both atoms on the hashed bond
are attached to more than two bonds. In this case
the hashed bond is treated like a solid bond. Wavy
bonds are always treated like solid bonds.
H-Dots and H-Dashes are also used to indicate
stereochemistry. H-Dots become hydrogen atoms
attached to carbon atoms by a wedged bond.
H-Dashes become hydrogen atoms attached by a
wedged hashed bond.
Example 4
Figure D-20: Cis and trans models
H H H H
cis-decalin trans-decalin
220 2D to 3D Conversion
Example 4 shows cis-decalin on the left and
trans-decalin on the right as they would be drawn in
ChemDraw to be read in by Chem3D. Of course,
you can specify a cis fusion with two H-Dots
instead of two H-Dashes.
As a general rule, the more stereo bonds you
include in your model, the greater is the probability
that Chem3D will make correct choices for chirality
and dihedral angles.
When converting two-dimensional structures,
specified in the current set of parameters. If
Chem3D tries to translate strained ring systems, the
ring closures will not be of the correct length or
angle.
Labels
Chem3D uses the atom labels in a two-dimensional
structure to determine the atom types of the atoms.
Unlabeled atoms are assumed to be carbon. Labels
are converted into atoms and bonds using the same
method as that used to convert the text in a text box
into atoms and bonds. Therefore, labels can contain
several atoms or even substructures.
CambridgeSoft
Appendix E: File Formats
Editing File Format Atom The remaining fields (Symbol, Charge, Maximum
Ring Size, Rectification type, Geometry, Number of
Types Double Bonds, Number of Triple Bonds, Number
of Delocalized Bonds, Bound to Order and Bound
Some file formats contain information describing to Type) contain information corresponding to the
the atom types that the file format understands. information in an Atom Types table.
Typically, these atom types are ordered by some set
of numbers, similar to the atom type numbers used File Format Examples
in the Atom Types table. If the file format needs to
support additional types of atoms, you can supply The following sections provide examples of the
those types by editing the file format atom types. files created when you save Chem3D files using the
provided file formats.
Chem3D 10 uses XML tables for storing file
formats. You can edit these tables in any text editor Alchemy File
or in Chem3D by selecting the table you want to
edit from the Parameter Tables list on the View The following is a sample Alchemy file1 (Alchemy)
menu. created using Chem3D for a model of
cyclohexanol. The numbers in the first column are
TIP: The XML files are in the path line numbers that are added for reference only.
...\Chem3D\C3D Items\ 1 19 19
ATOMS BONDS
2 1 C3 -1.1236 -0.177 0.059
Name
3 2 C3 -0.26 -0.856 -1.0224
Each atom type is described by a name. This name 4 3 C3 1.01 -0.0491 -1.3267
is a number found in files of the format described 5 4 C3 1.838 0.1626 -0.0526
by the file format. All names must be unique. The
6 5 C3 0.9934 0.8543 1.0252
records in the table window are sorted by name.
7 6 C3 -0.2815 0.0527 1.3275
8 7 O3 -2.1621 -1.0585 0.3907
NOTE: While names are similar to atom type numbers,
they do not have to correspond to the atom type numbers of 9 8H -1.4448 0.8185 -0.3338
atom types. In some cases, however, they do correspond. 10 9H -0.8497 -0.979 -1.9623
11 10 H 0.0275 -1.8784 -0.6806
12 11 H 1.6239 -0.5794 -2.0941
Description 13 12 H 0.729 0.9408 -1.7589
The second field contains a description of the atom 14 13 H 2.197 -0.8229 0.3289
type, such as C Alkane. This description is included 1. Alchemy III is a registered trademark
for your reference only. of Tripos Associates, Inc.

Chem & BioOffice 2006 /Chem3D File Formats 221

File Format Examples
 15 14 H 2.7422 0.7763 -0.282 the X coordinate, the fourth field is the
16 15 H 1.5961 0.9769 1.9574 Y coordinate and the fifth field is the
Z coordinate.
17 16 H 0.7156 1.8784 0.679
Administrator

18 17 H -0.8718 0.6068 2.0941 NOTE: Atom types in the Alchemy file format are
19 18 H -0.004 -0.9319 1.7721 user-definable. See Editing File Format Atom Types
20 19 H -2.7422 -0.593 0.9688 on page 221 for instructions on modifying or creating an
21 1 1 2 SINGLE atom type.
22 2 1 6 SINGLE
3. Lines 2140 each contain 4 fields describing
23 3 1 7 SINGLE
information about each of the bonds in the
24 4 1 8 SINGLE molecule. The first field is the bond number
25 5 2 3 SINGLE (ranging from 1 to the number of bonds), the
26 6 2 9 SINGLE second field is the serial number of the atom
27 7 2 10 SINGLE where the bond begins, the third field is the
serial number of the atom where the bond
28 8 3 4 SINGLE
ends, and the fourth field is the bond type. The
29 9 3 11 SINGLE possible bond types are: SINGLE, DOUBLE,
30 10 3 12 SINGLE TRIPLE, AMIDE, or AROMATIC. Note that
31 11 4 5 SINGLE all the bond order names are padded on the
32 12 4 13 SINGLE right with spaces to eight characters.
33 13 4 14 SINGLE
34 14 5 6 SINGLE FORTRAN Formats
35 15 5 15 SINGLE The FORTRAN format for each record of the
36 16 5 16 SINGLE Alchemy file is as follows:
37 17 6 17 SINGLE
38 18 6 18 SINGLE Line Description FORTRAN
40 19 7 19 SINGLE Number Format
Each line represents a data record containing one or
more fields of information about the molecule. 1 number of atoms, I5, 1X,
number of bonds ATOMS,1X,I5,
Each field is delimited by spaces or a tab. The fields
1X, BONDS
used by Chem3D are described below:

1. Line 1 contains two fields. The first field is the 220 atom serial I6,A4,3(F9.4)
total number of atoms in the molecule and the number, type, and
second field is the total number of bonds. coordinates

2. Lines 220 each contain 5 fields of information

2140 bond id, from I6,I5,I6,2X,A8
about each of the atom in the molecule. The atom, to atom,
first field is the serial number of the atom. The bond type
second field is the atom type, the third field is

222 File Formats CambridgeSoft

File Format Examples
Cartesian Coordinate Files
The Cartesian coordinate file format (Cart Coords,
Cart Coords 2) interprets text files that specify
models in terms of the X, Y, and Z coordinates of
the atoms. This file format can also interpret
fractional cell coordinates in orthogonal or non-
orthogonal coordinate systems.
Atom Types in Cartesian Coordinate
Files
Two file formats are supplied with Chem3D that
interpret Cartesian coordinate files. The difference
between the two file formats are the codes used to
convert atom type numbers in the file into atom
types used by Chem3D.
In Cartesian coordinates 1, atom types are
numbered according to the numbering used by N.L.
Allinger in MM2. These numbers are also generally
followed by the program PC Model.
In Cartesian coordinates 2, the atom type number
for all atom types is computed by multiplying the
atomic number of the element by 10 and adding the
number of valences as specified by the geometry of
the atom type. These numbers are also generally
followed by the program MacroModel.
For example, the atom type number for C Alkane (a
tetrahedral carbon atom) is 64.
To examine the atom types described by a file
format, see Editing File Format Atom Types on
page 221.
Chem & BioOffice 2006 /Chem3D
The Cartesian Coordinate File Format
The format for Cartesian coordinate files is as
follows:
1. The first line of data contains the number of
atoms in the model.
Optionally, you can follow the number of
atoms in the file with crystal cell parameters for
the crystal structure: a, b, c, , , and .
Following the cell parameters, you can also
include an exponent. If you include an
exponent, then all of the fractional cell
coordinates will be divided by 10 raised to the
power of the exponent.
2. The first line of a Cartesian coordinate file is
followed by one line of data for each atom in
the model. Each line describing an atom begins
with the symbol for the atom. This symbol
must correspond to a symbol in the Elements
table. The symbol can include a charge, such as
N+. The symbol is followed by the serial
number.
3. The serial number is followed by the three
coordinates of the atom. If you have specified
crystal cell parameters in the first line of the
file, then these numbers are the fractional cell
coordinates. Otherwise, the three numbers are
X, Y, and Z Cartesian coordinates.
4. Following the coordinates is the atom type
number of the atom type for this atom. This
number must correspond to the code of an
atom type record specified in the file format
atom type table. For more information, see
Editing File Format Atom Types on page
221.
5. Following the atom type number is the connec-
tion table for the atom. You can specify up to
ten other atoms. The connection table for a
Cartesian coordinate file can be listed in one of
two ways: by serial number or by position.
File Formats 223
File Format Examples
 Connection tables by serial number use the
serial number of each atom to determine the
number that appears in the connection table of
other atoms. All serial numbers must,
Administrator
6. To create multiple views of the same set of
atoms, you can flow the descriptions of the
atoms with an equal number of lines corre-
sponding to the same atoms with different

therefore, be unique. coordinates. Chem3D generates independent

Connection tables by position use the relative
positions of the atoms in the file to determine
the number for each atom that will appear in
the connection table of other atoms. The first
atom is number 1, the second is 2, etc.
views using the additional sets of coordinates.
Samples of Cartesian coordinate files with
connection tables by position and serial number for
a model of cyclohexanol are shown below. To
clearly illustrate the difference between the two
formats, the serial number of the oxygen has been
set to 101.

19
C 1 0.706696 1.066193 0.50882 1 2 4 7 8
C 2 -0.834732 1.075577 0.508789 1 1 3 9 10
C 3 -1.409012 0.275513 -0.668915 1 2 6 11 12
C 4 1.217285 -0.38632 0.508865 1 1 5 13 14
C 5 0.639328 -1.19154 -0.664444 1 4 6 15 16
C 6 -0.89444 -1.1698 -0.646652 1 3 5 17 18
O 101 1.192993 1.809631 1.59346 6 1 19
H 9 1.052597 1.559525 -0.432266 5 1
H 10 -1.211624 2.125046 0.457016 5 2
H 11 -1.208969 0.640518 1.465607 5 2
H 12 -2.524918 0.2816 -0.625809 5 3
H 13 -1.11557 0.762314 -1.629425 5 3
H 14 0.937027 -0.8781 1.470062 5 4
H 15 2.329758 -0.41023 0.437714 5 4
H 16 1.003448 -2.24631 -0.618286 5 5
H 17 1.005798 -0.76137 -1.627 5 5
H 18 -1.295059 -1.73161 -1.524567 5 6
H 19 -1.265137 -1.68524 0.271255 5 6
H 102 2.127594 1.865631 1.48999 21 7

224 File Formats CambridgeSoft

File Format Examples
Following is an example of a Cartesian Coordinate An example of a Cartesian Coordinate File with
file with Connection table by Position for Connection Table by Serial Number for
Cyclohexanol. Cyclohexanol follows.

Element X, Y and Z Positions of Other Atoms

Symbol Coordinates to which C(1) is Bonded

C 1 0.706691.0
6 6619
0.5
3 08820 1 2 4 7 8

Serial Atom Type

Number Text Number

19
C 1 0.706696 1.066193 0.50882 1 2 4 9 10
C 2 -0.834732 1.075577 0.508789 1 1 3 10 11
C 3 -1.409012 0.275513 -0.668915 1 2 6 12 13
C 4 1.217285 -0.38632 0.508865 1 1 5 14 15
C 5 0.639328 -1.19154 -0.664444 1 4 6 16 17
C 6 -0.89444 -1.1698 -0.646652 1 3 5 18 19
O 101 1.192993 1.809631 1.59346 6 1 102
H 9 1.052597 1.559525 -0.432266 5 1
H 10 -1.211624 2.125046 0.457016 5 3
H 11 -1.208969 0.640518 1.465607 5 3
H 12 -2.524918 0.2816 -0.625809 5 4
H 13 -1.11557 0.762314 -1.629425 5 4
H 14 0.937027 -0.8781 1.470062 5 5
H 15 2.329758 -0.41023 0.437714 5 5
H 16 1.003448 -2.24631 -0.618286 5 6
H 17 1.005798 -0.76137 -1.627 5 6
H 18 -1.295059 -1.73161 -1.524567 5 7
H 19 -1.265137 -1.68524 0.271255 5 7
H 102 2.127594 1.865631 1.48999 21 10
1

Chem & BioOffice 2006 /Chem3D File Formats 225

File Format Examples
 Components of a Cartesian coordinate File with
Connection Table by Serial Number for C(1) of 2 to End Atom coordi- A3, 1X, I4, 3(1X,
Cyclohexanol is shown below. nates F11.6), 1X, I4,
10(1X, I4)
Administrator

Element X, Y and Z Serial Numbers of Other Atoms Cartesian coordinate File (Fractional Crystal Cell
Symbol Coordinates to which C(1) is Bonded
Parameters):
C 1 0.706691.0
6 66193
0.508820 1 2 4 9 101
Line Description FORTRAN
Serial Atom Type Number Format
Number Text Number

1 Number of I3, 6(1X, F), I

Atoms, Crystal
Components of a Cartesian coordinate File with Cell Parameters
Crystal coordinate Parameters for C(1) is shown
below.
2 to End Atom coordi- A3, 1X, I4, 3(1X,
Number nates F11.6), 1X, I4,
a b c Exponent
of Atoms
10(1X,I4)
43 10.23 12.568.12 90.0 120.0
90.0 4

C 1 1578 -2341 5643 1 20 21 22

Fractional Cell
Coordinates
FORTRAN Formats
The FORTRAN format for the records in a
Cartesian coordinate file with a connection table by
serial number or position and a Cartesian
coordinate file with fractional crystal cell
parameters are listed in the following tables:
Cartesian coordinate File (Connection Table by
Serial Number or Position):
Cambridge Crystal Data
Bank Files
The specific format of Cambridge Crystal Data
Bank files (CCDB) used by Chem3D is the FDAT
format, described on pages 2642 of the data file
specifications of the Cambridge Structural
Database, Version 1 File Specifications from the
Cambridge Crystallographic Data Centre. For
further details about the FDAT format, please refer
to the above publication or contact the Cambridge
Crystallographic Data Centre.

As described in the specifications of the Cambridge

Line Description FORTRAN
Crystal Data Bank format, bonds are automatically
Number Format
added between pairs of atoms whose distance is less
than that of the sum of the covalent radii of the two
1 Number of I3
Atoms atoms. The bond orders are guessed based on the
ratio of the actual distance to the sum of the

226 File Formats CambridgeSoft

File Format Examples
covalent radii. The bond orders, bond angles, and 3. Beginning with line 3, the atom type number is
the atom symbols are used to determine the atom followed by the serial number of the atom to
types of the atoms in the model. which the new atom is bonded and the distance
to that atom. In an Internal coordinates file, the
origin atom is always the first distance-defining
atom in the file. All distances are measured in
Bond Type Actual Distance / Sum
Angstroms.
of Covalent Radii
4. Beginning with line 4, the distance is followed
by the serial number of the first angle-defining
Triple 0.81
atom and the angle between the newly defined
atom, the distance-defining atom, and the first
Double 0.87 angle-defining atom. All angles are measured in
degrees.
Delocalized 0.93 5. Beginning with line 5, the serial number of a
second angle-defining atom and a second
Single 1.00 defining angle follows the first angle. Finally, a
number is given that indicates the type of the
second angle. If the second angle type is zero,
Internal Coordinates File the second angle is a dihedral angle: New Atom
Distance-defining Atom First Angle-
Internal coordinates files (INT Coords) are text defining Atom Second Angle-defining Atom.
files that describe a single molecule by the internal Otherwise the third angle is a bond angle: New
coordinates used to position each atom. The serial Atom Distance-defining Atom Second
numbers are determined by the order of the atoms Angle-defining Atom. If the second angle type
in the file. The first atom has a serial number of 1, is 1, then the new atom is defined using a
the second is number 2, etc. Pro-R/Pro-S relationship to the three defining
atoms; if the second angle type is -1, the rela-
The format for Internal coordinates files is as tionship is Pro-S.
follows:
NOTE: You cannot position an atom in terms of a
1. Line 1 is a comment line ignored by Chem3D. later-positioned atom.
Each subsequent line begins with the atom
type number of an atom type. The following is a sample of an Internal coordinates
output file for cyclohexanol which was created
2. Line 2 contains the atom type number of the from within Chem3D:
Origin atom.
1
1 1 1.54146
1 2 1.53525 1 111.7729
1 1 1.53967 2 109.7132 3 -55.6959 0
1 4 1.53592 1 111.703 2 55.3112 0
1 3 1.53415 2 110.7535 1 57.0318 0

Chem & BioOffice 2006 /Chem3D File Formats 227

File Format Examples
 6 1 1.40195 2 107.6989 3 -172.6532 0
5 1 1.11742 2 109.39 4 109.39 -1
5 2 1.11629 1 109.41 3 109.41 1
Administrator

5 2 1.11568 1 109.41 3 109.41 -1

5 3 1.11664 2 109.41 6 109.41 -1
5 3 1.11606 2 109.41 6 109.41 1
5 4 1.11542 1 109.41 5 109.41 1
5 4 1.11493 1 109.41 5 109.41 -1
5 5 1.11664 4 109.41 6 109.41 1
5 5 1.11617 4 109.41 6 109.41 -1
5 6 1.11664 3 109.41 5 109.41 1
5 6 1.11606 3 109.41 5 109.41 -1
21 7 0.942 1 106.8998 2 59.999 0

5 6

Bonds the bond) the bond is removed from the model.

This is useful if you want to describe multiple
Bonds are indicated in Internal coordinates files in fragments in an internal coordinates file.
two ways.

First, a bond is automatically created between each Atom Type

Text Numbers

atom (except the Origin atom) and its distance- Bond

Lengths
defining atom. Origin Atom 1 First
Angles

Second, if there are any rings in the model, ring- Second Atom 1 1 1.54146 Second
Angles
closing bonds are listed at the end of the file. If
there are ring-closing bonds in the model, a blank Third Atom 1 2 1.53525 1 111.7729

line is included after the last atom definition. For Fourth Atom 1 1 1.53967 2 109.7132 3 -55.6959 0
each ring-closure, the serial numbers of the two
atoms which comprise the ring-closing bond are Distance-defining
Atoms
First Angle-
defining Atoms
Second Angle-
defining Atoms
Indicates
Dihedral
listed on one line. The serial number of the first
atom is 1, the second is 2, etc. In the prior Internal Components of an Internal coordinates File for
coordinates output example of cyclohexanol, the C(1) through C(4) of Cyclohexanol
numbers 5 and 6 are on a line at the end of the file,
and therefore the ring closure is between the fifth In this illustration, the origin atom is C(1). C(2) is
atom and the sixth atom. connected to C(1), the origin and distance defining
atom, by a bond of length 1.54146 . C(3) is
If a bond listed at the end of an Internal coordinates connected to C(2) with a bond of length 1.53525 ,
format file already exists (because one of the atoms and at a bond angle of 111.7729 degrees with C(1),
on the bond is used to position the other atom on defined by C(3)-C(2)-C(1). C(4) is attached to C(1)

228 File Formats CambridgeSoft

File Format Examples
with a bond of length 1.53967 , and at a bond Ignored by
angle of 109.7132 degrees with C(2), defined by Comment
Chem3D
C(4)-C(1)-C(2). C(4) also forms a dihedral angle of
-55.6959 degrees with C(3), defined by C(4)-C(1)- Origin Atom I4
C(2)-C(3).
Second Atom I4, 1X, I3,
This portion of the Internal coordinates file for 1X, F9.5
C(1) through C(4) of Cyclohexanol can be
Third Atom I4, 2(1X, I3,
represented by the following structural diagram: 1X, F9.5)

Fourth Atom to I4, 3(1X, I3,

1.540 4 Last Atom 1X, F9.5), I4

1
Blank Line
109.713
1.541
-55.698 Dihedral Angle
Ring Closure 2(1X, I4)
111.771
2 Atoms

1.535 3 MacroModel
MacroModel is produced within the Department of
Chemistry at Columbia University, New York, N.Y.
FORTRAN Formats The MacroModel file format is defined in the
MacroModel Structure Files version 2.0
The FORTRAN formats for the records in an documentation. The following is a sample
Internal coordinates file are as follows: MacroModel file created using Chem3D. The
following file describes a model of cyclohexanol.
Line Number Description FORTRAN
Format

19 cyclohexanol
3 2 1 6 1 7 1 18 1 0 0 0 0 -1.396561 0.350174 1.055603 0
3 1 1 3 1 8 1 9 1 0 0 0 0 -0.455032 -0.740891 1.587143 0
3 2 1 4 1 10 1 11 1 0 0 0 0 0.514313 -1.222107 0.49733 0
3 3 1 5 1 12 1 13 1 0 0 0 0 1.302856 -0.04895 -0.103714 0
3 4 1 6 1 14 1 15 1 0 0 0 0 0.372467 1.056656 -0.627853 0
3 1 1 5 1 16 1 17 1 0 0 0 0 -0.606857 1.525177 0.4599 0
41 1 1 0 0 0 0 0 0 0 0 0 0 -2.068466 -0.083405 0.277008 0
41 2 1 0 0 0 0 0 0 0 0 0 0 -1.053284 -1.603394 1.96843 0

Chem & BioOffice 2006 /Chem3D File Formats 229

File Format Examples
 41 2 1 0 0 0 0 0 0 0 0 0 0 0.127151 -0.3405 2.451294 0
41 3 1 0 0 0 0 0 0 0 0 0 0 1.222366 -1.972153 0.925369 0
41 3 1 0 0 0 0 0 0 0 0 0 0 -0.058121 -1.742569 -0.306931 0
Administrator

41 4 1 0 0 0 0 0 0 0 0 0 0 1.972885 0.38063 0.679077 0

41 4 1 0 0 0 0 0 0 0 0 0 0 1.960663 -0.413223 -0.928909 0
41 5 1 0 0 0 0 0 0 0 0 0 0 0.981857 1.921463 -0.992111 0
41 6 1 0 0 0 0 0 0 0 0 0 0 -1.309372 2.283279 0.037933 0
41 6 1 0 0 0 0 0 0 0 0 0 0 -0.033539 2.031708 1.272888 0
41 1 1 0 0 0 0 0 0 0 0 0 0 -2.052933 0.717285 1.881104 0
42 15 1 0 0 0 0 0 0 0 0 0 0 0.275696 0.374954 -2.411163 0

Each line represents a data record containing one or Atom colors are ignored by Chem3D. This
more fields of information about the model. Each field will contain a zero if the file was created
field is delimited by space(s) or a tab. using Chem3D.
The fields in the MacroModel format file used by
Chem3D are: NOTE: Atom types are user-definable. See Editing File
Format Atom Types on page 221 for instructions on
1. Line 1 contains 2 fields: the first field is the
number of atoms and the second field is the modifying or creating an atom type.
name of the molecule. The molecule name is
the file name when the file is created using For example, the following illustrates the atom and
Chem3D. bond components for C6 and bond 3 of
2. Lines 2-19 each contain 17 fields describing cyclohexanol:
information about one atom and its attached
bond. The first field contains the atom type.
The second through thirteenth fields represent Each pair of numbers represents an
atom to which this atom is bondedAtom Color
6 pairs of numbers describing the bonds that
this atom makes to other atoms. The first 3115116
117
10000-0.606
185
.52
750
1.45
77 90
900
number of each pair is the serial number of the
other atom, and the second number is the bond Atom TypS
eerial Nu
Bmober
nd Type
X Y Z
Coordinates
type. The fourteenth field is the X coordinate,
the fifteenth field is the Y coordinate, the
sixteenth field is the Z coordinate and finally, FORTRAN Formats
and the seventeenth field is the color of the
atom. The FORTRAN format for each record of the
MacroModel format is as follows:

Line Description FORTRAN

Number Format

230 File Formats CambridgeSoft

File Format Examples
 of Chemical Information and Computer Science,
1 number of 1X,I5,2X,A Volume 32, Number 3, 1992, pages 244255. The
atoms and mole-
following is a sample MDL MolFile file created
cule name (file
using Chem3D Pro. This file describes a model of
name
cyclohexanol (the line numbers are added for
reference only):
MDL MolFile
The MDL MolFile1 format is defined in the article 1. MDL MACCS-II is a product of MDL
Description of Several Chemical Structure File Information Systems, Inc. (previously called
Formats Used by Computer Programs Developed Molecular Design, Limited).
at Molecular Design Limited found in the Journal
1 cyclohexanol
2
3
4 19 19 0 0 0
5 -1.3488 0.1946 1.0316 C 0 0 0 0 0
6 -0.4072 -0.8965 1.5632 C 0 0 0 0 0
7 0.5621 -1.3777 0.4733 C 0 0 0 0 0
8 1.3507 -0.2045 -0.1277 C 0 0 0 0 0
9 0.4203 0.9011 -0.6518 C 0 0 0 0 0
10 -0.559 1.3696 0.4359 C 0 0 0 0 0
11 -0.3007 0.4266 -1.7567 O 0 0 0 0 0
12 -2.0207 -0.239 0.253 H 0 0 0 0 0
13 -2.0051 0.5617 1.8571 H 0 0 0 0 0
14 -1.0054 -1.7589 1.9444 H 0 0 0 0 0
15 0.1749 -0.4961 2.4273 H 0 0 0 0 0
16 1.27 -2.1277 0.9014 H 0 0 0 0 0
17 -0.0103 -1.8981 -0.3309 H 0 0 0 0 0
18 2.0207 0.225 0.6551 H 0 0 0 0 0
19 2.0084 -0.5688 -0.9529 H 0 0 0 0 0
20 1.0296 7659 -1.0161 H 0 0 0 0 0
21 -1.2615 2.1277 0.0139 H 0 0 0 0 0
22 0.0143 1.8761 1.2488 H 0 0 0 0 0
23 0.3286 0.2227 -2.4273 H 0 0 0 0 0
24 1 2 1 0 0 0
25 1 6 1 0 0 0

Chem & BioOffice 2006 /Chem3D File Formats 231

File Format Examples
 26 1 8 1 6 0 0
27 1 9 1 1 0 0
28 2 3 1 6 0 0
Administrator

29 2 10 1 0 0 0
30 2 11 1 1 0 0
31 3 4 1 0 0 0
32 3 12 1 0 0 0
33 3 13 1 6 0 0
34 4 5 1 0 0 0
35 4 14 1 1 0 0
36 4 15 1 6 0 0
37 5 6 1 1 0 0
38 5 7 1 6 0 0
39 5 16 1 0 0 0
40 6 17 1 0 0 0
41 6 18 1 1 0 0
42 7 19 1 6 0 0

Each line represents either a blank line, or a data
record containing one or more fields of
information about the structure. Each field is
delimited by a space(s) or a tab.
The fields in the MDL MolFile format used by
Chem3D Pro are discussed below:
1. Line 1 starts the header block, which contains
the name of the molecule. The molecule name
is the file name when the file was created using
Chem3D Pro.
2. Line 2 continues the Header block, and is a
blank line.
3. Line 3 continues the Header block, and is
another blank line.
number of bonds, the third field is the number
of atom lists, the fourth field is an unused field
and the fifth field is the stereochemistry.
NOTE: Chem3D Pro ignores the following fields: number
of atom lists, the unused field and stereochemistry. These
fields will always contain a zero if the file was created using
Chem3D Pro.
5. Lines 523 (the Atom block) each contain 9
fields which describes an atom in the molecule:
The first field is the X coordinate, the second
field is the Y coordinate, the third field is the Z
coordinate, the fourth field is the atomic
symbol, the fifth field is the mass difference,
the sixth field is the charge, the seventh field is

4. Line 4 (the Counts line) contains 5 fields which

describes the molecule: The first field is the
number of atoms, the second field is the

232 File Formats CambridgeSoft

File Format Examples
 the stereo parity designator, the eighth field is FORTRAN Formats
the number of hydrogens and the ninth field is
The FORTRAN format for each record of the
the center.
MDL MolFile format is as follows:
NOTE: Chem3D Pro ignores the following fields: mass
difference, charge, stereo parity designator, number of Line Description FORTRAN
hydrogens, and center. These fields contain zeros if the file was Number Format
created using Chem3D Pro.
1 Molecule name A
6. Lines 2442 (the Bond block) each contain 6 (file name)
fields which describe a bond in the molecule:
the first field is the from-atom id, the second 2 Blank line
field is the to-atom id, the third field is the
bond type, the fourth field is the bond stereo
designator, the fifth field is an unused field and 3 Blank line
the sixth field is the topology code.
4 Number of atoms 5I3
NOTE: Chem3D Pro ignores the unused field and Number of bonds
topology code. These fields will contain zeros if the file was
created using Chem3D Pro. 523 Atom coordi- 3F10.4,1X,A2,5I3
nates, atomic
Limitations symbol

The MDL MolFile format does not support

2442 Bond id, from 6(1X,I2)
non-integral charges in the same way as Chem3D
atom, to atom,
Pro. For example, in a typical MDL MolFile format
and bond type
file, the two oxygens in a nitro functional group
(NO2) contain different charges: -1 and 0. In
Chem3D models, the oxygen atoms each contain a MSI MolFile
charge of -0.500.
The MSI MolFile is defined in Chapter 4,
Chem-Note File Format in the Centrum:
Chem-Note Application documentation, pages
4-1 to 4-5. The following is a sample MSI MolFile
file created using Chem3D Pro for cyclohexanol
(the line numbers are added for purposes of
discussion only):
1 ! Polygen 133
2 Polygen Corporation: ChemNote molecule file (2D)
3 * File format version number
4 90.0928

Chem & BioOffice 2006 /Chem3D File Formats 233

File Format Examples
 5 * File update version number
6 92.0114
7 * molecule name
Administrator

8 cyclohexanol-MSI
9 empirical formula
10 Undefined Empirical Formula
11 * need 3D conversion?
12 0
13 * 3D displacement vector
14 0.000 0.000 0.000
15 * 3D rotation matrix
16 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000
17 * 3D scale factor
18 0
19 * 2D scale factor
20 1
21 * 2D attributes
22 100000000000000
23 * 3D attributes
24 00000000000
25 * Global display attributes
26 1 0 1 12 256
27 * Atom List
28 * Atom# Lbl Type x y x y z bits chrg ichrg frag istp lp chrl ring frad name seg grp FLAGS
29 1 C 10 0 0 -1 0.46 0.2 0 0 0 0 0 0 0 0 0 C 1 0 -1 0 0 0 0 0 0 [C]
30 2 C 10 0 0 1.2 -1.1 0.2 0 0 0 0 0 0 0 0 0 C 2 0 -1 0 0 0 0 0 0 [C]
30 2 C 10 0 0 1.2 -1.1 0.2 0 0 0 0 0 0 0 0 0 C 2 0 -1 0 0 0 0 0 0 [C]
31 3 C 10 0 0 0.1 -1.6 0.7 0 0 0 0 0 0 0 0 0 C 3 0 -1 0 0 0 0 0 0 [C]
32 4 C 10 0 0 1.3 -1.1 0 0 0 0000000C40-1000000[C]
33 5 C 10 0 0 1.2 0.48 0 0 0 0 0 0 0 0 0 0 C 5 0 -1 0 0 0 0 0 0 [C]
34 6 C 10 0 0 0 1.01 -1 0 0 0 0 0 0 0 0 0 C 6 0 -1 0 0 0 0 0 0 [C]
35 7 O 45 0 0 0 2.42 -1 0 0 0 0 0 0 0 0 0 O 7 0 -1 0 0 0 0 0 0 [O]
36 8 H 8 0 0 0.6 2.72 -1 0 0 0 0 0 0 0 0 0 H 7 0 -1 0 0 0 0 0 0 [H]
37 9 H 1 0 0 2.1 0.86 -1 0 0 0 0 0 0 0 0 0 H 8 0 -1 0 0 0 0 0 0 [H]
38 10 H 1 0 0 1.4 0.86 0.8 0 0 0 0 0 0 0 0 0 H 9 0 -1 0 0 0 0 0 0 [H]
39 11 H 1 0 0 1.1 -1.4 -1 0 0 0 0 0 0 0 0 0 H 10 0 -1 0 0 00 00[H]

234 File Formats CambridgeSoft

File Format Examples
40 12 H 1 0 0 2.2 -1.4 0.2 0 0 0 0 0 0 0 0 0 H 11 0 -1 0 0 0000 [H]
41 13 H 1 0 0 0 0.72 -2 0 0 0 0 0 0 0 0 0 H 12 0 -1 0 0000 0 [H]
42 14 H 1 0 0 0.1 -2.7 0.7 0 0 0 0 0 0 0 0 0 H 13 0 -1 0 0 0000 [H]
43 15 H 1 0 0 0.3 -1.3 1.7 0 0 0 0 0 0 0 0 0 H 14 0 -1 0 0 0 00 [H]
44 16 H 1 0 0 -1 -1.5 -1 0 0 0 0 0 0 0 0 0 H 15 0 -1 0 0 0000 [H]
45 17 H 1 0 0 -2 -1.5 0.9 0 0 0 0 0 0 0 0 0 H 16 0 -1 0 0 0000 [H]
46 18 H 1 0 0 -1 0.85 1.2 0 0 0 0 0 0 0 0 0 H 17 0 -1 0 0 0000 [H]
47 19 H 1 0 0 -2 0.83 0 0 0 0 0 0 0 0 0 0 H 18 0 -1 0 0 0000 [H]
48 * Bond List
49 * Bond# bond_type atom1 atom2 cis/trans length locked ring Sh_type Sh_nr Qorder Qtopol Qs
50 11120 0.000 0 0 0 0 [S] 0 0
51 21160 0.000 0 0 0 0 [S] 0 0
52 3 1 1 18 0 0.000 0 0 0 0 [S] 0 0
53 4 1 1 19 0 0.000 0 0 0 0 [S] 0 0
54 51230 0.000 0 0 0 0 [S] 0 0
55 6 1 2 16 0 0.000 0 0 0 0 [S] 0 0
56 7 1 2 17 0 0.000 0 0 0 0 [S] 0 0
57 81340 0.000 0 0 0 0 [S] 0 0
58 9 1 3 14 0 0.000 0 0 0 0 [S] 0 0
59 10 1 3 15 0 0.000 0 0 0 0 [S] 0 0
60 11 1 4 5 0 0.000 0 0 0 0 [S] 0 0
61 12 1 4 11 0 0.000 0 0 0 0 [S] 0 0
62 13 1 4 12 0 0.000 0 0 0 0 [S] 0 0
63 14 1 5 6 0 0.000 0 0 0 0 [S] 0 0
64 15 1 5 9 0 0.000 0 0 0 0 [S] 0 0
65 16 1 5 10 0 0.000 0 0 0 0 [S] 0 0
66 17 1 6 7 0 0.000 0 0 0 0 [S] 0 0
67 18 1 6 13 0 0.000 0 0 0 0 [S] 0 0
68 19 1 7 8 0 0.000 0 0 0 0 [S] 0 0
69 * Bond Angles
70 * bond1 bond2 angle locked
71 * Dihedral Angles
72 * at1-cons at1 at2 at2-cons angle locked
73 * Planarity data
74 * User data area
75 * End of File

Chem & BioOffice 2006 /Chem3D File Formats 235

File Format Examples
 The MSI MolFile1 format is broken up into several
sections. Section headers are preceded by a *.
Blank lines also contain a *. Each line is either a
blank line, a header line or a data record containing
Administrator
one or more fields of information about the
structure. Individual fields are delimited by space(s)
or a tab. The fields in the MSI MolFile format file
used by Chem3D Pro are discussed below.
The field value for Carbon 6 from the example file
is included in parentheses for reference:
1. Line 1 is a standard header line for MSI
MolFile format files.
2. Line 2 normally indicates the application which
created the file.
3. Line 3 is the header for the File format version
number section.
4. Line 4 indicates the file format version number.
The format for this field is YY.MMDD.
5. Line 5 is the header for the File update version
number section.
6. Line 6 indicates the file update version number.
The format for this field is YY.MMDD.
7. Line 7 is the header for the molecule name
section.
8. Line 8 contains the field molecule name. This
field contains either the file name, or Unde-
fined Name.
9. Line 9 is the header for the empirical formula.
10. Line 10 contains the empirical formula field.
This field contains either the empirical formula
or Undefined Empirical Formula.
11. Lines 1124 each contains information
concerning conversions from 3D to 2D.
12. Line 25 is the header for the Global display
attributes section.
1. Molecular Simulations MOLFILE
(ChemNote) is a product of Molecular
Simulations, Inc.
236 File Formats
13. Line 26 contains 5 fields describing the global
display attributes: Line thickness (1), font style
(0), type face (1), type size (12), font (256).
These values are specific to the platform that is
generating the file.
14. .Line 27 contains the header for the Atom Lists
section.
15. Line 28 contains a listing of all the possible
fields for the atom list section. When the file is
created using Chem3D Pro the following fields
are used: Atom#,Lbl, Type, and x,y,z.
16. Lines 2947 each contains 28 fields describing
information about each of the atoms in the
structure: the first field is the atom number (6),
the second field is the atom label (C), the third
field is the atom type (10), the fourth field and
fifth fields contain 2D coordinates, and contain
zeros when the file is created using Chem3D
Pro, the sixth field is the X coordinate (-0.113)
and the fifth field is the Y coordinate (1.005),
the sixth field is the Z coordinate (-0.675), the
seventh through fifteenth fields are ignored
and contain zeros when the file is created by
Chem3D Pro, the sixteenth field is, again, the
atom label (C), the eighteenth field is, again, the
atom number (6), the nineteenth field is the
segment field, the twentieth field is the
coordination field, the twenty first field is
ignored, the twenty-second field is called the
saturation field: if the atom is attached to any
single, double or delocalized bonds this field is
1 (not saturated) otherwise this field is 0. The
twenty-third through the twenty-sixth fields are
ignored and contain zeros when the file is
created using Chem3D Pro, the twenty-seventh
field is, again, the atom label (C).
NOTE: Atom types in the Molecular Simulations
MolFile format are user-definable. For more
information, see Editing File Format Atom Types
on page 221.
CambridgeSoft
File Format Examples
17. Line 48 contains the header for the Bond List FORTRAN Formats
section.
18. Line 49 contains a listing of all the possible The FORTRAN format for each record of the
fields for the bond list section. When the file is Molecular Simulations MolFile format is as follows:
created by Chem3D Pro the following fields
are used: Bond#, Bond_type, atom 1, atom 2 Line Description FORTRAN
and cis/trans and Qorder. Number Format
19. Lines 5068 each contain 4 fields describing
information about each of the bonds in the 29-47 atom list, field I,1X,A,3(1X,I),3F9.
structure: the first field is the internal bond value 3,1X,I,F4.1,7(1X,I),
number (6), the second field is the bond type 1X,A,I,8(1X,I),
(1), the third and fourth fields are the atom [,A, ]
serial numbers for the atoms involved in the
bond [atom 1 (2), atom 2 (16)], the fifth field is 50-68 bond list, field I,4(1X,I),F9.3,4(2X
the cis/trans designator (this is 0 if it does not values ,I),1X, [,A1, ]
apply), the sixth through tenth fields are ,2(1X,I)
ignored, and contain zeros if the file is created
using Chem3D Pro, the eleventh field contains
the bond order ([S] meaning single), the twelfth
and thirteenth fields are ignored and contain
MOPAC
zeros if the file is created using Chem3D Pro.
The specific format of the MOPAC files used by
20. Lines 6973 are each a section header for 3D Chem3D is the MOPAC Data-File format. This
conversion use. This section only contains the format is described on pages 1-5 through 1-7 of the
header name only (as shown) when the file is Description of MOPAC section and page 3-5 of
created using Chem3D Pro. the Geometry Specification section in the
21. Line 74 is a header for the section User data MOPAC Manual (fifth edition). For further details
area. This section contains the header name about the MOPAC Data-File format, please refer to
only (as shown) when the file is created using the above publication.
Chem3D Pro.
22. Line 75 is a header that indicates the End of The following is a sample MOPAC output file from
File. Chem3D for cyclohexanol:
Line 1:
Line 2: Cyclohexanol
Line 3:
Line 4a: C 0 0 0 0 0 0 0 0 0
Line 4b: C 1.54152 1 0 0 0 0 1 0 0
Line 4c: C 1.53523 1 111.7747 1 0 0 2 1 0
Line 4d: C 1.53973 1 109.7114 1 -55.6959 1 1 2 3
Line 4e: C 1.53597 1 111.7012 1 55.3112 1 4 1 2

Chem & BioOffice 2006 /Chem3D File Formats 237

File Format Examples
 Line 4f: C 1.53424 1 110.7535 1 57.03175 1 3 2 1
Line 4g: O 1.40196 1 107.6989 1 -172.662 1 1 2 3
Line 4h: H 1.11739 1 107.8685 1 62.06751 1 1 2 3
Administrator

Line 4I: H 1.11633 1 110.0751 1 -177.17 1 2 1 4

Line 4j: H 1.11566 1 109.4526 1 65.43868 1 2 1 4
Line 4k: H 1.11665 1 109.9597 1 178.6209 1 3 2 1
Line 4l: H 1.1161 1 109.5453 1 -63.9507 1 3 2 1
Line 4m: H 1.11542 1 109.4316 1 -66.0209 1 4 1 2
Line 4n: H 1.11499 1 110.549 1 176.0838 1 4 1 2
Line 4o: H 1.11671 1 109.93 1 -178.296 1 5 4 1
Line 4p: H 1.11615 1 109.4596 1 64.43501 1 5 4 1
Line 4q: H 1.11664 1 110.0104 1 -178.325 1 6 3 2
Line 4r: H 1.11604 1 109.6082 1 64.09581 1 6 3 2
Line 4s: H 0.94199 1 106.898 1 -173.033 1 7 1 2

The following illustrates the components of the a bond angle of 109.711411 degrees from C(2). C(4)
MOPAC Output File from Chem3D for C(1) also forms a dihedral angle of
Through C(4) of Cyclohexanol -55.695877 degrees with C(3).
The action integers listed next to each measurement
Element Bond Action Bond Action Dihedral Action Connectivity
Symbol Lengths Integers Angles Integers Angles Integers Atoms are instructions to MOPAC which are as follows:

1st Atom C 0.000000 0 0.000000 0 0.000000 0 0 0 0 1Optimize this internal coordinate

2nd Atom C 1.541519 1 0.000000 0 0.000000 0 1 0 0
0Do not optimize this internal coordinate
3rd Atom C 1.535233 1 111.774673 1 0.000000 0 2 1 0
-1Reaction coordinate or grid index
4th Atom C 1.539734 1 109.711411 1 -55.695877 1 1 2 3
When you create a MOPAC file from within
Chem3D, an action integer of 1 is automatically
assigned to each non-zero bond length, bond angle,
The internal coordinates section of the MOPAC and dihedral angle for each atom record in the file.
Data-File format contains one line of text for each
atom in the model. Each line contains bond lengths, FORTRAN Formats
bond angles, dihedral angles, action integers, and
The description of the MOPAC Data-File format
connectivity atoms.
for each line is as follows:
As shown in the illustration above, C(1) is the origin
atom. C(2) is connected to C(1) with a bond of
length 1.541519 . C(3) is connected to C(2) with a Line Description Read by Written
bond of length 1.535233 , and is at a bond angle Number Chem3D by
of 111.774673 degrees from C(1). C(4) is connected Chem3D
to C(1) with a bond of length 1.539734 , and is at

238 File Formats CambridgeSoft

File Format Examples
 The ATOM record contains atomic coordinate
1 Keywords for No No records for standard groups, and the HETATM
Calculation record contains atomic coordinate records for
Instructions non-standard groups. The CONECT record
contains the atomic connectivity records.
2 Molecule Title No Yes
NOTE: The COMPND record is created by Chem3D to
3 Comment No No include the title of a Chem3D model only when you are saving
a file using the Protein Data Bank file format. This record
4a-s Internal coor- Yes Yes is not used when opening a file.
dinates for
molecule The following is an example of a Protein Data Bank
Output File from Chem3D for L-Alanine.
5 Blank line, Yes Yes
terminates
geometry defi- COMPND Alanine.pdb
nition HETATM 1 N 0 -0.962 1
HETATM 2 C 0 -0.049 0
The FORTRAN format for each line containing HETATM 3 C 0.6 0.834 -1
internal coordinate data in the MOPAC Data-File is
HETATM 4 C -2 0.834 1
FORMAT(1X, 2A, 3(F12.6, I3), 1X, 3I4).
HETATM 5 O 0.3 1.737 -1
HETATM 6 O 1.8 0.459 0
Protein Data Bank Files HETATM 7 H 0.9 -1.398 1
The Protein Data Bank file format (Protein DB) is HETATM 13 H -1 -1.737 1
taken from pages 3, 1415, and 1718 of the HETATM 8 H -1 -0.642 -1
Protein Data Bank Atomic coordinate and HETATM 9 H -2 1.564 0
Bibliographic Entry Format Description dated HETATM 10 H -1 1.41 1
January, 1985.
HETATM 11 H -2 0.211 1
A Protein Data Bank file can contain as many as 32 HETATM 12 H 2.4 1.06 -1
different record types. Only the COMPND, CONECT 1 2 7 13
ATOM, HETATM, and CONECT records are
CONECT 2 1 3 4 8
used by Chem3D; all other records in a Protein
Data Bank file are ignored. The COMPND record CONECT 3 2 5 6
contains the name of the molecule and identifying CONECT 4 2 9 10 11
information. CONECT 5 3
CONECT 6 3 12
CONECT 7 1
CONECT 13 1
CONECT 8 2

Chem & BioOffice 2006 /Chem3D File Formats 239

File Format Examples
 CONECT 9 4
7-10 UNUSED No
CONECT 10 4
CONECT 11 4
11-70 Name of Molecule Yes
Administrator

CONECT 12 6
END The full description of the ATOM and HETATM
The ATOM or HETATM record contains the record formats in Protein Data Bank files is as
record name, followed by the serial number of the follows:
atom being described, the element symbol for that
atom, then the X, Y, and Z Cartesian coordinates
for that atom. Column Column Used by
Number Description Chem3D
A CONECT record is used to describe the atomic
connectivity. The CONECT records contain the
1-6 Record Name Yes
record name, followed by the serial number of the
(HETATM or
atom whose connectivity is being described, then
ATOM)
the serial numbers of the first atom, second atom,
third atom and fourth atom to which the described
atom is connected. 7-11 Atom Serial Number Yes

Record Chem3D 12 UNUSED No

Name File Title

COMPND Alanine.pdb 1316 Atom Name Yes

(Element Symbol)
Record Serial Element X Y Z
Name Number Symbol Coord. Coord. Coord.

17 Alternate Location No
HETATM 1 N 0.038 -0.962 0.943
Indicator
Record Serial 1st Atom 2nd Atom 3rd Atom 4th Atom
Name Number Serial Serial Serial Serial
Number Number Number Number
1820 Residue Name Optional
CONECT 2 1 3 4 8
21 UNUSED No
FORTRAN Formats
22 Chain Identifier No
The full description of the COMPND record
format in Protein Data Bank files is as follows:
2326 Residue Sequence No
Number
Column Column Used by
Number Description Chem3D
27 Code for insertions of No
residues
1-6 Record Name Yes
(COMPND)

240 File Formats CambridgeSoft

File Format Examples
2830 UNUSED No 2226 Serial Number of Third Yes
Bonded Atom
3138 X Orthogonal Yes
coordinates 2731 Serial Number of Yes
Fourth Bonded Atom
3946 Y Orthogonal coor- Yes
dinates 3236 Hydrogen Bonds, No
Atoms in cols. 711 are
4754 Z Orthogonal coor- Yes Donors
dinates
3741 Hydrogen Bonds No
5560 Occupancy No
4246 Salt Bridge, Atoms in No
6166 Temperature Factor No cols. 711 have Nega-
tive Charge
67 UNUSED No
4751 Hydrogen Bonds, No
Atoms in cols 711 are
6870 Footnote Number No
Acceptors
The full description of the CONECT record
format in Protein Data Bank files is as follows: 5256 Hydrogen Bonds No

5761 Salt Bridge, Atoms in No

Column Column Used by cols. 711 have Positive
Number Description Chem3D Charge

16 Record Name Yes The FORTRAN formats for the records used in
(CONECT) the Protein Data Bank file format are as follows:

711 Atom Serial Number Yes

Line Description FORTRAN Format

1216 Serial Number of First Yes

Bonded Atom COMPND COMPND, 4X, 60A1

1721 Serial Number of Yes ATOM ATOM, 2X, I5,1X,A4,

Second Bonded Atom 1X, A3,10X, 3F8.3,16X

HETATM HETATM,
I5,1X,A4,14X,3F8.3,16X

Chem & BioOffice 2006 /Chem3D File Formats 241

File Format Examples
 1-2-3-4-5-6,1-6,2-7H,3-8H,4-9H,5-10H,6-11H,1-
CONECT CONECT, 5I5, 30X 12O-13H,1-14H,2-15H, 3-16H,4-17H,5-18H,6-
19H.@
ROSDAL
Administrator

The Rosdal Structure Language1 file format is
defined in Appendix C: Rosdal Syntax, pages
91108, of the MOLKICK Users Manual. The
Rosdal format is primarily used for query searching
in the Beilstein Online Database. Rosdal format
files are for export only. The following is a sample
Rosdal format file created using Chem3D Pro for
cyclohexanol:
1. Rosdal is a product of Softron, Inc.
SMD
The Standard Molecular Data 2SMD file) file
format is defined in the SMD File Format version
4.3 documentation, dated 04-Feb-1987. The
following is a sample SMD file produced using
Chem3D Pro for cyclohexanol (the line numbers
are added for purposes of discussion only).
2. SMD format - H. Bebak AV-IM-AM
Bayer AG.

Line 1 >STRT Cyclohexane

Line 2 DTCR Chem3D 00000 05-MAY-92 12:32:26
Line 3 >CT Cyclohexan 00039
Line 4 19 19 (A2,5I2) (6I3)
Line 5 C 0 0 0
Line 6 C 0 0 0
Line 7 C 0 0 0
Line 8 C 0 0 0
Line 9 C 0 0 0
Line 10 C 0 0 0
Line 11 H 0 0 0
Line 12 H 0 0 0
Line 13 H 0 0 0
Line 14 H 0 0 0
Line 15 H 0 0 0
Line 16 O 0 0 0
Line 17 H 0 0 0
Line 18 H 0 0 0
Line 19 H 0 0 0
Line 20 H 0 0 0
Line 21 H 0 0 0
Line 22 H 0 0 0

242 File Formats CambridgeSoft

File Format Examples
 Line 23 H 0 0 0
Line 24 1 2 1
Line 25 1 6 1
Line 26 1 12 1
Line 27 1 14 1
Line 28 2 3 1
Line 29 2 7 1
Line 30 2 15 1
Line 31 3 4 1
Line 32 3 8 1
Line 33 3 16 1
Line 34 4 5 1
Line 35 4 9 1
Line 36 4 17 1
Line 37 5 6 1
Line 38 5 10 1
Line 39 5 18 1
Line 40 6 11 1
Line 41 6 19 1
Line 42 12 13 1
Line 43 >CO ANGSTROEM 0020
Line 44 4 (3I10)
Line 45 -6903 13566 -4583
Line 46 -14061 808 125
Line 47 -4424 -8880 7132
Line 48 7577 -12182 -1855
Line 49 14874 594 -6240
Line 50 5270 10234 -13349
Line 51 -18551 -4300 -8725
Line 52 -9815 -18274 9852
Line 53 4047 -17718 -10879
Line 54 19321 5600 2685
Line 55 10636 19608 -16168
Line 56 -2794 21139 6600
Line 57 2876 15736 11820
Line 58 -14029 20018 -10310

Chem & BioOffice 2006 /Chem3D File Formats 243

File Format Examples
 Line 59 -22477
Line 60 -806
Line 61 14642
Administrator
Line 62 23341
Line 63 1740
Each line is either a blank line, a block header line
or a data record containing multiple fields of
information about the structure. The SMD file is
broken down into several blocks of information.
The header for each block starts with a > sign.
Individual fields are delimited by space(s) or a tab.
The fields in the SMD format file used by Chem3D
Pro are discussed below:
1. Line 1 starts the block named STRT. This
block contains the molecule name. The
molecule name is the file name when the file
was created using Chem3D Pro.
2. Line 2 starts the block named DTCR. The
information in this line includes the name of
the application that created the file and the date
and time when the file was generated.
3. Line 3 starts the block named CT which
contains the connection table of the
compound(s). Also on this line is a 10 character
description of the connection table. This will
be the same as the file name when the file is
generated using Chem3D Pro. Finally, the
number of records contained within the CT
block is indicated, 39 in the above example.
4. Line 4 of the CT Block contains four fields.
The first field is the number of atoms, the
second field is the number of bonds, the third
field is the FORTRAN format for the number
of atoms, and the fourth field is the
FORTRAN format for the number of bonds.
5. Lines 523 of the CT Block each contain 4
fields describing an atom. The first field is the
element symbol (first letter uppercase, second
lowercase). The second field is the total
244 File Formats
3450 6965
-4365 16672
-18918 3566
-2014 -13035
5536 -22837
number of hydrogens attached to the atom, the
third field is the stereo information about the
atom and the fourth field is the formal charge
of the atom.
NOTE: If the file is created using Chem3D Pro, the
number of hydrogens, the stereo information and the
formal charge fields are not used, and will always
contain zeros.
6. Lines 2442 of the CT Block each contains 3
fields describing a bond between the two
atoms. The first field is the serial number of the
atom from which the bond starts, the second
field is the serial number of atom where the
bond ends, and the third field is the bond
order.
7. Line 43 starts the block named CO, The infor-
mation in this block includes the Cartesian
coordinates of all the atoms from the CT block
and indicates the type of coordinates used,
Angstroms in this example. Also in this line is
the number of lines in the block, 20 in this
example.
8. Line 44 contains two fields. The first field
contains the exponent used to convert the
coordinates in the lines following to the coor-
dinate type specified in line 43. The second
field is the FORTRAN format of the atom
coordinates.
9. Lines 4565 each contains three fields
describing the Cartesian coordinates of an
atom indicated in the CT block. The first field
is the X coordinate, the second field is the Y
coordinate and the third field is the Z coordi-
nate.
CambridgeSoft
File Format Examples
SYBYL MOL File The following is an example of a file in SYBYL
format produced from within Chem3D. This file
The SYBYL MOL File format (SYBYL) is defined describes a model of cyclohexanol.
in Chapter 9, SYBYL File Formats, pages 91
through 95, of the 1989 SYBYL Programming
Manual.
19 MOL Cyclohexanol0
1 1 1.068 0.3581 -0.7007C
2 1 -0.207 1.2238 -0.7007C
3 1 -1.473 0.3737 -0.5185C
4 1 1.1286 -0.477 0.5913C
5 1 -0.139 -1.324 0.7800C
6 1 -1.396 -0.445 0.7768C
7 8 2.1708 1.2238 -0.7007O
8 13 1.0068 -0.343 -1.5689H
9 13 -0.284 1.7936 -1.6577H
10 13 -0.147 1.9741 0.1228H
11 13 -2.375 1.032 -0.4983H
12 13 -1.589 -0.314 -1.3895H
13 13 1.2546 0.202 1.4669H
14 13 2.0091 -1.161 0.5742H
15 13 -0.077 -1.893 1.7389H
16 13 -0.21 -2.076 -0.0419H
17 13 -2.308 -1.081 0.8816H
18 13 -1.372 0.2442 1.6545H
19 13 2.9386 0.6891 -0.8100H
19 MOL
1 1 2 1
2 1 4 1
3 1 7 1
4 1 8 1
5 2 3 1
6 2 9 1
7 2 10 1
8 3 6 1
9 3 11 1

Chem & BioOffice 2006 /Chem3D File Formats 245

File Format Examples
 10 3 12 1
11 4 5 1
12 4 13 1
Administrator

13 4 14 1
14 5 6 1
15 5 15 1
16 5 16 1
17 6 17 1
18 6 18 1
19 7 19 1
0 MOL

The following illustration shows the components of The format for SYBYL MOL files is as follows:
the SYBYL Output File from Chem3D for C(6)
and Bond 3 of Cyclohexanol. 1. The first record in the SYBYL MOL File
contains the number of atoms in the model, the
word MOL, the name of the molecule, and
the center of the molecule.
Number Molecule
of Atoms Name Center
2. The atom records (lines 220 in the cyclohex-
19 MOL Cyclohexanol 0
anol example) contain the Atom ID in column
6 1 -1.3959 -0.4449 0.7768C 1, followed by the Atom Type in column 2, and
the X, Y and Z Cartesian coordinates of that
Atom
ID
Atom
Type
X
Coord
Y
Coord
Z
Coord
atom in columns 35.
Number
of Bonds
3. The first record after the last atom records
19 MOL contains the number of bonds in the molecule,
3 1 7 1 followed by the word MOL.
Bond From-Atom To-Atom Bond 4. The bond records (lines 2240 in the cyclohex-
Number Type

Number
anol example) contain the Bond Number in
of Features column 1, followed by the Atom ID of the
atom where the bond starts (the From-
0 MOL
Atom) in column 2 and the Atom ID of the
atom where the bond stops (the To-Atom) in
column 3. The last column in the bond records
is the bond type. Finally the last line in the file
is the Number of Features record, which
contains the number of feature records in the
molecule. Chem3D does not use this informa-
tion.

246 File Formats CambridgeSoft

File Format Examples
FORTRAN Formats
Number of Features I4,1X,'MOL'
The FORTRAN format for each record of the record
SYBYL MOL File format is as follows:
SYBYL MOL2 File
Line Description FORTRAN Format
The SYBYL MOL21 file format (SYBYL2) is
Number of Atoms/File I4,1X,'MOL',20A2,11 defined in Chapter 3, File Formats, pages 3033
Name X,I4 3050, of the 1991 SYBYL Programming Manual. The
following is a sample SYBYL MOL2 file created
using Chem3D Pro. This file describes a model of
Atom records 2I4,3F9.4,2A2
cyclohexanol (the line numbers are added for
reference only):
Number of Bonds record I4,1X,'MOL'

Bond records 3I4,9X,I4

1. SYBYL is a product of TRIPOS Associ-

ates, Inc., a subsidiary of Evans &
Sutherland.
Line 1 # Name: CYCLOHEXANOL
Line 2
Line 3 @<TRIPOS>MOLECULE
Line 4 CYCLOHEXANOL
Line 5 19 19 0 0 0
Line 6 SMALL
Line 7 NO_CHARGES
Line 8
Line 9
Line 10 @<TRIPOS>ATOM
Line 11 1 C -1.349 0.195 1.032 C.3
Line 12 2 C -0.407 -0.896 1.563 C.3
Line 13 3 C 0.562 -1.378 0.473 C.3
Line 14 4 C 1.351 -0.205 -0.128 C.3
Line 15 5 C 0.42 0.9 -0.652 C.3
Line 16 6 C -0.559 1.37 0.436 C.3
Line 17 7 H -2.021 -0.239 0.253 H
Line 18 8 H -1.005 -1.759 1.944 H
Line 19 9 H 0.175 -0.496 2.427 H

Chem & BioOffice 2006 /Chem3D File Formats 247

File Format Examples
 Line 20 10 H 1.27 -2.128 0.9 H
Line 21 11 H -0.01 -1.898 -0.331 H
Line 22 12 H 2.021 0.225 0.655 H
Administrator

Line 23 13 H 2.008 -0.569 -0.953 H

Line 24 14 H 1.03 1.766 -1.016 H
Line 25 15 O -0.3 0.427 -1.757 O.sp
Line 26 16 H -1.262 2.128 0.014 H
Line 27 17 H 0.014 1.876 1.249 H
Line 28 18 H -2.005 0.562 1.857 H
Line 29 19 H 0.329 0.223 -2.427 H.sp
Line 30 @<TRIPOS>BOND
Line 31 1 31 2 1
Line 32 2 1 6 1
Line 33 3 1 7 1
Line 34 4 1 18 1
Line 35 5 2 3 1
Line 36 6 2 8 1
Line 37 7 2 9 1
Line 38 8 3 4 1
Line 39 9 3 10 1
Line 40 10 3 11 1
Line 41 11 4 5 1
Line 42 12 4 12 1
Line 43 13 4 13 1
Line 44 14 5 6 1
Line 45 15 5 14 1
Line 46 16 5 15 1
Line 47 17 6 16 1
Line 48 18 6 17 1
Line 49 19 15 19 1

Each line is either a blank line, a section header or a information. Record type indicators (RTI) break
data record containing multiple fields of the information about the molecule into sections.
information about the compound. The SYBYL RTIs are always preceded by an @ sign.
MOL2 file is broken down into several sections of Individual fields are delimited by space(s) or a tab.

248 File Formats CambridgeSoft

File Format Examples
The fields in the SYBYL MOL2 format file used by
Chem3D Pro are as follows:
1. Line 1 is a comment field. The pound sign
preceding the text indicates a comment line.
Name: is a field designating the name of
molecule. The molecule name is the file name
when the file is created using Chem3D Pro.
2. Line 2 is a blank line.
3. Line 3, @<TRIPOS>MOLECULE, is a
Record Type Indicator (RTI) which begins a
section containing information about the
molecule(s) contained in the file.
NOTE: There are many additional RTIs in the
SYBYL MOL2 format. Chem3D Pro uses only
@<TRIPOS>MOLECULE,
@<TRIPOS>ATOM and
@<TRIPOS>BOND.
4. Line 4 contains the name of the molecule. The
name on line 4 is the same as the name on line
1.
5. Line 5 contains 5 fields describing information
about the molecule: The first field is the
number of atoms, the second field is the
number of bonds, the third field is the number
of substructures, the fourth field is the number
of features and the fifth field is the number of
sets.
NOTE: Chem3D Pro ignores the following fields: number
of substructures, number of features and number of sets.
These fields will contain zeros if the file was created using
Chem3D Pro.
6. Line 6 describes the molecule type. This field
contains SMALL if the file is created using
Chem3D Pro.
Chem & BioOffice 2006 /Chem3D
7. Line 7 describes the charge type associated
with the molecule. This field contains
NO_CHARGES if the file is created using
Chem3D Pro.
8. Line 8, blank in the above example, might
contain internal SYBYL status bits associated
with the molecule.
9. Line 9, blank in the above example, might
contain comments associated with the mole-
cule.
NOTE: Four asterisks appear in line 8 when there
are no status bits associated with the molecule but there
is a comment in Line 9.
10. Line 10, @<TRIPOS>ATOM, is a Record
Type Indicator (RTI) which begins a section
containing information about each of the
atoms associated with the molecule.
11. Lines 1129 each contain 6 fields describing
information about an atom: the first field is the
atom id, the second field is the atom name, the
third field is the X coordinate, the fourth field
is the Y coordinate, the fifth field is the Z
coordinate and the sixth field is the atom type.
NOTE: Atom types are user-definable See Editing
File Format Atom Types on page 221 for instructions
on modifying or creating an atom type.
12. Line 30, @<TRIPOS>BOND, is a Record
Type Indicator (RTI) which begins a section
containing information about the bonds
associated with the molecule.
13. .Lines 3149 each contain 4 fields describing
information about a bond: the first field is the
bond id, the second field is the from-atom id,
the third field is the to-atom id, and the fourth
field is the bond type.
File Formats 249
File Format Examples
 FORTRAN Formats 5 Number of 4(1X,I2)
The FORTRAN format for each record of the atoms/number of
SYBYL MOL2 File format is as follows: bonds
Administrator

1129 Atom type, name, I4,6X,A2,3X,

coordinates and id 3F9.3,2X,A5
Line Description FORTRAN
Number Format
3149 Bond id, from-atom, 3I4,3X,A2
1 Molecule name (file # ,5X, to-atom, bond type
name) Name:
,1X,A

250 File Formats CambridgeSoft

File Format Examples
Appendix F: Parameter Tables
Parameter Table Over- Parameter Use
view Table

Chem3D uses the parameter tables, containing
information about elements, bond types, atom
types, and other parameters, for building and for
analyzing your model.
The parameter tables must be located in the C3D
Items directory in the same directory as the
Chem3D application.
Parameter Table Use
4-Membered Ring Bond angles for bonds in
Angles.xml 4-membered rings. In force
field analysis, angle bending
portion of the force field for
bonds in 4-membered rings.
4-Membered Ring Computes the portion of the
Torsionals.xml force field for the torsional
angles in your model for
atoms in 4-membered rings.

Chem3D uses several parameter tables to calculate Angle Bending Standard bond angles. In
bond lengths and bond angles in your model. To Parameters.xml force field analysis, angle
apply this information, select Apply Standard bending portion of the force
measurements in the Building Control panel. field for bonds.

Calculating the MM2 force field of a model requires

Atom Types.xml Contains atom types available
special parameters for the atoms and bonds in your
for building models.
model. The MM2 force field is calculated during
Energy Minimization, Molecular Dynamics, and
Steric Energy computations. Bond Stretching Standard bond lengths. In
Parameters.xml force field analysis, bond
The use of the parameter tables are described in the stretching and electrostatic
following table: portions of force field for
bonds.
Parameter Use
Table Conjugated Bond lengths for bonds
Pisystem involved in Pi systems. Pi
Atoms.xml system portion of the force
3-Membered Ring Bond angles for bonds in
field for pi atoms.
Angles.xml 3-membered rings. In force
field analysis, angle bending
portion of the force field for
bonds in 3-membered rings.

Chem & BioOffice 2006 /Chem3D Parameter Tables 251

 Parameter Use
Table
Administrator
Conjugated Pi system portion of the force
Pisystem field for pi bonds.
Bonds.xml
Electronegativity Adjusts optimal bond length
Adjustments.xml between two atoms when one
atom is attached to an atom
that is electronegative.
Elements.xml Contains elements available
for building models.
MM2 Atom Type van der Waals parameters for
Parameters.xml computing force field for
each atom.
MM2 Constants used for
Constants.xml computing MM2 force field.
Out-of-Plane Parameters to assure atoms in
Bending Parame- trigonal planar geometry
ters.xml remain planar. In force field
analysis, parameters to assure
atoms in trigonal planar
geometry remain planar.
References.xml Contains information about
where parameter information
is derived.
Substructures.xml Contains predrawn substruc-
tures available for speeding
up model building.
252 Parameter Tables
Parameter Use
Table
Torsional Parame- Computes the portion of the
ters.xml force field for the torsional
angles in your model.
VDW Interac- Adjusts specific VDW inter-
tions.xml actions, such as hydrogen
bonding.
Parameter Table Fields
Most of the tables contain the following types of
fields:
Atom Type Numbers
Quality
Reference
Atom Type Numbers
The first column in a parameter table references an
atom type using an Atom Type number. An Atom
Type number is assigned to an atom type in the
Atom Types table. For example, in Chem3D, a
dihedral type field, 1114, in the Torsional
Parameters table indicates a torsional angle between
carbon atoms of type alkane (Atom Type number 1)
and carbon atoms of type alkyne (Atom Type
number 4). In the 3-membered ring table, the angle
type field, 22-22-22, indicates an angle between
three cyclopropyl carbons (Atom Type number 22)
in a cyclopropane ring.
Quality
The quality of a parameter indicates the relative
accuracy of the data.
Quality Accuracy Level
CambridgeSoft
Parameter Table Fields

1 Parameter guessed by Chem3D.
2 Parameter theorized but not
confirmed.
3 Parameter derived from experi-
mental data.
4 Parameter well confirmed.
Reference
The reference for a measurement corresponds to a
reference number in the References table.
References indicate where the parameter data was
derived.
Estimating Parameters
In certain circumstances Chem3D may estimate
parameters.
For example, during an MM2 analysis, a non-MM2
atom type is encountered in your model. Although
the atom type is defined in the Atom Types table,
the necessary MM2 parameter will not be defined
for that atom type. For example, torsional
parameters are missing. This commonly occurs for
inorganic complexes, which MM2 does not cover
adequately. More parameters exist for organic
compounds.
In this case, Chem3D makes an educated guess
wherever possible. A message indicating an error in
your model may appear before you start the
analysis. If you choose to ignore this, you can
determine the parameters guessed after the analysis
is complete.
Chem & BioOffice 2006 /Chem3D
To view the parameters used in an MM2 analysis:
From the Calculations menu, point to MM2,
and choose Show Used Parameters.
Estimated parameters have a Quality value of
1.
Creating Parameters
The MM2 force field parameters are based on a
limited number of MM2 atom types. These atom
types cover the common atom types found in
organic compounds. As discussed in the previous
section, parameters may be missing from structures
containing other than an MM2 atom type.
NOTE: Adding or changing parameter tables is not
recommended unless you are sure of the information your are
adding. For example, new parameter information that is
documented in journals.
NOTE: A method for guessing at missing MM2
Parameters can be found in Development of an Internal
Searching Algorithm for Parameterization of the
MM2/MM3 Force Fields, Journal of Computational
Chemistry, Vol 12, No. 7, 844849 (1991).
To add a new parameter to a parameter table:
1. From the View menu, point to Parameter
Tables and choose the parameter table to open.
The parameter table appears.
2. Right click on a row header and choose Append
Row from the context menu.
A blank row is inserted.
3. Type the information for the new parameter.
4. Close and Save the file.
Parameter Tables 253
Estimating Parameters
 The new parameter is added to the file.
NOTE: Do not include duplicate parameters. If duplicate
parameters exist in a parameter table it is indeterminate
Administrator
which parameter will be used when called for in a calculation.
NOTE: If you do want to make changes to any of the
parameters used in Chem3D, we strongly recommend that
you make a back up copy of the original parameter table and
remove it from the C3DTABLE directory.
The Elements
The Elements table (Elements.xml) contains the
elements for use in building your models.
To use an element in a model, type its symbol in the
Replacement text box (or paste it, after copying the
cell in the Symbol field to the Clipboard) and
press the Enter key when an atom is selected, or
double-click an atom. If no atom is selected, a
fragment is added.
Four fields comprise a record in the Elements table:
the symbol, the covalent radius, the color, and the
atomic number.
Symbol
Normally you use only the first column of the
Elements table while building models. If you are
not currently editing a text cell, you can quickly
move from one element to another by typing the
first letter or letters of the element symbol.
Covalent Radius
The covalent radius is used to approximate bond
lengths between atoms.
254 Parameter Tables
Color
The colors of elements are used when the Color by
Element check box is selected in the control panel.
To change the color of an element:
Double-click the current color.
The Color Picker dialog box appears in which
you can specify a new color for the element.
Atom Types
The Atom Types table Atom Types.xml) contains
the atom types for use in building your models.
Normally you use only the first column of the Atom
Types table while building models. To use an atom
type in a model, type its name in the Replacement
text box (or paste it, after copying the name cell to
the Clipboard) and press the Enter key when an
atom is selected, or when you double-click an atom.
If no atom is selected, a fragment is added.
Twelve fields comprise an atom type record: name,
symbol, van der Waals radius, text number, charge,
the maximum ring size, rectification type, geometry,
number of double bonds, number of triple bonds,
number of delocalized bonds, bound-to order and
bound-to type.
Name
The records in the Atom Types table are ordered
alphabetically by atom type name. Atom type names
must be unique.
Symbol
This field contains the element symbol associated
with the atom type. The symbol links the Atom
Type table and the Elements table. The element
symbol is used in atom labels and when you save
files in file formats that do not support atom types,
such as MDL MolFile.
CambridgeSoft
The Elements
van der Waals Radius
The van der Waals (VDW) radius is used to specify
the size of atom balls and dot surfaces when
displaying the Ball & Stick, Cylindrical Bonds or
Space Filling models.
The Close Contacts command in the Measurements
submenu of the Structure menu determines close
contacts by comparing the distance between pairs
of non-bonded atoms to the sum of their van der
Waals radii.
The van der Waals radii specified in the Atom Types
table do not affect the results of an MM2
computation. The radii used in MM2 computations
are specified in the MM2 Atom Types table.
NOTE: The space filling model display is set in the Model
Display tab of the Model Settings dialog box. The
appearance of VDW dot surfaces is specified for the entire
model in the Atom Display tab of the Model Settings dialog
box, or for individual atoms using the Right-click Atom
Dots submenu in the Model Explorer.
Text Number (Atom Type)
Text numbers are used to determine which
measurements apply to a given group of atoms in
other parameter tables.
For example, C Alkane has an atom type number
of 1and O Alcohol has an atom type number of 6.
To determine the standard bond length of a bond
between a C Alkane atom and an O Alcohol atom,
you should look at the 1-6 record in the Bond
Stretching table.
Charge
The charge of an atom type is used when assigning
atom types to atoms in a model.
Chem & BioOffice 2006 /Chem3D
When the information about an atom is displayed,
the atom symbol is always followed by the charge.
Charges can be fractional. For example, the charge
of a carbon atom in a cyclopentadienyl ring should
be 0.200.
Maximum Ring Size
The maximum ring size field indicates whether the
corresponding atom type should be restricted to
atoms found in rings of a certain size. If this cell is
zero or empty, then this atom type is not restricted.
For example, the maximum ring size of
C Cyclopropane is 3.
Rectification Type
The rectification type specifies the type of atom
used to fill open valences. Rectification atoms are
added or deleted as you build your model if you
have selected the Automatically Rectify checkbox
from the Model Build tab of the Model Settings
dialog box.
Possible rectification types are:
D
H
H Alcohol
H Amide
H Amine
H Ammonium
H Carboxyl
H Enol
H Guanidine
H Thiol
NOTE: When you specify a rectification type, the bound-to
type of the rectification type should not conflict with the atom
type. If there is no rectification type for an atom, it is never
rectified.
For example, if the rectification type of O Carboxyl is H
Carboxyl, the bound-to type of H Carboxyl should be either
Parameter Tables 255
Atom Types
 O Carboxyl or empty. Otherwise, when assigning atom types,
hydrogen atoms bound to O Carboxyl atoms are not assigned
H Carboxyl.
Administrator
Bound-to Order
Specifies the order of the bond acceptable between
this atom type and the atom type specified in the

bound-to type.
Geometry
For example, for C Carbonyl, only double bonds
The geometry for an atom type describes both the can be formed to bound-to type O Carboxylate. If
number of bonds that extend from this type of there is no bound-to type specified, this field is not
atom and the angles formed by those bonds. used.
Possible geometries are: Possible bond orders are:
0 Ligand Single
1 Ligand Double
5 Ligands Triple

Bent Delocalized

Linear NOTE: The bound-to order should be consistent with the

Octahedral number of double, triple, and delocalized bonds for this atom
Square planar type. If the bound-to type of an atom type is not specified, its
bound-to order is ignored.
Tetrahedral
Trigonal bipyramidal
Bound-to Type
Trigonal planar
Specifies the atom type that this atom must be
Trigonal pyramidal
bound to. If there is no restriction, this field is
empty. Used conjunction with the Bound-to Order
NOTE: Standard bond angle parameters are used only
field.
when the central atom has a tetrahedral, trigonal or bent
geometry. Non-blank Bound-to-Type values:
C Alkene
Number of Double Bonds, C Carbocation
Triple Bonds, and Delocal- C Carbonyl
ized Bonds C Carboxylate
C Cyclopentadienyl
The number of double bonds, number of triple
bonds, and number of delocalized bonds are C Cyclopropene
integers ranging from zero to the number of ligands C Epoxy
as specified by the geometry. Chem3D uses this C Isonitrile
information both to assign atom types based on the
bond orders and to assign bond orders based on C Metal CO
atom types. C Thiocarbonyl

256 Parameter Tables CambridgeSoft

Atom Types
 H Alcohol References
H Thiol
The References table (References.xml) contains
N Ammonium information concerning the source for other
N Azide Center parameters. Use of the References table does not
affect the other tables in any way.
N Azide End
Two fields are used for each reference record: the
N Isonitrile
reference number and the reference description.
N Nitro
O Carbonyl Reference Number
O Carboxylate The reference number is an index by which the
references are organized. Each measurement also
O Epoxy
contains a reference field that should contain a
O Metal CO reference number, indicating the source for that
measurement.
O Nitro
O Oxo Reference Description
O Phosphate
The reference description contains whatever text
P Phosphate you need to describe the reference. Journal
references or bibliographic data are common
S Thiocarbonyl
examples of how you can describe your references.

Substructures Bond Stretching Parame-

The Substructure table (Substructures.xml)
contains substructures to use in your model.
To use a substructure simply type its name in the
Replacement text box (or paste it, after copying the
name cell to the Clipboard) and press the Enter key
when an atom(s) is selected, or double-click an
atom. You can also copy the substructures picture
to the Clipboard and paste it into a model window.
The substructure is attached to selected atom(s) in
the model window. If no atom is selected, a
fragment is added. You can also define your own
substructures and add them to the table. The table
below shows the substructure table window with
the substructure records open (triangles facing
down). Clicking a triangle closes the record. The
picture of the substructure is minimized.
ters
The Bond Stretching Parameters table (Bond
Stretching Parameters.xml) contains information
about standard bond lengths between atoms of
various atom types. In addition to standard bond
lengths are information used in MM2 calculations
in Chem3D.
The Bond Stretching table contains parameters
needed to compute the bond stretching and
electrostatic portions of the force field for the
bonds in your model.
The Bond Stretching Parameters record consists of
six fields: Bond Type, KS, Length, Bond Dpl,
Quality, and Reference.

Chem & BioOffice 2006 /Chem3D Parameter Tables 257

Substructures
 Bond Type
The Bond Type field contains the atom type
numbers of the two bonded atoms.
Administrator
For example, Bond Type 1-2 is a bond between an
alkane carbon and an alkene carbon.
KS
The KS, or bond stretching force constant field,
contains a proportionality constant which directly
impacts the strength of a bond between two atoms.
The larger the value of KS for a particular bond
between two atoms, the more difficult it is to
compress or to stretch that bond.
Length
The third field, Length, contains the bond length
for a particular bond type. The larger the number in
the Length field, the longer is that type of bond.
Bond Dipole
The Bond Dpl field contains the bond dipole for a
particular bond type. The numbers in this cell give
an indication of the polarity of the particular bond.
A value of zero indicates that there is no difference
in the electronegativity of the atoms in a particular
bond. A positive bond dipole indicates that the
atom type represented by the first atom type
number in the Bond Type field is less
electronegative than the atom type represented by
the second atom type number. Finally, a negative
bond dipole means that the atom type represented
by the first atom type number in the Bond Type
field is more electronegative than the atom type
represented by the second atom type number.
For example, the 1-1 bond type has a bond dipole
of zero since both alkane carbons in the bond are of
the same electronegativity. The 1-6 bond type has a
bond dipole of 0.440 since an ether or alcohol oxy-
258 Parameter Tables
gen is more electronegative than an alkane carbon.
Finally, the 1-19 bond type has a bond dipole
of - 0.600 since a silane silicon is less
electronegative than an alkane carbon.
NOTE: The 1-5 bond type has a dipole of zero, despite the
fact that the carbon and hydrogen atoms on this bond have
unequal electronegativity. This approximation drastically
reduces the number of dipoles to be computed and has been
found to produce acceptable results.
Record Order
The order of the records in the Bond Stretching
table window is as follows:
1. Records are sorted by the first atom type
number in the Bond Type field. For example,
the record for bond type 1-3 is before the
record for bond type 2-3.
2. For records where the first atom type number
is the same, the records are sorted by the
second atom type number in the Bond Type
field. For example, bond type 1-1 is before the
record for bond type 1-2.
Angle Bending
(4-Membered Ring Angle Bending, 3-Membered
Ring Angle Bending)
The Angle Bending table (Angle Bending
Parameters.xml) contains information about bond
angles between atoms of various atom type. In
addition to standard bond angles are information
used in MM2 Calculations in Chem3D. Angle
bending parameters are used when the central atom
has four or fewer attachments and the bond angle is
not in a three or four membered ring. In three and
four membered rings, the parameters in the
3-Membered Ring Angles.xml and 4-Membered
Ring Angles.xml are used.
CambridgeSoft
Angle Bending
The Angle Bending table contains the parameters
used to determine the bond angles in your model.
In Chem3D Pro, additional information is used to
compute the angle bending portions of the MM2
force field for the bond angles in your model.
The 4-membered Ring Angles table contains the
parameters that are needed to determine the bond
angles in your model that are part of 4-membered
rings. In Chem3D, additional information is used to
compute the angle bending portions of the MM2
force field for any bond angles in your model which
occur in 4-membered rings.
The 3-membered Ring Angles table contains the
parameters that are needed to determine the bond
angles in your model that are part of 3-membered
rings. In Chem3D, additional information is used to
compute the angle bending portions of the MM2
force field for any bond angles in your model which
occur in 3-membered rings.
Each of the records in the Angle Bending table, the
4-Membered Ring Angles table and the 3-
Membered Ring Angles table consists of seven
fields: Angle Type, KB, XR2, XRH, XH2, other non-hydrogen atom is a carbon.
Quality, and Reference.
Angle Type
The first field, Angle Type, contains the atom type
numbers of the three atoms which describe the
bond angle.
For example, angle type 1-2-1 is a bond angle
formed by an alkane carbon bonded to an alkene
carbon which is bonded to another alkane carbon.
Notice that the alkene carbon is the central atom of
the bond angle.
KB
The KB, or the angle bending constant, contains a
measure of the amount of energy required to
deform a particular bond angle. The larger the value
Chem & BioOffice 2006 /Chem3D
of KB for a particular bond angle described by
three atoms, the more difficult it is to compress or
stretch that bond angle.
XR2
XR2, the third field, contains the optimal value
of a bond angle where the central atom of that bond
angle is not bonded to any hydrogen atoms. In the
XR2 notation, X represents the central atom of a
bond angle and R represents any non-hydrogen
atom bonded to X.
For example, the optimal value of the 1-1-3 angle
type for 2,2-dichloropropionic acid is the XR2
bond angle of 107.8, since the central carbon (C-2)
has no attached hydrogen atoms.
The optimal value of the 1-8-1 angle type for
N,N,N-triethylamine is the XR2 bond angle of
107.7, because the central nitrogen has no attached
hydrogen atoms. Notice that the central nitrogen
has a trigonal pyramidal geometry, thus one of the
attached non-hydrogen atoms is a lone pair, the
XRH
The XRH field contains the optimal value of a
bond angle where the central atom of that bond
angle is also bonded to one hydrogen atom and one
non-hydrogen atom. In the XRH notation, X
and R are the same as XR2, and H represents a
hydrogen atom bonded to X.
For example, the optimal value of the 1-1-3 angle
type for 2-chloropropionic acid is the XRH bond
angle of 109.9, since the central carbon (C-2) has
one attached hydrogen atom. The optimal value of
the 1-8-1 angle type for N,N-diethylamine is the
XRH value of 107.7, because the central N has
one attached hydrogen atom. In this case the
XR2 and XRH values for the 1-8-1 angle type
Parameter Tables 259
Angle Bending
 are identical. As in the N,N,N-triethylamine
example above, the only attached non-hydrogen
atom is a lone pair.
Administrator
XH2
XH2 is the optimal value of a bond angle where
the central atom of that bond angle is also bonded
to two hydrogen atoms.
For example, the optimal value of the 1-1-3 angle
type for propionic acid is the XH2 bond angle of
110.0, since the central carbon (C-2) has two
attached hydrogen atoms.
Record Order
When sorted by angle type, the order of the records
in the Angle Bending table, the 4-Membered Ring
Angles table and the 3-Membered Ring Angles
table is as follows:
1. Records are sorted by the second atom type
number in the Angle Type field. For example,
the record for bond angle type 1-2-1 is before
the record for bond angle type 1-3-1.
2. For multiple records where the second atom
type number is the same, the records are sorted
by the first atom type number in the Angle
Type field. For example, the record for bond
angle type 1-3-2 is listed before the record for
bond angle type 2-3-2.
3. For multiple records where the first two atom
type numbers are the same, the records are
sorted by the third atom type number in the
Angle Type field. For example, the record for
bond angle type 1-1-1 is listed before the
record for bond angle type 1-1-2.
Pi Atoms
The Pi Atoms table (Conjugated Pisystem
Atoms.xml) contains the parameters which are used
to correct bond lengths and angles for pi atoms in
260 Parameter Tables
your model. In Chem3D, additional information is
used to compute the pi system portions of the
MM2 force field for the pi atoms in your model.
The records in the Pi Atoms table are comprised of
six fields: Atom Type, Electron, Ionization,
Repulsion, Quality, and Reference.
Atom Type
The Atom type number field contains the atom
type number to which the rest of the Conjugated
Pisystem Atoms record applies.
Electron
The Electron field contains the number of
electrons that a particular pi atom contributes to the
pi system.
For example, an alkene carbon, atom type number
2, contributes 1 electron to the pi system whereas a
pyrrole nitrogen, atom type number 40, contributes
2 electrons to the pi system.
Ionization
The Ionization field contains the amount of energy
required to remove a pi electron from an isolated pi
atom. The units of the ionization energy by electron
volts (eV). The magnitude of the ionization energy
is larger the more electronegative the atom.
For example, an alkene carbon has an ionization
energy of -11.160 eV, and the more electronegative
pyrrole nitrogen has an ionization energy of -13.145
eV.
Repulsion
The Repulsion field contains a measure of:
The energy required to keep two electrons,
each on separate pi atoms, from moving apart
and
CambridgeSoft
Pi Atoms
 The energy required to keep two electrons,
occupying the same orbital on the same pi
atom, from moving apart.
The units of the repulsion energy are electron
volts (eV). The repulsion energy is more
positive the more electronegative the atom.
For example, an alkene carbon has an repulsion
energy of 11.134 eV, and the more electronegative
pyrrole nitrogen has an repulsion energy of 17.210
eV.
Pi Bonds
The Pi Bonds table (Conjugated PI System
Bonds.xml) contains parameters used to correct
bond lengths and bond angles for bonds that are
part of a pi system. In Chem3D, additional
information is used to compute the pi system
portions of the MM2 force field for the pi bonds in
a model.
There are five fields in records in the Pi Bonds
table: Bond Type, dForce, dLength, Quality, and
Reference.
Bond Type
The Bond Type field is described by the atom type
numbers of the two bonded atoms.
For example, bond type 2-2 is a bond between two
alkene carbons.
dForce
The dForce field contains a constant used to
decrease the bond stretching force constant of a
particular conjugated double bond. The force
constant Kx for a bond with a calculated pi bond
order x is:
Kx = K2 - (1 - x) * dForce
where K2 is the force constant for a non-
conjugated double bond, taken from the Bond
Stretching table.
Chem & BioOffice 2006 /Chem3D
The higher the value of Kx for the bond between
two pi atoms, the more difficult it is to compress or
stretch that bond.
dLength
The dLength field contains a constant used to
increase the bond length of any conjugated double
bond. The bond length lx for a bond with a
calculated pi bond order x is:
lx = l2 + (1 - x) * dLength
where l2 is the bond length of a non-conjugated
double bond, taken from the Bond Stretching
table. The higher the value of lx for the bond
between two pi atoms, the longer that bond is.
Record Order
When sorted for Bond Type, the order of the
records in the Conjugated Pisystem Bonds table is
as follows:
1. Records are sorted by the first atom type
number in the Bond Type field. For example,
the record for bond type 2-2 is listed before the
record for bond type 3-4.
2. For records where the first atom type number
is the same, the records are sorted by the
second atom type number in the Bond Type
field. For example, the record for bond type 2-
2 is listed before the record for bond type 2-3.
Electronegativity Adjust-
ments
The parameters contained in the Electronegativity
Adjustments table (Electronegativity
Adjustments.xml) are used to adjust the optimal
bond length between two atoms when one of the
atoms is attached to a third atom which is
electronegative.
Parameter Tables 261
Pi Bonds
 For example, the carbon-carbon single bond length
in ethane is different than that in ethanol. The MM2
parameter set has only a single parameter for
carbon-carbon single bond lengths (1.523). The
Administrator
use of electronegativity correction parameters
allows the C-C bond in ethanol to be corrected. The
electronegativity parameter used in the
Electronegativity Corrections table is the 1-1-6
angle type, where atom type 1 is a C Alkane and
atom type 6 is an O Alcohol. The value of this
parameter is -0.009. Thus the C-C bond length in
ethanol is 0.009 shorter than the standard C-C
bond length.
MM2 Constants
The MM2 Constants table (MM2 Constants.xml)
contains parameters which Chem3D uses to
compute the MM2 force field.
Cubic and Quartic Stretch
Constants
Integrating the Hooke's Law equation provides the
Hooke's Law potential function which describes
the potential energy of the ball and spring model.
The shape of this potential function is the classical
potential well.
dV
------- = F = dx
dx
The Hooke's Law potential function is quadratic,
thus the potential well created is symmetrical. The
real shape of the potential well is asymmetric and is
defined by a complicated function called the Morse
Function, but the Hooke's Law potential function
works well for most molecules.
x x 1--- kx 2
V( x)=
0 dV = k0 xdx = 2 for 1-1-1 angles and thus require separate constants
262 Parameter Tables
Certain molecules contain long bonds which are
not described well by Hooke's Law. For this reason
the MM2 force field contains a cubic stretch term.
The cubic stretch term allows for an asymmetric
shape of the potential well, thereby allowing these
long bonds to be handled. However, the cubic
stretch term is not sufficient to handle abnormally
long bonds. Thus the MM2 force field contains a
quartic stretch term to correct for problems caused
by these abnormally long bonds.
Type 2 (-CHR-) Bending Force
Parameters for C-C-C Angles
-CHR- Bending K for 1-1-1 angles -CHR- Bending
K for 1-1-1 angles in 4-membered rings -CHR-
Bending K for 22-22-22 angles in 3-membered
rings
These constants are distinct from the force
constants specified in the Angle Bending table. The
bending force constant (K) for the 1-1-1 angle (1 is
the atom type number for the C Alkane atom type)
listed in the MM2 Angle Bending parameters table
is for an alkane carbon with two non-hydrogen
groups attached. Angle bending parameters for
carbons with one or two attached hydrogens differ
from those for carbons with no attached hydrogens.
Because carbons with one or two attached
hydrogens frequently occur, separate force
constants are used for these bond angles.
The -CHR- Bending K for 1-1-1 angles allows more
accurate force constants to be specified for the
Type 1 (-CH2-) and Type 2 (-CHR-) interactions. In
addition, the -CHR- Bending K for 1-1-1 angles in
4-membered rings and the -CHR- Bending K for
22-22-22 angles (22 is the atom type number for the
C Cyclopropane atom type) in 3-membered rings
differ from the aforementioned -CHR- Bending K
to be accurately specified.
CambridgeSoft
MM2 Constants
Stretch-Bend Parameters
X-B,C,N,O-Y Stretch-Bend interaction force
constant X-B,C,N,O-H Stretch-Bend interaction
force constant X-Al,S-Y Stretch-Bend force
constant X-Al,S-H Stretch-Bend force constant X-
Si,P-Y Stretch-Bend force constant X-Si,P-H
Stretch-Bend force constant X-Ga,Ge,As,Se-Y
Stretch-Bend force constant
The stretch-bend parameters are force constants
for the stretch-bend interaction terms in the prior
list of elements. X and Y represent any non-
hydrogen atom.
When an angle is compressed, the MM2 force field
uses the stretch-bend force constants to lengthen
the bonds from the central atom in the angle to the
other two atoms in the angle.
For example, the normal C-C-C bond angle in
cyclobutane is 88.0, as compared to a C-C-C bond
angle of 110.8 in cyclohexane. The stretch-bend
force constants are used to lengthen the C-C bonds
in cyclobutane to 1.550, from a C-C bond length
of 1.536 in cyclohexane.
Sextic Bending Constant
Sextic bending constant (* 10**8)
Chem3D uses the sextic bending constant to
increase the energy of angles with large
deformations from their ideal value.
Dielectric Constants
Dielectric constant for charges Dielectric constant
for dipoles
The dielectric constants perform as inverse
proportionality constants in the electrostatic energy
terms. The constants for the charge and dipole
terms are supplied separately so that either can be
partially or completely suppressed.
Chem & BioOffice 2006 /Chem3D
The charge-dipole interaction uses the geometric
mean of the charge and dipole dielectric constants.
For example, when you increase the Dielectric
constant for dipoles, a decrease in the
Dipole/Dipole energy occurs. This has the effect of
reducing the contribution of dipole-dipole
interactions to the total steric energy of a molecule.
Electrostatic and van der
Waals Cutoff Parameters
Cutoff distance for charge/charge interactions
Cutoff distance for charge/dipole interactions
Cutoff distance for dipole/dipole interactions
Cutoff distance for van der Waals interactions
These parameters define the minimum distance at
which the fifth-order polynomial switching
function is used for the computation of the listed
interactions.
MM2 Atom Types
The MM2 Atom Types table (MM2 Atom
Types.xml) contains the van der Waals parameters
used to compute the force field for each atom in
your model.
Each MM2 Atom Type record contains eight fields:
Atom type number, R*, Eps, Reduct, Atomic
Weight, Lone Pairs, Quality, and Reference.
Atom type number
The Atom Type number field is the atom type to
which the rest of the MM2 Atom Type Parameter
record applies. The records in the MM2 Atom Type
table window are sorted in ascending order of
Atom Type Atom type number.
Parameter Tables 263
MM2 Atom Types
 R*
The R* field is the van der Waals radius of the
particular atom. The larger the van der Waals radius
Administrator
of an atom is, the larger that atom.
NOTE: Chem3D uses the van der Waals radius, R*, in
the MM2 Atom Types table for computation. It is not the
same as the van der Waals radius in the Atom Types table,
which is used for displaying the model.
Eps
The Eps or Epsilon field is a constant which is
proportional to the depth of the potential well. As
the value of epsilon increases, the depth of the
potential well increases, as does the strength of the
repulsive and attractive interactions between this
atom and other atoms.
NOTE: For specific VDW interactions, the R* and Eps
values from the VDW Interactions table are used instead of
values in the MM2 Atom Types table. See VDW
Interactions later in the chapter for more information.
Reduct
Reduct, the fourth field, is a constant used to orient
the center of the electron cloud on a hydrogen atom
toward the nucleus of the carbon atom to which it
is bonded by approximately 10% of the distance
between the two atoms.
Any atom in a van der Waals potential function
must possess a spherical electron cloud centered
about its nucleus. For most larger atoms this is a
reasonable assumption, but for smaller atoms such
as hydrogen it is not a good assumption. Molecular
mechanics calculations based on spherical electron
clouds centered about hydrogen nuclei do not give
accurate results.
264 Parameter Tables
However, it is a reasonable compromise to assume
that the electron cloud about hydrogen is still
spherical, but that it is no longer centered on the
hydrogen nucleus. The Reduct constant is
multiplied by the normal bond length to give a new
bond length which represents the center of the
repositioned electron cloud.
The value of the Reduct field for all non-hydrogen
atoms is zero.
Atomic Weight
The fifth field, Atomic Weight, is the atomic weight
of atoms represented by this atom type number.
NOTE: The atomic weight is for the isotopically pure
element, i.e. the atomic weight for atom type number 1 is
12.000, the atomic weight of 12C.
Lone Pairs
The Lone Pairs field contains the number of lone
pairs around a particular atom type. Notice that an
amine nitrogen, atom type number 8, has one lone
pair and an ether oxygen, atom type number 6, has
two lone pairs. Lone pairs are treated explicitly for
atoms such as these, which have distinctly
non-spherical electron distributions. For atom types
such as O Carbonyl, which have more nearly
spherical electron distributions, no explicit lone
pairs are necessary.
NOTE: Lone pairs are added automatically to atoms
which require them at the beginning of an MM2
computation.
Torsional Parameters
The Torsional Parameters table (Torsional
Parameters.xml) contains parameters used to
compute the portions of the MM2 force field for
the torsional angles in your model. The 4-
CambridgeSoft
Torsional Parameters
Membered Ring Torsional Parameters
(4-membered Ring Torsionals.xml) contains
torsional parameters for atoms in 4-membered
rings.
Each of the records in the Torsional Parameters
table and the 4-Membered Ring Torsional
Parameters table consists of six fields: Dihedral
Type, V1, V2, V3, Quality, and Reference.
Dihedral Type
The Dihedral Type field contains the atom type
numbers of the four atom types which describe the
dihedral angle.
For example, angle type 1-2-2-1 is a dihedral angle
formed by an alkane carbon bonded to an alkene
carbon which is first bonded to a second alkene
carbon which is bonded to another alkane carbon.
In other words, angle type 1-2-2-1 is the dihedral
angle between the two methyl groups of 2-butene.
The two alkene carbons are the central atoms of the
dihedral angle.
V1
The V1, or 360 Periodicity Torsional constant,
field contains the first of three principal torsional
constants used to compute the total torsional
energy in a molecule. V1 derives its name from the
fact that a torsional constant of 360 periodicity can
have only one torsional energy minimum and one
torsional energy maximum within a 360 period.
The period starts at -180 and ends at 180.
A positive value of V1 means that a maximum
occurs at 0 and a minimum occurs at 180 in a
360 period. A negative value of V1 means that a
minimum occurs at 0 and a maximum occurs at
180 in a 360 period. The significance of V1 is
explained in the example following the V2
discussion.
Chem & BioOffice 2006 /Chem3D
V2
The V2, or 180 Periodicity Torsional constant,
field contains the second of three principal
torsional constants used to compute the total
torsional energy in a molecule. V2 derives its name
from the fact that a torsional constant of 180
periodicity can have only two torsional energy
minima and two torsional energy maxima within a
360 period.
A positive value of V2 indicates there are minima at
0 and +180, and there are maxima at -90 and
+90 in a 360 period. A negative value of V2
causes the position of the maxima and minima to be
switched, as in the case of V1 above. The
significance of V2 is explained in the following
example.
A good example of the significance of the V1 and
V2 torsional constants exists in the 1-2-2-1
torsional parameter of 2-butene. The values of V1
and V2 in the Torsional Parameters table are -0.100
and 10.000 respectively.
Because a positive value of V2 indicates that there
are minima at 0 and +180, these minima signify
cis-2-butene and trans-2-butene respectively.
Notice that V2 for torsional parameters involving
torsions about carbon-carbon double bonds all
have values ranging from approximately V2=8.000
to V2=16.250. In addition, V2 torsional parameters
involving torsions about carbon-carbon single
bonds all have values ranging from approximately
V2=-2.000 to V2=0.950.
The values of V2 for torsions about carbon-carbon
double bonds are higher than those values for
torsions about carbon-carbon single bonds. A
consequence of this difference in V2 values is that
the energy barrier for rotations about double bonds
is much higher than the barrier for rotations about
single bonds.
Parameter Tables 265
Torsional Parameters
 The V1 torsional constant creates a torsional energy
difference between the conformations represented
by the two torsional energy minima of the V2
constant. As discussed previously, a negative value
Administrator
of V1 means that a torsional energy minimum
occurs at 0 and a torsional energy maximum
occurs at 180. The value of V1=-0.100 means that
cis-2-butene is a torsional energy minimum that is
0.100 kcal/mole lower in energy than the torsional
energy maximum represented by trans-2-butene.
The counterintuitive fact that the V1 field is
negative can be understood by remembering that
only the total energy can be compared to
experimental results. In fact, the total energy of
trans-2-butene is computed to be 1.423 kcal/mole
lower than the total energy of cis-2-butene. This
corresponds closely with experimental results. The
negative V1 term has been introduced to
compensate for an overestimation of the energy
difference based solely on van der Waals repulsion
between the methyl groups and hydrogens on
opposite ends of the double bond. This example
illustrates an important lesson:
There is not necessarily any correspondence
between the value of a particular parameter used in
MM2 calculations and value of a particular physical
property of a molecule.
V3
The V3, or 120 Periodicity Torsional constant,
field contains the third of three principal torsional
constants used to compute the total torsional
energy in a molecule. V3 derives its name from the
fact that a torsional constant of 120 periodicity can
have three torsional energy minima and three
torsional energy maxima within a 360 period. A
positive value of V3 indicates there are minima at -
266 Parameter Tables
60, +60 and +180 and there are maxima at -
120, 0, and +120 in a 360 period. A negative
value of V3 causes the position of the maxima and
minima to be reversed, as in the case of V1 and V2
above. The significance of V3 is explained in the
following example.
The 1-1-1-1 torsional parameter of n-butane is an
example of the V3 torsional constant. The values of
V1, V2 and V3 in the Torsional Parameters table are
0.200, 0.270 and 0.093 respectively. Because a
positive value of V3 indicates that there are minima
at -60, +60 and +180 and there are maxima at -
120, 0, and +120, the minima at 60 signify the
two conformations of n-butane in which the methyl
groups are gauche to one another. The +180
minimum represents the conformation in which the
methyl groups are anti to one another. The
maximum at 0 represents the conformation in
which the methyl groups are eclipsed. The maxima
at 120 conform n-butane in which a methyl
group and a hydrogen are eclipsed.
The V1 and V2 torsional constants in this example
affect the torsional energy in a similar way to the V1
torsional constant for torsions about a carbon-
carbon double bond (see previous example).
NOTE: The results of MM2 calculations on hydrocarbons
do not correspond well with the experimental data on
hydrocarbons when only the V3 torsional constant is used
(when V1 and V2 are set to zero). However, including
small values for the V1 and V2 torsional constants in the
MM2 calculations for hydrocarbons dramatically improve
the correspondence of the MM2 results with experimental
results. This use of V1 and V2 provides little
correspondence to any particular physical property of
hydrocarbons.
CambridgeSoft
Torsional Parameters
Record Order
When sorted by Dihedral Angle, the order of the
records in the Torsional Parameters table and the
4-Membered Ring Torsional Parameters table is as
follows:
1. Records are sorted by the second atom type
number in the Dihedral Type field. For
example, the record for dihedral type 1-1-1-1 is
listed before the record for dihedral
type 1-2-1-1.
2. For records where the second atom type
number is the same, the records are sorted by
the third atom type number in the Dihedral
Type field. For example, the record for dihedral
type 1-1-1-1 is listed before the record for
dihedral type 1-1-2-1.
3. For multiple records where the second and
third atom type numbers are the same, the
records are sorted by the first atom type
number in the Dihedral Type field. For
example, the record for dihedral type 5-1-3-1 is
listed before the record for dihedral type 6-1-3-
1.
4. For multiple records where the first, second
and third atom type numbers are the same, the
records are sorted by the fourth atom type
number in the Dihedral Type field. For
example, the record for dihedral type 5-1-3-1 is
listed before the record for dihedral
type 5-1-3-2.
Out-of-Plane Bending
The Out-of-Plane Bending table (Out-of-Plane
Bending Parameters.xml) contains parameters
which are used to ensure that atoms with trigonal
planar geometry remain planar in MM2
calculations.
Chem & BioOffice 2006 /Chem3D
There are four fields in records in the Out-of-Plane
Bending Parameters table: Bond Type, Force
Constant, Quality and Reference.
Bond Type
The first field is the Bond Type which is described
by the atom type numbers of the two bonded
atoms.
For example, Bond Type 2-3 is a bond between an
alkene carbon and a carbonyl carbon.
Force Constant
The Force Constant field, or the out-of-plane
bending constant, field contains a measure of the
amount of energy required to cause a trigonal
planar atom to bend out-of-plane, i.e., to become
non-planar. The larger the value of Force Constant
for a particular atom, the more difficult it is to
coerce that atom to be non-planar.
Record Order
When sorted by Bond Type, the order of the
records in the Out-of-Plane Bending Parameters
table is as follows:
1. Records are sorted by the first atom type
number in the Bond Type field. For example,
the record for bond type 2-1 is before the
record for bond type 3-1.
2. For records where the first atom type number
is the same, the records are sorted by the
second atom type number in the Bond Type
field. For example, the record for bond type 2-
1 is before the record for bond type 2-2.
NOTE: Out-of-plane bending parameters are not
symmetrical. For example, the force constant for a 2-3 bond
refers to the plane about the type 2 atom. The force constant
for a 3-2 bond refers to the plane about the type 3 atom.
Parameter Tables 267
Out-of-Plane Bending
 VDW Interactions
The parameters contained in the VDW parameters
table (VDW Interaction.xml) are used to adjust
Administrator
specific VDW interactions in a molecule, such as
hydrogen bonding, to provide better
correspondence with experimental data in
calculating the MM2 force field.
For example, consider the VDW interaction
between an Alkane carbon (Atom Type 1) and a
hydrogen (Atom Type 5). Normally, the VDW
energy is based on the sum of the VDW radii for
these atoms, found for each atom in the Atom
Types table (1.900 for Atom type number 1 +
1.400 for Atom type number 2 = 3.400).
However, better correspondence between the
computed VDW energy and experimental data is
found by substituting this sum with the value found
in the VDW Interactions table for this specific atom
type pair (Atom Types 1-5 = 3.340). Similarly, an
268 Parameter Tables
Eps parameter is substituted for the geometric
mean of the Eps parameters for a pair of atoms if
their atom types appear in the VDW Interactions
table.
Record Order
When sorted by Atom Type, the order of the
records in VDW Interactions table window is as
follows:
Records are sorted by the first atom type number in
the Atom Type field. For example, the record for
Atom Type 1-36 is before the record for atom type
2-21.
For records where the first atom type number is the
same, the records are sorted by the second atom
type number in the Atom Type field. For example,
the record for atom type 2-21 is before the record
for atom type 2-23.
CambridgeSoft
VDW Interactions
Appendix G: Computation Concepts
Computational
Chemistry Overview
Computational chemistry allows the exploration of
molecules by using a computer when an actual
laboratory investigation may be inappropriate,
impractical, or impossible.
Aspects of computational chemistry include:
Figure G-21: Computational Chemistry Methods
Molecular modeling.
Computational methods.
Computer-Aided Molecular Design (CAMD).
Chemical databases.
Molecular mechanicsapplies the laws of
classical physics to the atoms in a molecule
without explicit consideration of electrons.
Quantum mechanicsrelies on the
Schrdinger equation to describe a molecule
with explicit treatment of electronic structure.
Quantum mechanical methods can be
subdivided into two classes: ab initio and
semiempirical.
Computational Chemistry Methods
Molecular Quantum
Mechanical Methods Mechanical Methods

Organic synthesis design.

Molecular modeling can be thought of as the

Semiempirical Ab Initio
rendering of a 2D or 3D model of a molecules Methods Methods
structure and properties. Computational methods,
on the other hand, calculate the structure and Chem3D provides the following methods:
property data necessary to render the model.
Within a modeling program such as Chem3D, Method
computational methods are referred to as
computation engines, while geometry engines and
graphics engines render the model. molecular MM2 Chem3D, Tinker
mechanics Tinker
Chem3D supports a number of powerful MM3,
computational chemistry methods and extensive MM3-
visualization options. protein Gaussian

AMBER,UFF,
Computational Methods Dreiding
Overview
Computational chemistry encompasses a variety of
mathematical methods which fall into two broad
categories:

Chem & BioOffice 2006 /Chem3D Computation Concepts 269

Computational Methods Overview
 Single point energy calculationThe
Method energy of a given geometry of the atoms in a
model which is the value of the PES at that
semi- extended Chem3D, point.
Administrator

empirical Hckel MOPAC, Gaussian Geometry optimizationA systematic

MOPAC, Gaussian modification of the atomic coordinates of a
other semi-
model resulting in a geometry where the forces
empirical
on each atom in the structure is zero. A
methods
3-dimensional arrangement of atoms in the
(AM1,
model representing a local energy minimum (a
MINDO/3,
stable molecular geometry to be found without
PM3, etc.)
crossing a conformational energy barrier).
Property calculationPredicts certain phys-
Ab initio RHF, UHF, Gaussian,
ical and chemical properties, such as charge,
MP2, etc. GAMESS
dipole moment, and heat of formation.
Molecular mechanical methods: MM2 Computational methods can perform more
(directly). MM3 and MM3-protein through the specialized functions, such as conformational
Chem3D Tinker interface. searches and molecular dynamics simulations.

Semiempirical Extended Hckel, MINDO/3, Choosing the Best Method

MNDO, MNDO-d, AM1 and PM3 methods
through Chem3D and CS MOPAC or Gaus-
sian.
Ab initio methods through the Chem3D Gaus-
sian or GAMESS interface.
Uses of Computational
Methods
Computational methods calculate the potential
energy surfaces (PES) of molecules. The potential
energy surface is the embodiment of the forces of
interaction among atoms in a molecule. From the
PES, structural and chemical information about a
molecule can be derived. The methods differ in the
way the surface is calculated and in the molecular
properties derived from the energy surface.
The methods perform the following basic types of
calculations:
Not all types of calculations are possible for all
methods and no one method is best for all
purposes. For any given application, each method
poses advantages and disadvantages. The choice of
method depend on a number of factors, including:
The nature and size of the molecule
The type of information sought
The availability of applicable experimentally
determined parameters (as required by some
methods)
Computer resources
The three most important of the these criteria are:
Model sizeThe size of a model can be a
limiting factor for a particular method. The
limiting number of atoms in a molecule
increases by approximately one order of
magnitude between method classes from ab
initio to molecular mechanics. Ab initio is limited
to tens of atoms, semiempirical to hundreds,
and molecular mechanics to thousands.

270 Computation Concepts CambridgeSoft

Computational Methods Overview
 Parameter AvailabilitySome methods
depend on experimentally determined parame-
ters to perform computations. If the model
contains atoms for which the parameters of a
particular method have not been derived, that
method may produce invalid predictions.
Molecular mechanics, for example, relies on
parameters to define a force-field. A force-field
is only applicable to the limited class of mole-
cules for which it is parametrized.
Computer resourcesRequirements
increase relative to the size of the model for
each of the methods.
Ab initio: The time required for performing
computations increases on the order of N4,
where N is the number of atoms in the model.
Semiempirical: The time required for
computation increases as N3 or N2, where N is
the number of atoms in the model.
MM2: The time required for performing
computations increases as N2, where N is the
number of atoms.
In general, molecular mechanical methods are
computationally less expensive than quantum
mechanical methods. The suitability of each
general method for particular applications can
be summarized as follows.
Molecular Mechanics Methods Applica-
tions Summary
Molecular mechanics in Chem3D apply to:
Systems containing thousands of atoms.
Organic, oligonucleotides, peptides, and
saccharides.
Gas phase only (for MM2).
Useful techniques available using MM2 methods
include:
Energy Minimization for locating stable
conformations.
Chem & BioOffice 2006 /Chem3D
Single point energy calculations for comparing
conformations of the same molecule.
Searching conformational space by varying one
or two dihedral angles.
Studying molecular motion using Molecular
Dynamics.
Quantum Mechanical Methods Applica-
tions Summary
Useful information determined by quantum
mechanical methods includes:
Molecular orbital energies and coefficients.
Heat of Formation for evaluating conforma-
tional energies.
Partial atomic charges calculated from the
molecular orbital coefficients.
Electrostatic potential.
Dipole moment.
Transition-state geometries and energies.
Bond dissociation energies.
Semiempirical methods available in Chem3D with
CS MOPAC or Gaussian apply to:
Systems containing up to 120 heavy atoms and 300
total atoms.
Organic, organometallics, and small oligomers
(peptide, nucleotide, saccharide).
Gas phase or implicit solvent environment.
Ground, transition, and excited states.
Ab initio methods available in Chem3D with
Gaussian or Jaguar apply to:
Systems containing up to 150 atoms.
Organic, organometallics, and molecular frag-
ments (catalytic components of an enzyme).
Gas or implicit solvent environment.
Study ground, transition, and excited states
(certain methods).
Computation Concepts 271
Computational Methods Overview
 Table 1: Comparison of Methods

Method Type Advantages Disadvantages Best For

Administrator

Molecular Mechanics Least intensive compu- Particular force field appli- Large systems
(Gaussian) tationallyfast and cable only for a limited (thousands of atoms)
useful with limited class of molecules
Uses classical physics computer resources Systems or processes with
Does not calculate elec- no breaking or forming of
Relies on force-field with Can be used for mole- tronic properties bonds
embedded empirical cules as large as
parameters enzymes Requires experimental
data (or data from ab initio)
for parameters

Semiempirical Less demanding Requires experimental Medium-sized systems

(MOPAC, Gaussian) computationally than data (or data from ab initio) (hundreds of atoms)
ab initio methods for parameters
Uses quantum physics Systems involving elec-
Capable of calculating Less rigorous than ab tronic transitions
Uses experimentally transition states and initio methods
derived empirical param- excited states
eters

Uses approximation
extensively

ab initio (Gaussian, Useful for a broad Computationally intensive Small systems

GAMESS) range of systems (tens of atoms)

Uses quantum physics Does not depend on Systems involving elec-

experimental data tronic transitions
Mathematically
rigorousno empirical Capable of calculating Molecules or systems
parameters transition states and without available experi-
excited states mental data
(new chemistry)

Systems requiring rigorous

accuracy

272 Computation Concepts CambridgeSoft

Computational Methods Overview
Potential Energy Surfaces
A potential energy surface (PES) can describe:
A molecule or ensemble of molecules having
constant atom composition (ethane, for
example) or a system where a chemical reaction
occurs.
Relative energies for conformations (eclipsed
and staggered forms of ethane).
Potential energy surfaces can differentiate between:
Molecules having slightly different atomic
composition (ethane and chloroethane).
Molecules with identical atomic composition
but different bonding patterns, such as propy-
lene and cyclopropane
Excited states and ground states of the same
molecule.
Potential Energy Surfaces (PES)
The true representation of a models potential
energy surface is a multi-dimensional surface whose
dimensionality increases with the number of atom
coordinates. Since each atom has three independent
variables (x, y, z coordinates), visualizing a surface
for a many-atom model is impossible. However,
you can generalize this problem by examining any 2
independent variables, such as the x and y
coordinates of an atom, as shown below.
Figure G-22: Potential energy surfaces
Saddle Point
Potential Energy
Local Minimum
Global Minimum
Chem & BioOffice 2006 /Chem3D
The main areas of interest on a potential energy
surface are the extrema as indicated by the arrows,
are as follows:
Global minimumThe most stable confor-
mation appears at the extremum where the
energy is lowest. A molecule has only one
global minimum.
Local minimaAdditional low energy
extrema. Minima are regions of the PES where
a change in geometry in any direction yields a
higher energy geometry.
Saddle pointA stationary point between
two low energy extrema. A saddle point is
defined as a point on the potential energy
surface for which the slope (first derivative) of
the surface is zero.
NOTE: At the energy minimum, the energy is not zero; the
first derivative (gradient) of the energy with respect to
geometry is zero.
All the minima on a potential energy surface of a
molecule represent stable stationery points where
the forces on each atom sums to zero. The global
minimum represents the most stable conformation;
the local minima, less stable conformations; and the
saddle points represent transition conformations
between minima.
Single Point Energy Calculations
Single point energy calculations can be used to
calculate properties of specific geometry of a
model. The values of these properties depend on
where the model lies on the potential surface as
follows:
A single point energy calculation at a global
minimum provides information about the
model in its most stable conformation.
A single point calculation at a local minimum
provides information about the model in one
of many stable conformations.
Computation Concepts 273
Computational Methods Overview
 A single point calculation at a saddle point
provides information about the transition state
of the model.
A single point energy calculation at any other
Administrator
point on the potential energy surface provides
information about that particular geometry,
not a stable conformation or transition state.
Single point energy calculations can be performed
before or after optimizing geometry.
NOTE: Do not compare values from different methods.
Different methods rely on different assumptions about a given
molecule, and the energies differ by an arbitrary offset.
Geometry Optimization
Geometry optimization is used to locate a stable
conformation of a model, and should be done
before performing additional computations or
analyses of a model.
Locating global and local energy minima is typically
done by energy minimization. Locating a saddle
point is optimizing to a transition state.
The ability of a geometry optimization to converge
to a minimum depends on the starting geometry,
the potential energy function used, and the settings
for a minimum acceptable gradient between steps
(convergence criteria).
Geometry optimizations are iterative and begin at
some starting geometry as follows:
1. The single point energy calculation is
performed on the starting geometry.
2. The coordinates for some subset of atoms are
changed and another single point energy calcu-
lation is performed to determine the energy of
that new conformation.
274 Computation Concepts
3. The first or second derivative of the energy
(depending on the method) with respect to the
atomic coordinates determines how large and
in what direction the next increment of geom-
etry change should be.
4. The change is made.
5. Following the incremental change, the energy
and energy derivatives are again determined
and the process continues until convergence is
achieved, at which point the minimization
process terminates.
The following illustration shows some concepts of
minimization. For simplicity, this plot shows a
single independent variable plotted in two
dimensions.
The starting geometry of the model determines
which minimum is reached. For example, starting at
(b), minimization results in geometry (a), which is
the global minimum. Starting at (d) leads to
geometry (f), which is a local minimum.The
proximity to a minimum, but not a particular
minimum, can be controlled by specifying a
minimum gradient that should be reached.
Geometry (f), rather than geometry (e), can be
reached by decreasing the value of the gradient
where the calculation ends.
In theory, if a convergence criterion (energy
gradient) is too lax, a first-derivative minimization
can result in a geometry that is near a saddle point.
CambridgeSoft
Computational Methods Overview
This occurs because the value of the energy
gradient near a saddle point, as near a minimum, is
very small. For example, at point (c), the derivative
of the energy is 0, and as far as the minimizer is
concerned, point (c) is a minimum. First derivative
minimizers cannot, as a rule, cross saddle points to
reach another minimum.
NOTE: If the saddle point is the extremum of interest, it is
best to use a procedure that specifically locates a transition
state, such as the CS MOPAC Pro Optimize To Transition
State command.
You can take the following steps to ensure that a
minimization has not resulted in a saddle point.
The geometry can be altered slightly and
another minimization performed. The new
starting geometry might result in either (a), or
(f) in a case where the original one led to (c).
The Dihedral Driver can be employed to
search the conformational space of the model.
For more information, see Tutorial 5:
Mapping Conformations with the Dihedral
Driver on page 62.
A molecular dynamics simulation can be run,
which will allow small potential energy barriers
to be crossed. After completing the molecular
dynamics simulation, individual geometries can
then be minimized and analyzed. For more
information see Appendix H: MM2
You can calculate the following properties with the
computational methods available through Chem3D
using the PES:
Steric energy
Heat of formation
Dipole moment
Charge density
COSMO solvation in water
Electrostatic potential
Chem & BioOffice 2006 /Chem3D
Electron spin density
Hyperfine coupling constants
Atomic charges
Polarizability
Others, such as IR vibrational frequencies
Molecular Mechanics
Theory in Brief
Molecular mechanics computes the energy of a
molecule in terms of a set of classical potential
energy functions. The potential energy functions
and the parameters used for their evaluation are
known as a force-field.
Molecular mechanical methods are based on the
following principles:
Nuclei and electrons are lumped together and
treated as unified particles (atoms).
Atoms are typically treated as spheres.
Bonds are typically treated as springs.
Non-bonded interactions between atoms are
described using potential functions derived
from classical mechanics.
Individual potential functions are used to
describe the different interactions: bond
stretching, angle bending, torsion (bond
twisting), and through-space (non-bonded)
interactions.
Potential energy functions rely on empirically
derived parameters (force constants, equilib-
rium values) that describe the interactions
between sets of atoms.
The sum of the interactions determines the
conformation of the molecule.
Molecular mechanical energies have no meaning
as absolute quantities. They can only be used to
compare relative steric energy (strain) between
two or more conformations of the same mole-
cule.
Computation Concepts 275
Molecular Mechanics Theory in Brief
 The Force-Field
Since molecular mechanics treats bonds as springs,
the mathematics of spring deformation (Hookes
Administrator
Law) is used to describe the ability of bonds to
stretch, bend, and twist. Non-bonded atoms
(greater than two bonds apart) interact through van
der Waals attraction, steric repulsion, and
electrostatic attraction and repulsion. These
properties are easiest to describe mathematically
when atoms are considered as spheres of
characteristic radii.
The total potential energy, E, of a molecule can be
described by the following summation of
interactions:
E= Stretching Energy + Bending Energy +
Torsion Energy + Non-bonded Interaction
Energy
The first three terms are the so-called bonded
interactions. In general, these bonded interactions
can be viewed as a strain energy imposed by a
model moving from some ideal zero strain
conformation. The last term, which represents the
non-bonded interactions, includes the two
interactions shown below.
The total potential energy can be described by the
following relationships between atoms. The
numbers refer to the atom positions in Figure G-23.
1. Bond Stretching: (1-2) bond stretching
between directly bonded atoms
2. Angle Bending: (1-3) angle bending between
two atoms that are adjacent to a third atom.
3. Torsion Energy: (1-4) torsional angle rotation
between atoms that form a dihedral angle.
4. Repulsion for atoms that are too close and
attraction at long range from dispersion forces
(van der Waals interaction).
5. Interactions from charges, dipoles, quadru-
poles (electrostatic interactions).
276 Computation Concepts
The following illustration shows the major
interactions.
Figure G-23Potential Energy Interactions
Different kinds of force-fields have been
developed. Some include additional energy terms
that describe other kinds of deformations, such as
the coupling between bending and stretching in
adjacent bonds, in order to improve the accuracy of
the mechanical model.
The reliability of a molecular mechanical force-field
depends on the parameters and the potential energy
functions used to describe the total energy of a
model. Parameters must be optimized for a
particular set of potential energy functions, and
thus are not transferable to other force fields.
MM2
Chem3D uses a modified version of Allingers
MM2 force field. For additional MM2 references
see Appendix H: MM2
The principal additions to Allingers MM2 force
field are:
A charge-dipole interaction term
A quartic stretching term
Cutoffs for electrostatic and van der Waals
terms with 5th order polynomial switching
function
Automatic pi system calculations when neces-
sary
CambridgeSoft
Molecular Mechanics Theory in Brief
 Torsional and non-bonded constraints. This simple parabolic model fails when bonds are
stretched toward the point of dissociation. The
Chem3D stores the parameters for the potential
Morse function would be the best correction for
energy function in tables. These tables may be
this problem. However, the Morse Function leads
viewed and edited from the Parameter Tables option
to a large increase in computation time. As an
of the View menu.
alternative, cubic stretch and quartic stretch
Each parameter is classified by a Quality number. constants are added to provide a result approaching
This number indicates the reliability of the data. a Morse-function correction.
The quality ranges from 4, where the data is derived
completely from experimental data (or ab initio The cubic stretch term allows for an asymmetric
data), to 1, where the data is guessed by Chem3D. shape of the potential well, allowing these long
bonds to be handled. However, the cubic stretch
The parameter table, MM2 Constants, contains term is not sufficient to handle abnormally long
adjustable parameters that correct for failings of the bonds. A quartic stretch term is used to correct
potential functions in outlying situations. problems caused by these very long bonds. With the
addition of the cubic and quartic stretch term, the
equation for bond stretching becomes:
NOTE: Editing of MM2 parameters should only be done
with the greatest of caution by expert users. Within a force-
field equation, parameters operate interdependently; changing E
S=
t7
r1
e
.
tK
c[
9
h
(
r
4
o
2
)+
r
C(
r
r
)
S
o
B
3
+Q
on

(r
r
)
o
s
ds
4
]
S
one normally requires that others be changed to compensate
for its effects.
Both the cubic and quartic stretch constants are
Bond Stretching Energy defined in the MM2 Constants table.

To precisely reproduce the energies obtained with

.
2
E =
Stre 7
1
tch 9K
4(
rr
o) s Allingers force field: set the cubic and quartic
Bonds
stretching constant to 0 in the MM2 Constants
tables.
The bond stretching energy equation is based on
Hooke's law. The Ks parameter controls the
stiffness of the springs stretching (bond stretching Angle Bending Energy
force constant), while ro defines its equilibrium
length (the standard measurement used in building E=
Be0.
021
nd 9
K(
1

4
b o
2
)18
models). Unique Ks and ro parameters are assigned Angles

to each pair of bonded atoms based on their atom
types (C-C, C-H, O-C). The parameters are stored
in the Bond Stretching parameter table. The
constant, 71.94, is a conversion factor to obtain the
final units as kcal/mole.
The result of this equation is the energy
contribution associated with the deformation of the
bond from its equilibrium bond length.
The bending energy equation is also based on
Hookes law. The Kb parameter controls the
stiffness of the springs bending (angular force
constant), while 0 defines the equilibrium angle.
This equation estimates the energy associated with
deformation about the equilibrium bond angle. The
constant, 0.02191418, is a conversion factor to
obtain the final units as kcal/mole.

Chem & BioOffice 2006 /Chem3D Computation Concepts 277

Molecular Mechanics Theory in Brief
 Unique parameters for angle bending are assigned
to each bonded triplet of atoms based on their atom
types (C-C-C, C-O-C, C-C-H). For each triplet of
atoms, the equilibrium angle differs depending on
Administrator
There are three additional angle bending force
constants available in the MM2 Constants table.
These are the -CHR-Bending constants,
specifically for carbons with one or two attached

what other atoms the central atom is bonded to. For hydrogens.
each angle there are three possibilities: XR2, XRH
or XH2. For example, the XH2 parameter would be The -CHR- Bending Kb for 1-1-1 angles1 allows
used for a C-C-C angle in propane, because the more accurate force constants to be specified for
other atoms the central atom is bonded to are both Type 1 (-CHR-) and Type 2 (-CHR-) interactions.
hydrogens. For isobutane, the XRH parameter
The -CHR-Bending Kb for 1-1-1 angles in
would be used, and for 2,2-dimethylpropane, the
XR2 parameter would be used. 4-membered rings and the -CHR- Bending Kb for
22-22-22 angles in 3-membered rings require
The effect of the Kb and 0 parameters is to separate constants for accurate specification.
broaden or steepen the slope of the parabola. The
larger the value of Kb, the more energy is required Torsion Energy
to deform an angle from its equilibrium value.
Shallow potentials are achieved with Kb values less =
Tw
ist [
n
1+
co

s]
)
(n
2
V
Torsions
than 1.0.
This term accounts for the tendency for dihedral
A sextic term is added to increase the energy of angles (torsionals) to have an energy minimum
angles with large deformations from their ideal occurring at specific intervals of 360/n. In
value. The sextic bending constant, SF, is defined in Chem3D, n can equal 1, 2, or 3.
the MM2 Constants table. With the addition of the
sextic term, the equation for angle bending
T=
w
V
(
1
1
is
2
+
tc)
+
o
V
(
2

2
+
1
sc2
V
)
+
o(
3
1
2
+
sc
3)
o s
becomes: Torsion s
The Vn/2 parameter is the torsional force constant. It determines the amplitude of the curve. The n signifies its periodicity. n shifts the entire curve about the rotation angle axis. The parameters are determined through curve-fitting techniques. Unique parameters for
torsional rotation are assigned to each bonded quartet of atoms based on their atom types (C-C-C-C, C-O-C-N, H-C-C-H).

E
B=
0
e.
0
nd
21
K[
(
9)
o+1
(
S
4
F)
o]18
A
b
ngles

2 6 Chem3D provides three torsional parameters
tables:
Torsional parameters
NOTE: The default value of the sextic force constant 4-Membered ring torsions
is 0.00000007. To precisely reproduce the energies 3-Membered ring torsions.
obtained with Allingers force field, set the sextic
bending constant to 0 in the MM2 Constants tables. Non-Bonded Energy
The non-bonded energy represents the pairwise
There are three parameter tables for the angle
sum of the energies of all possible interacting
bending parameters:
non-bonded atoms within a predetermined
cut-off distance.
Angle Bending parameters 1. The numbers in the angle definitions
3-Membered Ring Angle Bending parameters refer to the Text column in the Atom
Types Table. 1 refers to C-alkane, and
4-Membered Ring Angle Bending parameters 22 refers to C-cyclopropane.

278 Computation Concepts CambridgeSoft

Molecular Mechanics Theory in Brief
The non-bonded energy accounts for repulsive
forces experienced between atoms at close
distances, and for the attractive forces felt at longer
distances. It also accounts for their rapid falloff as
the interacting atoms move farther apart by a few
Angstroms.
For certain interactions, values in the VDW
interactions parameter table are used instead of
those in the MM2 atom types table. These
situations include interactions where one of the
atoms is very electronegative relative to the other,
such as in the case of a water molecule.

van der Waals Energy Cutoff Parameters for van der Waals
Repulsive forces dominate when the distance Interactions
between interacting atoms becomes less than the The use of cutoff distances for van der Waals terms
sum of their contact radii. In Chem3D repulsion is greatly improves the computational speed for large
modeled by an equation which combines an molecules by eliminating long range, relatively
exponential repulsion with an attractive dispersion insignificant, interactions from the computation.
interaction (1/R6):
Chem3D uses a fifth-order polynomial switching
function so that the resulting force field maintains
Evan der W=
aals (290000
e12.5/R
-2.2R-6
5 ) second-order continuity. The cutoff is implemented
i j gradually, beginning at 90% of the specified cutoff
where distance. This distance is set in the MM2 Constants
rij table.
R= * *
Ri +R j
The van der Waals interactions fall off as 1/r6, and
The parameters include: can be cut off at much shorter distances, for
example 10. This cut off speeds the computations
Ri* and Rj*the van der Waals radii for the significantly, even for relatively small molecules.
atoms
Epsilon ()determines the depth of the NOTE: To precisely reproduce the energies obtained with
attractive potential energy well and how easy it Allingers force field: set the van der Waals cutoff constants
is to push atoms together to large values in the MM2 Constants table.
rijwhich is the actual distance between the
atoms Electrostatic Energy
At short distances the above equation favors
repulsive over dispersive interactions. To q
iq

j
E =
Electrostatic
compensate for this at short distances (R=3.311) i j D r
ij
this term is replaced with:
The electrostatic energy is a function of the charge
on the non-bonded atoms, q, their interatomic
E =
van d3
er.
3
1W

7
6
a6
aR
ls -2
distance, rij, and a molecular dielectric expression,
i j
D, that accounts for the attenuation of electrostatic
The R* and Epsilon parameters are stored in the interaction by the environment (solvent or the
MM2 Atom Types table. molecule itself).

Chem & BioOffice 2006 /Chem3D Computation Concepts 279

Molecular Mechanics Theory in Brief
 In Chem3D, the electrostatic energy is modeled
using atomic charges for charged molecules and
bond dipoles for neutral molecules.
There are three possible interactions accounted for
Administrator
Bond dipole parameters, , for each atom pair are
stored in the bond stretching parameter table. The
charge, q, is stored in the atom types table. The
molecular dielectric expression is set to a constant

by Chem3D: value between 1.0 and 5.0 in the MM2 Atom types
table.
charge/charge
dipole/dipole NOTE: Chem3D does not use a distance-dependent
dipole/charge. dielectric.

Each type of interaction uses a different form of the

electrostatic equation as shown below: Cutoff Parameters for Electrostatic Inter-
actions
charge/charge contribution
The use of cutoff distances for electrostatic terms,
iq
q as for van der Waals terms, greatly improves the

j
E=
332
.0538 2 computational speed for large molecules by
i j Dr
qij
eliminating long-range interactions from the
where the value 332.05382 converts the result to computation.
units of kcal/mole.
As in the van der Waals calculations, Chem3D uses
dipole/dipole contribution a fifth-order polynomial switching function to
maintain second-order continuity in the force-field.

The switching function is invoked as minimum
=
E
14
.338(
c8
o
3c
so
ics
o)
j s
ij
values for charge/charge, charge/dipole, or
i jD
r

ij
dipole/dipole interactions are reached. These
where the value 14.388 converts the result from cutoff values are located in the MM2 Constants
ergs/mole to kcal/mole, is the angle between the parameter table.
two dipoles i and j, i and j are the angles the
dipoles form with the vector, rij, connecting the two Since the charge-charge interaction energy between
at their midpoints, and D is the (effective) two point charges separated by a distance r is
proportional to 1/r, the charge-charge cutoff must
dielectric constant.
be rather large, typically 30 to 40, depending on
the size of the molecule. The charge-dipole, dipole-
dipole/charge contribution
dipole interactions fall off as 1/r2, 1/r3 and can be
q cutoff at much shorter distances, for example 25
=
E6
91
. 202
i j
(
coj)
s and 18 respectively. To precisely reproduce the
i j ij D
r Dq
energies obtained with Allingers force field: set the
where the value 69.120 converts the result to units cutoff constants to large values (99, for example) in
of kcal/mole. the MM2 Constants table.

280 Computation Concepts CambridgeSoft

Molecular Mechanics Theory in Brief
OOP Bending
Atoms that are arranged in a trigonal planar
fashion, as in sp2 hybridization, require an
additional term to account for out-of-plane (OOP)
bending. MM2 uses the following equation to
describe OOP bending:
( )
2 6
= K
[
b
o +
S(
F
o)]
O
oP
uft
lane
The form of the equation is the same as for angle
bending, however, the value used is angle of
deviation from coplanarity for an atom pair and
is set to zero. The illustration below shows the
determined for atom pairs DB.
Figure G-24: Determination of
D converge. This method is called the self-
x
C calculation.
A
y 4. A pi bond order is computed from the pi
B molecular orbitals.
The special force constants for each atom pair are
located in the Out of Plane bending parameters
table. The sextic correction is used as previously
described for Angle Bending. The sextic constant,
SF, is located in the MM2 Constants table.
Pi Bonds and Atoms with Pi Bonds
For models containing pi systems, MM2 performs a
Pariser-Parr-Pople pi orbital SCF computation for
each system. A pi system is defined as a sequence of
three or more atoms of types which appear in the
Conjugate Pi system Atoms table. Because of this
computation, MM2 may calculate bond orders
other than 1, 1.5, 2, and so on.
NOTE: The method used is that of D.H. Lo and M.A.
Whitehead, Can. J. Chem., 46, 2027(1968), with
heterocycle parameter according to G.D. Zeiss and M.A.
Whitehead, J. Chem. Soc. (A), 1727 (1971). The SCF
Chem & BioOffice 2006 /Chem3D
computation yields bond orders which are used to scale the
bond stretching force constants, standard bond lengths and
twofold torsional barriers.
The following is a step-wise overview of the
process:
1. A Fock matrix is generated based on the
favorability of electron sharing between pairs
of atoms in a pi system.
2. The pi molecular orbitals are computed from
the Fock matrix.
3. The pi molecular orbitals are used to compute
a new Fock matrix, then this new Fock matrix
is used to compute better pi molecular orbitals.
Step 2 and 3 are repeated until the computation
of the Fock matrix and the pi molecular orbitals
consistent field technique or a pi-SCF
5. The pi bond order is used to modify the bond
length(BLres) and force constant (Ksres) for
each bond in the pi system.
6. The modified values of Ksres and BLres are
used in the molecular mechanics portion of the
MM2 computation to further refine the mole-
cule.
Stretch-Bend Cross Terms
Stretch-bend cross terms are used when a coupling
occurs between bond stretching and angle bending.
For example, when an angle is compressed, the
MM2 force field uses the stretch-bend force
constants to lengthen the bonds from the central
atom in the angle to the other two atoms in the
angle.
1
=
K(
r
sbr
o)
(
)
o
Stre
/B 2
tc
enhd
Computation Concepts 281
Molecular Mechanics Theory in Brief
 The force constant (Ksb) differs for different atom Molecular Dynamics Simula-
combinations. tion
The seven different atom combinations where Molecular dynamics simulates molecular motion.
Administrator

force constants are available for describing the
situation follow:
X-B, C, N, O-Y
B-B, C, N, O-H
X-Al, S-Y
X-Al, S-H
X-Si, P-Y
X-Si, P-H
X-Ga, Ge, As, Se-Y, P-Y
where X and Y are any non-hydrogen atom.
User-Imposed Constraints
Additional terms are included in the force field
when constraints are applied to torsional angles and
non-bonded distances by the Optimal field in the
Measurements table. These terms use a harmonic
potential function, where the force constant has
been set to a large value (4 for torsional constraints
and 106 for non-bonded distances) in order to
enforce the constraint.
For torsional constraints the additional term and
force constant is described by:
This simulation is useful because motion is inherent
to all chemical processes: vibrations, like bond
stretching and angle bending, give rise to IR spectra;
chemical reactions, hormone-receptor binding, and
other complex processes are associated with many
kinds of intramolecular and intermolecular
motions.
The MM2 method of molecular dynamics
simulation uses Newtons equations of motion to
simulate the movement of atoms.
Conformational transitions and local vibrations are
the usual subjects of molecular dynamics studies.
Molecular dynamics alters the values of the
intramolecular degrees of freedom in a stepwise
fashion. The steps in a molecular dynamics
simulation represent the changes in atom position
over time, for a given amount of kinetic energy.
The Molecular Dynamics (MM2) command in the
Calculations menu can be used to compute a
molecular dynamics trajectory for a molecule or
fragment in Chem3D. A common use of molecular
dynamics is to explore the conformational space
accessible to a molecule, and to prepare sequences
of frames representing a molecule in motion. For
more information on Molecular Dynamics see
Chapter 8, MM2 and MM3 Computations on
page 157.

Molecular Dynamics Formulas

=
4
(
o)
2

Torsions
The molecular dynamics computation consists of a
For non-bonded distance constraints the additional series of steps that occur at a fixed interval, typically
term and force constant is: about 2.0 fs (femtoseconds, 1.0 x 10-15 seconds). The
Beeman algorithm for integrating the equations of
motion, with improved coefficients (B. R. Brooks)
=
16
0
(rr
o)2
is used to compute new positions and velocities of
Distance
each atom at each step.

282 Computation Concepts CambridgeSoft

Molecular Mechanics Theory in Brief
Each atom (i) is moved according to the following
formula:
xi = xi + vit + (5ai ai old) (t)2/8
Similarly, each atom is moved for y and z, where xi,
yi, and zi are the Cartesian coordinates of the atom,
vi is the velocity, ai is the acceleration, aiold is the
acceleration in the previous step, and t is the time
between the current step and the previous step. The
potential energy and derivatives of potential energy
(gi) are then computed with respect to the new
Cartesian coordinates.
New accelerations and velocities are computed at
each step according to the following formulas (mi is
the mass of the atom):
aiveryold = aiold
aiold = ai
ai = gi / mi
vi = vi + (3ai + 6aiold aiveryold) t / 8
Methods Available in CS
MOPAC
CS MOPAC methods include both open shell and
closed shell Hartree-Fock approximations.
Configuration interaction may be estimated by
either iterative self-consistent field (SCF) or multi-
electron (MECI) methods. For semi-empirical
methods, you may choose between five
Hamiltonian approximations.
RHF
The default Hartree-Fock method assumes that the
molecule is a closed shell and imposes spin
restrictions. The spin restrictions allow the Fock
matrix to be simplified. Since alpha (spin up) and
beta (spin down) electrons are always paired, the
basic RHF method is restricted to even electron
closed shell systems.
Chem & BioOffice 2006 /Chem3D
Further approximations are made to the RHF
method when an open shell system is presented.
This approximation has been termed the 1/2
electron approximation by Dewar. In this method,
unpaired electrons are treated as two 1/2 electrons
of equal charge and opposite spin. This allows the
computation to be performed as a closed shell. A
CI calculation is automatically invoked to correct
errors in energy values inherent to the 1/2 electron
approximation. For more information see
Configuration Interaction on page 283.
With the addition of the 1/2 electron
approximation, RHF methods can be run on any
starting configuration.
UHF
The UHF method treats alpha (spin up) and beta
(spin down) electrons separately, allowing them to
occupy different molecular orbitals and thus have
different orbital energies. For many open and
closed shell systems, this treatment of electrons
results in better estimates of the energy in systems
where energy levels are closely spaced, and where
bond breaking is occurring.
UHF can be run on both open and closed shell
systems. The major caveat to this method is the
time involved. Since alpha and beta electrons are
treated separately, twice as many integrals need to
be solved. As your models get large, the time for the
computation may make it a less satisfactory
method.
Configuration Interaction
The effects of electron-electron repulsion are
underestimated by SCF-RHF methods, which
results in the overestimation of energies.
SCF-RHF calculations use a single determinant that
includes only the electron configuration that
describes the occupied orbitals for most molecules
in their ground state. Further, each electron is
Computation Concepts 283
Molecular Mechanics Theory in Brief
 assumed to exist in the average field created by all
other electrons in the system, which tends to
overestimate the repulsion between electrons.
Repulsive interactions can be minimized by
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allowing the electrons to exist in more places (i.e.
more orbitals, specifically termed virtual orbitals).
The multi-electron configuration interaction
(MECI) method in MOPAC addresses this problem
by allowing multiple sets of electron assignments
(i.e., configurations) to be used in constructing the
molecular wave functions. Molecular wave
functions representing different configurations are
combined in a manner analogous to the LCAO
approach.
For a particular molecule, configuration interaction
uses these occupied orbitals as a reference electron
configuration then promotes the electrons to
unoccupied (virtual) orbitals. These new states,
Slater determinants or microstates in MOPAC, are
then linearly combined with the ground state
configuration. The linear combination of
microstates yields an improved electronic
configuration and hence a better representation of
the molecule.
Approximate Hamilto-
nians in MOPAC
There are five approximation methods available in
MOPAC:
MINDO/3
MNDO
AM1
PM3
Ultra MNDO-d
The potential energy functions modify the HF
equations by approximating and parameterizing
aspects of the Fock matrix.
284 Computation Concepts
The approximations in semiempirical MOPAC
methods play a role in the following areas of the
Fock operator:
The basis set used in constructing the 1-elec-
tron atom orbitals is a minimum basis set of
only the s and p Slater Type Orbitals (STOs)
for valence electrons.
The core electrons are not explicitly treated.
Instead they are added to the nucleus. The
nuclear charge is termed Neffective.
For example, Carbon as a nuclear charge of +6-
2 core electrons for a effective nuclear charge
of +4.
Many of the 2-electron Coulomb and
Exchange integrals are parameterized based on
element.
Choosing a Hamiltonian
Overall, these potential energy functions may be
viewed as a chronological progression of
improvements from the oldest method, MINDO/3
to the newest method, PM3. However, although the
improvements in each method were designed to
make global improvements, they have been found
to be limited in certain situations.
The two major questions to consider when
choosing a potential function are:
Is the method parameterized for the elements
in the model?
Does the approximation have limitations
which render it inappropriate for the model
being studied?
For more detailed information see the MOPAC
online manual.
MINDO/3 Applicability and Limitations
MINDO/3 (Modified Intermediate Neglect of
Diatomic Overlap revision 3) is the oldest method.
Using diatomic pairs, it is an INDO (Intermediate
CambridgeSoft
Approximate Hamiltonians in MOPAC
Neglect of Diatomic Orbitals) method, where the
degree of approximation is more severe than the
NDDO methods MNDO, PM3 and AM1. This
method is generally regarded to be of historical
interest only, although some sulfur compounds are
still more accurately analyzed using this method.
The following table shows the diatomic pairs that
are parameterized in MINDO/3. An x indicates
parameter availability for the pair indicated by the
row and column. Parameters of dubious quality are
indicated by (x).
Sterically crowded molecules are too unstable,
for example, neopentane.
Four-membered rings are too stable, for
example, cubane.
Hydrogen bonds are virtually non-existent, for
example, water dimer. Overly repulsive
nonbonding interactions between hydrogens
and other atoms are predicted. In particular,
simple H-bonds are generally not predicted to
exist using MNDO.
Hypervalent compounds are too unstable, for
example, sulfuric acid.
Activation barriers are generally too high.
Non-classical structures are predicted to be
unstable relative to the classical structure, for
example, ethyl radical.
Oxygenated substituents on aromatic rings are
out-of-plane, for example, nitrobenzene.

The peroxide bond is systematically too short

by about 0.17 .

The C-O-C angle in ethers is too large.

AM1 Applicability and Limitations

AM1 may be applied to the shaded elements in the
table below:
MNDO Applicability and Limitations
MNDO may be applied to the shaded elements in
the table below:

Important factors relevant to AM1 are:

AM1 is similar to MNDO; however, there are
changes in the core-core repulsion terms and
The following limitations apply to MNDO: reparameterization.

Chem & BioOffice 2006 /Chem3D Computation Concepts 285

Approximate Hamiltonians in MOPAC
 AM1 is a distinct improvement over MNDO, PM3 Applicability and Limitations
in that the overall accuracy is considerably
PM3 (Parameterized Model revision 3) may be
improved. Specific improvements are:
applied to the shaded elements in the following
The strength of the hydrogen bond in the table:
Administrator

water dimer is 5.5 kcal/mol, in accordance

with experiment.
Activation barriers for reaction are markedly
better than those of MNDO.
Hypervalent phosphorus compounds are
considerably improved relative to MNDO.
In general, errors in Hf obtained using
AM1 are about 40% less than those given by
MNDO. The following apply to PM3:
AM1 phosphorus has a spurious and very
PM3 is a reparameterization of AM1.
sharp potential barrier at 3.0. The effect of
this is to distort otherwise symmetric PM3 is a distinct improvement over AM1.
geometries and to introduce spurious Hypervalent compounds are predicted with
activation barriers. A good example is given considerably improved accuracy.
by P4O6, in which the nominally equivalent Overall errors in Hf are reduced by about
P-P bonds are predicted by AM1 to differ by
40% relative to AM1.
0.4. This is by far the most severe
limitation of AM1. Little information exists regarding the limita-
tions of PM3. This should be corrected natu-
Alkyl groups have a systematic error due to rally as results of PM3 calculations are
the heat of formation of the CH2 fragment reported.
being too negative by about 2 kcal/mol.
The barrier to rotation in formamide is practi-
Nitro compounds, although considerably cally non-existent. In part, this can be
improved, are still systematically too positive corrected by the use of the MMOK option.
in energy. The MMOK option is used by default in CS
The peroxide bond is still systematically too MOPAC. For more information about MMOK
short by about 0.17. see the online MOPAC Manual.

286 Computation Concepts CambridgeSoft

Approximate Hamiltonians in MOPAC

Ultra MNDO-d Applicability and Limi-
tations
MNDO-d (Modified Neglect of Differential
Overlap with d-Orbitals) may be applied to the
shaded elements in the table below:
MNDO-d is a reformulation of MNDO with an
extended basis set to include d-orbitals. This
method may be applied to the elements shaded in
Chem & BioOffice 2006 /Chem3D
the table below. Results obtained from MNDO-d
are generally superior to those obtained from
MNDO. The MNDO method should be used
where it is necessary to compare or repeat
calculations previously performed using MNDO.
The following types of calculations, as indicated by
MOPAC keywords, are incompatible with
MNDO-d:
COSMO (Conductor-like Screening Model)
solvation
POLAR (polarizability calculation)
GREENF (Greens Function)
TOM (Miertus-Scirocco-Tomasi self-consis-
tent reaction field model for solvation)
Computation Concepts 287
Approximate Hamiltonians in MOPAC
Administrator

288 Computation Concepts CambridgeSoft

Approximate Hamiltonians in MOPAC
Appendix H: MM2
Overview
This appendix contains miscellaneous information
about the MM2 parameters and force field.
MM2 Parameters
The original MM2 parameters include the elements
commonly used in organic compounds: carbon,
hydrogen, nitrogen, oxygen, sulfur and halogens.
The atom type numbers for these atom types range
from 1 to 50.
The MM2 parameters were derived from three
sources:
1. Most of the parameters were provided by
Dr. N. L. Allinger.
2. Several additional parameters were provided by
Dr. Jay Ponder, author of the TINKER
program.
3. Some commonly used parameters that were
not provided by Dr. Allinger or Dr. Ponder are
provided by CambridgeSoft Corporation.
However, most of these parameters are esti-
mates which are extrapolated from other
parameters.
The best source of information on the MM2
parameter set is Molecular Mechanics, Burkert, Ulrich
and Allinger, Norman L., ACS Monograph 177,
American Chemical Society, Washington, DC, 1982.
A method for developing reasonable guesses for
parameters for non-MM2 atom types can be found
in Development of an Internal Searching
Chem & BioOffice 2006 /Chem3DI
Algorithm for Parameterization of the MM2/MM3
Force Fields, Journal of Computational Chemistry,
Vol 12, No. 7, 844-849 (1991).
Other Parameters
The rest of the parameters consist of atom types
and elements in the periodic table which were not
included in the original MM2 force field, such as
metals. The rectification type of all the non-MM2
atom types in the Chem3D Parameter tables is
Hydrogen (H). The atom type numbers for these
atom types range from 111 to 851. The atom type
number for each of the non-MM2 atom types in the
MM2 Atom Type Parameters table is based on the
atomic number of the element and the number of
ligands in the geometry for that atom type. To
determine an atom type number, the atomic
number is multiplied by ten, and the number of
ligands is added.
For example, Co Octahedral has an atomic number
of 27 and six ligands. Therefore the atom type
number is 276.
In a case where different atom types of the same
element have the same number of ligands (Iridium
Tetrahedral, Atom Type # 774 and Iridium Square
Planar, Atom Type # 779), the number nine is used
for the second geometry.
Viewing Parameters
To view the parameters used by Chem3D to
perform MM2 computations:
From the View menu, point to Parameter
Tables, and choose a table.
The table you chose opens in a window.
MM2 289
Viewing Parameters
 Editing Parameters
You can edit the parameters that come with
Chem3D. Parameters that you add or change can be
Administrator
guesses or approximations that you make, or values
obtained from current literature.
In addition, there are several adjustable parameters
available in the MM2 Constants table.
NOTE: Before performing any editing we strongly
recommend that you create back-up copies of all the
parameter files located in the C3DTable directory.
To add a new parameter to the Torsional
parameters table:
1. From the View menu, point to Parameter
Tables and choose Torsional Parameters.
The Torsional Parameters table opens in a
window.
2. Enter the appropriate data in each field of the
parameter table. Be sure that the name for the
parameter is not duplicated elsewhere in the
table.
3. Close and Save the table.
The MM2 Force Field in
Chem3D
Chem3D includes a new implementation of
Norman L. Allingers MM2 force field based in
large measure on work done by Jay W. Ponder of
Washington University. This appendix does not
attempt to completely describe the MM2 force
field, but discusses the way in which the MM2 force
field is implemented and used in Chem3D and the
differences between this implementation, Allingers
MM2 program (QCPE 395), and Ponders
TINKER system (M.J. Dudek and J.W. Ponder, J.
Comput. Chem., 16, 791-816 (1995)).
290 MM2
For a review of MM2 and applications of molecular
mechanics methods in general, see Molecular
Mechanics, by U. Burkert and N. L. Allinger, ACS,
Washington, D.C., USA, 1982. Computational
Chemistry, by T. Clark, Wiley, N.Y., USA, 1985, also
contains an excellent description of molecular
mechanics.
For a description of the TINKER system and the
detailed rationale for Ponders additions to the
MM2 force field, visit the TINKER home page at
http://dasher.wustl.edu/tinker.
For a description and review of molecular
dynamics, see Dynamics of Proteins and Nucleic Acids, J.
Andrew McCammon and Stephen Harvey,
Cambridge University Press, Cambridge, UK, 1987.
Despite its focus on biopolymers, this book
contains a cogent description of molecular
dynamics and related methods, as well as
information applicable to other molecules.
Chem3D Changes to
Allingers Force Field
The Chem3D implementation of the Allinger Force
Field differs in these areas:
1. A charge-dipole interaction term
2. A quartic stretching term
3. Cutoffs for electrostatic and van der Waals
terms with a fifth-order polynomial switching
function
4. Automatic pi system calculation when neces-
sary
Charge-Dipole Interaction
Term
Allingers potential function includes one of two
possible electrostatic terms: one based on bond
dipoles, or one based on partial atomic charges. The
addition of a charge-dipole interaction term allows
for a combined approach, where partial charges are
CambridgeSoft
The MM2 Force Field in Chem3D
represented as bond dipoles, and charged groups,
such as ammonium or phosphate, are treated as
point charges.
Quartic Stretching Term
With the addition of a quartic bond stretching term,
troublesome negative bond stretching energies
which appear when long bonds are treated by
Allingers force field are eliminated.
The quartic bond stretching term is required
primarily for molecular dynamics; it has little or no
effect on low energy conformations.
To precisely reproduce energies obtained with
Allingers force field:
Set the quartic stretching constant in the MM2
Constants table window to zero.
The quartic term is eliminated.
Electrostatic and van der
Waals Cutoff Terms
The cutoffs for electrostatic and van der Waals
terms greatly improve the computation speed for
large molecules by eliminating long range
interactions from the computation.
To precisely reproduce energies obtained with
Allingers force field:
Set the cutoff distances to large values (greater
than the diameter of the model).
Every interaction is then computed.
The cutoff is implemented gradually, beginning at
50% of the specified cutoff distance for charge and
charge-dipole interactions, 75% for dipole-dipole
interactions, and 90% for van der Waals
interactions. Chem3D uses a fifth-order polynomial
switching function so that the resulting force field is
second-order continuous.
Chem & BioOffice 2006 /Chem3DI
Because the charge-charge interaction energy
between two point charges separated by a distance
r is proportional to 1/r, the charge-charge cutoff
must be rather large, typically 30 or 40. The
charge-dipole, dipole-dipole, and van der Waals
energies, which fall off as 1/r2, 1/r3, and 1/r6,
respectively, can be cut off at much shorter
distances, for example, 25, 18, and 10,
respectively. Fortunately, since the van der Waals
interactions are by far the most numerous, this
cutoff speeds the computation significantly, even
for relatively small molecules.
Pi Orbital SCF Computation
Chem3D determines whether the model contains
any pi systems, and performs a Pariser-Parr-Pople
pi orbital SCF computation for each system. A pi
system is defined as a sequence of three or more
atoms of types which appear in the Pi Atoms table
window (PIATOMS.xml).
The method used is that of D.H. Lo and M.A.
Whitehead, Can. J. Chem., 46, 2027 (1968), with
heterocycle parameters according to G.D. Zeiss and
M.A. Whitehead, J. Chem. Soc. (A), 1727 (1971). The
SCF computation yields bond orders which are
used to scale the bond stretching force constants,
standard bond lengths, and twofold torsional
barriers.
A step-wise overview of the process used to do pi
system calculations is as follows:
5. A matrix called the Fock matrix is initialized to
represent the favorability of sharing electrons
between pairs of atoms in a pi system.
6. The pi molecular orbitals are computed from
the Fock matrix.
7. The pi molecular orbitals are used to compute
a new Fock matrix, then this new Fock matrix
is used to compute better pi molecular orbitals.
MM2 291
Chem3D Changes to Allingers Force Field
 8. step 6 and Step 7 are repeated until the compu-
tation of Fock matrix and the pi molecular
orbitals converge. This method is called the
self-consistent field technique or a pi-SCF
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calculation.
9. A pi bond order is computed from the pi
molecular orbitals.
10.The pi bond order is used to modify the bond
length (BLres) and force constant (KSres) for
each sigma bond in the pi system.
292 MM2
11.The values of KSres and BLres are used in the
molecular mechanics portion of the MM2
computation to further refine the molecule.
To examine the computed bond orders after an
MM2 computation:
1. In the Pop-up Information control panel,
select Bond Order.
2. Position the pointer over a bond.
The information box contains the newly computed
bond orders for any bonds that are in a pi system.
CambridgeSoft
Chem3D Changes to Allingers Force Field
Appendix I: MOPAC
Overview
The appendix contains miscellaneous information
about MOPAC.
You can find additional information about MOPAC
by visiting the MOPAC home page at:
http://www.cachesoftware.com/mopac/index.shtml
MOPAC background
Potential energy functions
Adding parameters to MOPAC
MOPAC Keywords used in CS MOPAC
Electronic configuration (includes using
MOPAC sparkles)
MOPAC Background
MOPAC was created by Dr. James Stewart at the
University of Texas in the 1980s. It implements
semi-empirical methodologies for analyzing
molecular models. (MOPAC stands for Molecular
Orbital PACkage.) Due to its complexity and
command line user interface, its use was limited
until the mid 1990s.
Since version 3.5 (1996), Chem3D has provided an
easy-to-use GUI interface for MOPAC that makes
it accessible to the novice molecular modeller, as
well as providing greater usability for the veteran
modeller. We are currently supporting MOPAC
2002.
MOPAC 2002 is copyrighted by Fujitsu, Ltd.CS
MOPAC is the licensed version that runs under
Chem3D.
Chem & BioOffice 2006 /Chem3D
Potential Functions
Parameters
MOPAC provides five potential energy functions:
MINDO/3, MNDO, PM3, AM1, and MNDO-d.
All are SCF (Self Consistent Field) methods. Each
function represents an approximation in the
mathematics for solving the Electronic Schrdinger
equation for a molecule.
Historically, these approximations were made to
allow ab initio calculations to be within the reach of
available computer technology. Currently, ab initio
methods for small molecules are within the reach of
desktop computers. Larger molecules, however, are
still more efficiently modeled on the desktop using
semi-empirical or molecular mechanics
methodologies.
To understand the place that the potential energy
functions in MOPAC take in the semi-empirical
arena, here is a brief chronology of the
approximations that comprise the semi-empirical
methods. The first approximation was termed
CNDO for Complete Neglect of Differential
Overlap. The next approximation was termed
INDO for Intermediate Neglect of Differential
Overlap, Next followed MINDO/3, which stands
for Modified Intermediate Neglect of Differential
Overlap. Next was MNDO, which is short for
Modified Neglect of Differential Overlap which
corrected MINDO/3 for various organic
molecules made up from elements in rows 1 and 2
of the periodic table. AM1 improved upon MNDO
markedly. Finally the most recent, PM3 is a
reparameterization of AM1. The approximations in
PM3 are the same as AM1.
MOPAC 293
Potential Functions Parameters
 This sequence of potential energy functions
represents a series of improvements to support the
initial assumption that complete neglect of diatomic
orbitals would yield useful data when molecules
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Automatic Keywords
The following contains keywords automatically sent
to MOPAC and some additional keywords you can
use to affect convergence.

proved too resource intensive for ab initio methods.

Adding Parameters to Keyword Description

MOPAC
Parameters are in constant development for use
with PM3 and AM1 potential functions. If you find
that the standard set of parameters that comes with
CS MOPAC does not cover an element that you
need, for example Cu, you can search the literature
for the necessary parameter and add it at run time
when performing a MOPAC job. This flexibility
greatly enhances the usefulness of MOPAC.
You can add parameters at run time using the
keyword EXTERNAL=name, where name is the
name of the file (and its full path) containing the
additional parameters.
A description of the required format for this file can
be found in Figure 3.4, page 43 of the MOPAC
2002 V.1.3 manual included on the CD-ROM.
EF Automatically sent to MOPAC to
specify the use of the Eigenvector
Following (EF) minimizer.
BFGS Prevents the automatic insertion
of EF and restores the BFGS mini-
mizer.
GEO-OK Automatically sent to MOPAC to
override checking of the Z-matrix.
MMOK Automatically sent to MOPAC to
specify Molecular Mechanics
correction for amide bonds. Use
the additional keyword NOMM to
turn this keyword off.

Using Keywords RMAX=n.nn The calculated/predicted energy

Selecting parameters for a MOPAC approximation
automatically inserts keywords in a window on the
General tab of the MOPAC Interface. You can edit
these keywords or use additional keywords to
perform other calculations or save information to
the *.out file.
CAUTION
Use the automatic keywords unless you are an advanced
MOPAC user. Changing the keywords may give
unreliable results.
For a complete list of keywords see the MOPAC
online manual.
change must be less than n.nn.
The default is 4.0.
RMIN=n.nn The calculated/predicted energy
change must be more than n.n.
The default value is 0.000.
PRECISE Runs the SCF calculations using a
higher precision so that values do
not fluctuate from run to run.
LET Overrides safety checks to make
the job run faster.

294 MOPAC CambridgeSoft

Adding Parameters to MOPAC
Keyword Description Keyword Data

RECALC=5 Use this keyword if the optimiza- BONDS Bond Order Matrix*
tion has trouble converging to a
transition state. The following table contains the keywords that
invoke additional computations. Terms marked
For descriptions of error messages reported by with an asterisk (*) appear in the *.out file.
MOPAC see Chapter 11, pages 325331, in the
MOPAC manual. Keyword Description

Additional Keywords CIS UV absorption energies*

Keywords that output the details of a particular NOTE: Performs C.I. using only
computation are shown in the following table. the first excited Singlet states and
Terms marked with an asterisk (*) appear in the does not include the ground state.
*.out file. Use MECI to print out energy
information in the *.out file.

Keyword Data
FORCE Vibrational Analysis*
ENPART All Energy Components* NOTE: Useful for determining
zero point energies and normal
FORCE Zero Point Energy vibrational modes. Use DFORCE
to print out vibration information
in *.out file.
FORCE Vibrational Frequencies*

MECI
NOMM No MM correction
Microstates used in MECI calcula-
tion* NOTE: By default, MOPAC
performs a molecular mechanics
none HOMO/LUMO Energies* (MM) correction for CONH
bonds.
none Ionization Potential*
PI Resolve density matrix*
*
none Symmetry
NOTE: Resolve density matrix
into sigma and pi bonds.
LOCALIZE Print localized orbitals

VECTORS Print final eigenvectors

(molecular orbital coefficients)

Chem & BioOffice 2006 /Chem3D MOPAC 295

Using Keywords
 To specify the charge in MOPAC:
Keyword Description
1. From the Calculations menu, point to
MOPAC Interface and choose a computation.
PRECISE Increase SCF criteria
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The MOPAC Interface dialog box appears.

NOTE: Increases criteria by 100
2. On the General tab, in the Keywords box, type
times. This is useful for increasing
the keyword CHARGE=n, where n is a positive
the precision of energies reported.
or negative integer (-2, -1, +1, +2).

T = n [M,H,D] Increase the total CPU time Different combinations of spin-up (alpha electrons)
allowed for the job. and spin-down (beta electrons) lead to various
electronic energies. These combinations are
NOTE: The default is 1h (1 hour) specified as the Spin Multiplicity of the molecule.
or 3600 seconds. The following table shows the relation between
total spin S, spin multiplicity, and the number of
unpaired electrons.
Specifying the Electronic
Configuration
Spin Keyword (# unpaired
MOPAC must have the net charge of the molecule electrons)
in order to determine whether the molecule is open
or closed shell. If a molecule has a net charge, be 0 SINGLET 0 unpaired
sure you have either specified a charged atom type
or added the charge.
1/2 DOUBLET 1 unpaired
CS MOPAC 2002 supports sparkles pure ionic
charges that can be used as counter-ions or to form 1 TRIPLET 2 unpaired
dipoles that mimic solvation effects.
1 1/2 QUARTET 3 unpaired
You can assign a charge using the Text Building tool
or by specifying it in MOPAC:
2 QUINTET 4 unpaired
To add the charge to the model:
2 1/2 SEXTET 5 unpaired
1. Click the Text Building tool.
To determine the appropriate spin multiplicity,
2. Click an atom in your model. consider whether:
3. Type a charge symbol. The molecule has an even or an odd number of
electrons.
For example, click a carbon and type + in a
text box to make it a carbocation.The charge is The molecule is in its ground state or an excited
automatically sent to MOPAC when you do a state.
calculation. To use RHF or UHF methods.

296 MOPAC CambridgeSoft

Specifying the Electronic Configuration
The following table shows some common
UHF (Open Shell)
permutations of these three factors:
Electronic State Spin State
RHF (Closed Shell)
Ground SINGLET
Electronic Spin Keywords to
State State Usea DOUBLET

OPEN(n1,n2)
TRIPLET

ROOT=n

C.I.=n
QUARTET
QUINTET

Ground SINGLET SEXTET

DOUBLET 1,2 Even-Electron Systems

TRIPLET 2,2
If a molecule has an even number of electrons, the
QUARTET 3,3 ground state and excited state configurations can be
QUINTET 4,4 Singlet, Triplet, or Quintet (not likely). Normally
the ground state is Singlet, but for some molecules,
SEXTET 5,5 symmetry considerations indicate a Triplet is the
1st Excited SINGLET 2 most stable ground state.
DOUBLET 2 2
Ground State, RHF
TRIPLET 2 3
The Ground State, RHF configuration is as follows:
QUARTET 2 4
Singlet ground statethe most common
QUINTET 2 5 configuration for a neutral, even electron stable
SEXTET 2 6 organic compound. No additional keywords
are necessary.
2nd Excited SINGLET 3
Triplet ground stateUse the following
DOUBLET 3 3 keyword combination: TRIPLET OPEN(2,2)
TRIPLET 3 3 Quintet ground stateUse the following
QUARTET 3 4 keyword combination: QUINTET OPEN(4,4)
QUINTET 3 5
NOTE: The OPEN keyword is normally necessary only
SEXTET 3 6 when the molecule has a high degree of symmetry, such as
a.
Do not use OPEN(n1,n2) for ground- molecular oxygen. The OPEN keyword increases the active
state systems except for high symmetry space available to the SCF calculation by including virtual
systems with open shells orbitals. This is necessary for attaining the higher multiplicity
configurations for even shell system. The OPEN keyword
also invokes the RHF computation using the 1/2 electron
approximation method and a C.I. calculation to correct the

Chem & BioOffice 2006 /Chem3D MOPAC 297

Specifying the Electronic Configuration
 final RHF energies. To see the states used in a C.I.
calculation, type MECI as an additional keyword. The
information is printed at the bottom of the *.out file.
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Ground State, UHF
For UHF computations, all unpaired electrons are
forced to be spin up (alpha).
Singlet ground statethe most common
configuration for a neutral, even electron,
stable organic compound. No additional
keywords are necessary.
UHF will likely converge to the RHF solution
for Singlet ground states.
Triplet or Quintet ground state: Use the
keyword TRIPLET or QUINTET.
NOTE: When a higher multiplicity is used, the UHF
solution yields different energies due to separate treatment of
alpha electrons.
Excited State, RHF
First Excited State: The first excited state is actually
the second lowest state (the root=2) for a given spin
system (Singlet, Triplet, Quintet).
To request the first excited state, use the following
sets of keywords:
First excited Singlet: ROOT=2 OPEN(2,2) SINGLET
(or specify the single keyword EXCITED)
First excited triplet: ROOT=2 OPEN (2,2)
TRIPLET C.I.=n, where n=3 is the simplest case.
First excited quintet: ROOT=2 OPEN (4,4)
QUINTET C.I.=n, where n=5 is the simplest case.
Second Excited State: The second excited state is
actually the third lowest state (the root=3) for a
given system (Singlet, Triplet, Quintet). To request
the second excited state use the following set of
keywords:
298 MOPAC
Second excited Singlet: OPEN(2,2) ROOT=3
SINGLET
Second excited triplet: OPEN(2,2) ROOT=3
TRIPLET C.I.=n, where n=3 is the simplest case.
Second excited quintet: OPEN(4,4) ROOT=3
QUINTET C.I.=n, where n=5 is the simplest case.
Excited State, UHF
Only the ground state of a given multiplicity can be
calculated using UHF.
Odd-Electron Systems
Often, anions, cations, or radicals are odd-electron
systems. Normally, the ground states and excited
state configuration can be doublet, quartet or
sextet.
Ground State, RHF
Doublet ground state: This is the most common
configuration. No additional keywords are
necessary.
Quartet: Use the following keyword combination:
QUARTET OPEN(3,3)
Sextet ground state: Use the following keyword
combination: SEXTET OPEN(5,5)
Ground State, UHF
For UHF computations all unpaired electrons are
forced to be spin up (alpha).
Doublet ground state: This is the most common
configuration for a odd electron molecule. No
additional keywords are necessary.
UHF will yield energies different from those
obtained by the RHF method.
Quartet and Sextet ground state: Use the keyword
QUARTET or SEXTET.
CambridgeSoft
Specifying the Electronic Configuration
Excited State, RHF Sparkles
First Excited State: The first excited state is actually Sparkles are used to represent pure ionic charges.
the second lowest state (the root=2) for a given spin They are roughly equivalent to the following
system (Doublet, Quartet, Sextet). To request the chemical entities:
first excited state use the following sets of
keywords. Chemical Equivalent to...
First excited doublet: ROOT=2 DOUBLET C.I.=n, symbol
where n=2 is the simplest case.
+ tetramethyl ammonium, potassium
First excited quartet: ROOT=2 QUARTET C.I.=n,
or cesium cation + electron
where n=4 is the simplest case.
First excited sextet: ROOT=2 SEXTET C.I.=n, where ++ barium di-cation + 2 electrons
n=5 is the simplest case.
Second Excited State: The second excited state is _ borohydride halogen, or nitrate
actually the third lowest state (the root=3) for a anion minus electron
given system (Singlet, Triplet, Quintet). To request
the second excited state use the following set of = sulfate, oxalate di-anion minus 2
keywords: electrons
Second excited doublet: ROOT=3 DOUBLET C.I.=n,
where n=3 is the simplest case. Sparkles are represented in Chem3D by adding a
charged dummy atom to the model.
Second excited quartet: ROOT=3 QUARTET C.I.=n,
where n=4 is the simplest case.
TIP: Dummy atoms are created with the uncoordinated
Second excited sextet: ROOT=3 SEXTET C.I.=n, bond tool. You must add the charge after creating the dummy.
where n=5 is the simplest case.
The output file shows the chemical symbol as XX.
NOTE: If you get an error indicating the active space is not
spanned, use C.I.> n for the simplest case to increase the
number of orbitals available in the active space. To see the
states used in a C.I. calculation, type MECI as an
additional keyword. The information is printed at the bottom
of the *.out file.

Excited State, UHF

Only the ground state of a given multiplicity can be
calculated using UHF.

Chem & BioOffice 2006 /Chem3D MOPAC 299

Specifying the Electronic Configuration
Administrator

300 MOPAC CambridgeSoft

Specifying the Electronic Configuration
Section II ChemFinder: Introduction
About ChemFinder Whats New in Chem-
ChemFinder is a database management system for
Finder 10?
anyone who works with chemical information. It ChemFinder 10 includes the following new
provides a place to store chemical structures, features:
physical properties, notes, tables of data, and charts GUI Improvements
based on that data. It takes the place of that box of Tabbed Windows
index cards youve been using to jot notes about
Find and Replace
interesting molecules and reactions, but does it
much better! With ChemFinder, you can search Struct=Name from the Context Menu
through data efficiently and quickly, and you can Subform Generator
organize the data instantly. BioViz improvements
Statistical Analysis
ChemFinder is integrated with the following
Details Window
CambridgeSoft products:
Filter Slider Adjustment
ChemDraw Histogram Improvements

Chem3D Better Selecting And Mouse-overs

More plotting flexibility
ChemDraw/Excel
Removal of Empty Points
Chem & BioOffice 2006

Chem & BioOffice 2006 /ChemFinder Introduction 301

About ChemFinder
Administrator

302 Introduction CambridgeSoft

Whats New in ChemFinder 10?
Chapter 13: ChemFinder Basics
Overview
ChemFinder is a database management system that
allows storage, retrieval, and searching of molecular
structures, text, and numerical data.
You create structures in ChemDraw or with the
built-in ChemDraw ActiveX control to store in
your ChemFinder database, and add related
numerical or textual data and comments. You can
use the Chem3D ActiveX control to view the
structures.
Use ChemFinder as a reference, together with one
of the CD-ROM databases provided. Use it as your
corporate database system, available to anyone on
your network. Use it as a registration system or
front-end search engine for your big mainframe
database. Use it as a custom viewer for your Oracle
data, with or without chemical structures. Use it to
keep track of what you find in your routine
literature scans. Use it to make a database to keep
the figures that go in your thesis or your next paper.
This chapter describes The ChemFinder GUI,
including each of The ChemFinder Toolbars, and
The Status Bar. Following that is a description of
Chem & BioOffice 2006 /ChemFinder
GUI Improvements in ChemFinder 10, a brief
description of opening a database, using a database,
and finally a discussion of the ChemFinder database
model.
The general steps for using ChemFinder are as
follows:
Create a form.
Create or open a database and link it to the
form.
Add or manipulate data.
Perform a search.
These steps are described in the Tutorials, and in
the detailed reference material in the manual.
The ChemFinder GUI
The ChemFinder GUI consists of menus, toolbars
and the form window. The central part of the form
window contains the work space where you create
and view structures and data. The toolbars contain
icons that change the way the pointer behaves or
that perform actions corresponding to menu
commands.
ChemFinder Basics 303
The ChemFinder GUI
 The components of the ChemFinder GUI are
shown below.
.

Main toolbar Title bar Record toolbar Search toolbar

Administrator

Menu
bar

Main form
S
Form
toolbar
O
Structure
window Framed
(shows BioViz data box
moused point)

Structure
box
(shows current
record) BioViz
Explorer window
window
(Database
panel visible)

Favorites tab
Database tab
Queries tab Details &
Filters tab Filter windows
New record
Details tab
indicator
Status Total
bar db size
Details for moused-over point Read-only Query Current Current
(in Structure window) indicator indicator record list size

The components of the ChemFinder GUI are

described below. Screen Description
Element
Screen Description
Element Current list size Displays the number of records
through which you are
browsing. Might be less than the
BioViz window Displays plotted data from
total database size if you have
ChemFinder databases.
recently performed a search.

304 ChemFinder Basics CambridgeSoft

The ChemFinder GUI
Screen Description
Element
Current record Displays the position within the
current hit list of the record you
are viewing.
Details window Displays details of selected (or
moused-over) point when a plot
window is displayed.
Explorer Has three tabs to display:
window
1. The database field hierarchy.
2. The query list that will be
saved with the form.
3. A Favorites list of file
paths.
Form toolbar Contains icons representing the
form-creation tools available in
ChemFinder. Click a tool icon
to select it. The selected tool
determines what action is
carried out when you drag in a
form window.
Framed data Displays data in a Data Box
box surrounded by a labeled frame.
Main form Displays data contained in one
record of the database.
Main toolbar Contains icons representing
general-purpose menu
commands such as copying,
saving, and printing. Click an
icon to perform the command.
Chem & BioOffice 2006 /ChemFinder
Screen Description
Element
Menu bar Contains all the commands
specific to the ChemFinder
application for manipulating
forms, tables, databases, and
their contents.
New record Displays ADD if you are in the
indicator process of adding a new record
that had not yet been
committed to the database.
Query indicator Displays QRY if you are in the
process of entering a search
query.
Read-only indi- Displays READ if the data-
cator base is read-only and cannot be
modified.
Record toolbar Contains icons for commands
in the Record menu. Click an
icon to perform the command.
Search toolbar Contains icons for commands
in the Search menu. Click an
icon to perform the command.
Status bar Displays information about the
current state of the ChemFinder
application.
Structure box Displays the chemical structure
of the current record.
ChemFinder Basics 305
The ChemFinder GUI
 Main Toolbar
Screen Description
Element The Main Toolbar contains the standard tools you
find in most modern applications: New, Open, and
Save; Cut, Copy, and Paste; Undo and Redo; Print
Administrator

Structure Displays structure of selected

and Help.
window (or moused-over) point when a
plot window is displayed.
New Save Layout
Form Form Paste Redo Print Help Mode
Table header Displays the name of a field.
Double-clicking on a table
header sorts on that field.

Title bar Contains the name of the appli-

Open Cut Copy Undo Switch to Database
cation or document as a Form Table Wizard
window title. Also, the title bar
can be dragged to move a In addition, it has three ChemFinder tools:
window. Layout Modeswitches between Layout
(Edit) Mode and View Mode. When the Layout
Total database Displays the total number of Mode button is depressed, the Form
size records in the current table. Toolbar is visible and an alignment grid
appear on the form.
The ChemFinder Toolbars Switch to Tableswitches between Form
View and Table View.
ChemFinder uses several toolbars to create and
manipulate the ChemFinder form and the database Database Wizardactivates the Database
records it displays. Toolbars are normally docked at Wizard to connect a database to a form.
the top and left side of the GUI, but they can be
Form Toolbar
torn off and placed anywhere on the screen for
your convenience. Which toolbars are visible is set The Form Toolbar contains the tools you need to
in the Toolbars submenu of the View menu. You create objects on a form. Use it to create a new
can also use the Toolbars submenu to customize the form, or to add an object to an existing form.
toolbars. A description of toolbar customization is
beyond the scope of this manual. (See Microsoft Selection
help for information on customizing toolbars.) tool Frame Text Button Subform

To select which toolbars are visible, choose Toolbars

from the View menu, and check or uncheck the
appropriate boxes.

Data box Framed box Picture Boolean Grid

The tools are described in detail in Chapter 15,

Creating and Editing Forms on page 335.

306 ChemFinder Basics CambridgeSoft

The ChemFinder GUI
Search Toolbar (not available) when you are not working in a data
or text field. Some options will be grayed out if the
The Search Toolbar contains the tools you need to
field type does not permit them.
query the database and work with the hitlists that
the query produces. Font Bold Italic Underline Color Alignment

Enter Retrieve Previous Restore Find

Query All Query List List

Point Size Subscript Superscript Bullets

The Status Bar

While you move among records, counters in the
Find Find Current Save List Restore Over
lower right corner of the ChemFinder window
Molecule Previous Current
List List change to indicate the current record, the current
list size, and the total size of the database. The lower
Record Toolbar left corner of the window displays help for menu
items and other information.
The Record Toolbar contains the tools you need to
browse a database or hitlist. It also has tools for When you first open a form, the current list size
adding, deleting, and changing records. equals the total database size. The total database
size changes only when you add or delete records.
First Go to Last Undo Omit If you search to find a subset of the entries in the
Record Record Record Changes Record database, then the current list size changes to
indicate the number of hits in the search.
To the left of these counters are three other
indicators that show the general status of the
database. The first displays the word READ when
Previous Next Add a Commit Delete you are using a read-only database, such as one that
Record Record Record Changes Record is on a CD-ROM, a read only form file, or if you
have selected Open as read only on the Open
Text Toolbar File dialog box.
The Text Toolbar contains standard text formatting
tools that you can use when entering or editing
information in data and text fields. It is grayed out The second indicator displays the word ADD
when you are entering a new record.

The third displays QRY when you are entering a

query.

To hide or show the Status Bar:

Chem & BioOffice 2006 /ChemFinder ChemFinder Basics 307

The ChemFinder GUI
 From the View menu, deselect or choose Status A dialog box appears where you can enter text
Bar. and set the search parameters.

Figure 9: Find and replace

GUI Improvements in
Administrator

ChemFinder 10
Create tabbed windows to save space. Drag a
dockable window over an existing docked window
until you see the outline of a tab at the bottom.

Figure 8: Creating tabbed windows

1. Drag

Struct=Name from the

Context Menu
The structure Copy As command has two new
options. In addition to SMILES, you may now copy
as Name or InChI1. The Name command
2. Tab outline appears invokes the CS Struct=Name utility.
Struct=Name generates systematic chemical
names with proper CIP stereochemistry
3. Final result descriptors.

The InChI command invokes the CambridgeSoft

Find and Replace
You can find-and-replace strings in both text and
memo fields, either across all records in the current
recordset, or in the current record. In either case,
find-and-replace is limited to the selected field.
To find text:
1. Right-click in a text or memo field.
2. Select Find or Replace.
implementation of the IUPAC InChI algorithm.
The InChI algorithm takes a chemical structure
and converts it into an alphanumeric string. A key
aspect of the InChI algorithm is that the
generated string is independent of the way that a
structure is drawn, producing a consistent
alphanumeric representation of different structural
representations of the same structural formula
(canonicalization).
Both commands place the data on the Clipboard,
allowing it to be copied into other applications.
1. InChI is a trademark of the Interna-
tional Union of Pure and Applied
Chemistry. InChI Material in Chem-
Draw is IUPAC 2005.

308 ChemFinder Basics CambridgeSoft

GUI Improvements in ChemFinder 10
To copy a structure as a name or InChI string:
1. Click in the Structure window to select it.
2. Right-click, and choose Name or InChI from
the Copy As submenu.
Figure 10: Copy As Name
3. Paste the data into the other application using
Ctrl+V or the Paste command on the Edit
menu.
Opening ChemFinder
To open the ChemFinder application:
Click Start, point to Programs (in Windows XP
All Programs), point to Chem & BioOffice 2006,
and select ChemFinder.
ChemFinder opens and the ChemFinder
dialog box appears.
The ChemFinder dialog box enables you to
perform the following tasks.
Blank FormOpen a blank form to create
your own form.
Database ConnectionAllows you to open
a blank form and connect it to a database. You
can create the form manually or choose to
Chem & BioOffice 2006 /ChemFinder
create it automatically. For more information,
see Connecting a Database to a Form on
page 317.
The Database WizardGuides you through
the process of setting up a form with a database
connection.
Existing tabAllows you to open an existing
form in your file system.
Recent tabAllows you to open a form on
the recently-used file list.
You can choose whether or not the ChemFinder
dialog box is displayed when ChemFinder opens by
doing the following:
1. From the File menu, choose Preferences.
2. In the Preferences dialog box, click the
General tab.
3. Select or deselect Show Startup Dialog.
If you choose to hide the ChemFinder dialog
box, ChemFinder will open a new blank form
by default when you open the application.
To open the ChemFinder dialog box when the
preference is set to hide:
From the File menu, choose New.
Using ChemFinder with
Databases
ChemFinder comes with the Microsoft Jet database
engine. ChemFinder maintains a table of chemical
informationstructure, formula, and molecular
weightand relies Jet to create a database system
for managing the rest of the data. If you have MS
Access installed on your computer, you can use it to
work with the relational part of the database (.mdb
file).
With ChemFinder 10 Ultra, you can use the
ChemFinder/Oracle Cartridge to manage all
chemical and relational data directly in Oracle,
without using DAO or ODBC.
ChemFinder Basics 309
Opening ChemFinder
 The Database Model A record is a set of related data items, one per field,
representing a single entry in the database.
A database is a collection of information. In
ChemFinder the information is organized into
increasing levels of complexity. At the simplest level
Administrator

is the data item itself, for example the, molecular

weight of furan.

A collection of records is a table. A table is defined

by a set of fields, generally set up once and rarely
modified, and a set of records which grows as
entries are added.
The data item is stored within a field, in this
example MolWeight. A field contains
information of a specific type. For example, a field
can contain numeric, text, or structure information.

In spreadsheet terminology:

A data item is found in a cell.

A field corresponds to a column.

A record corresponds to a row.

A table corresponds to a worksheet.

A database is a storehouse for tablespossibly one,

possibly more than one. A database containing only
one table is known as a simple (or flat or flat-file)
database.

310 ChemFinder Basics CambridgeSoft

Using ChemFinder with Databases
Databases containing multiple tables are called
relational. Relational databases are discussed
further in Chapter 16, Relational Data and
Subforms on page 361.
A form displays data from a single table, but may
contain subforms that display data from other
tables. If the tables have a field in common, then
any record retrieved in the form calls up the related
records in the subform.
Understanding Forms and
Databases
There is an important distinction between forms
and databases. Databases are where data is actually
stored. A form is used only to display the
Chem & BioOffice 2006 /ChemFinder
information stored in the database. No data is
stored in a form. The form acts like a window,
letting you select which fields and tables you want
to view.
ChemFinder lets you create more than one form to
access the same database. For example, you may
want to create one sample form for working with
structural data and a more complicated one to
include literature or lab data. By switching between
forms, you can look at just those fields you want to
see. For more information, see Chapter 16,
Relational Data and Subforms on page 361.
ChemFinder Basics 311
Using ChemFinder with Databases
Administrator

312 ChemFinder Basics CambridgeSoft

Using ChemFinder with Databases
Chapter 14: ChemFinder Tutorials
Overview
The general steps for using ChemFinder are:
1. Create a form.
2. Create or open a database and link it to the
form.
3. Add or manipulate data.
4. Perform a search.
The tutorials introduce you to ChemFinder basic
functions. Tutorial 1: Creating Forms walks you
through the basics of form creation. Tutorial 2:
Opening a Database works with an existing
database, showing you how to link it to your form.
Tutorial 3: Creating Your Own Database teaches
you how to create your own simple database and
link it to your form.
Tutorial 4: Searching a Database illustrates the
basics of searching databases and Tutorial 5:
Reaction Queries expands on this to include
reaction databases. Tutorial 6: Using BioViz
introduces the new Chemfinder plotting feature.
Finally, Tutorial 7: Working with Subforms,
illustrates ChemFinder relational database
capabilities.
You may want to use the Quick Reference card
while you perform the tutorials.
Perform the tutorials in the sequence they are
presented because each tutorial develops on and
refers to the previous ones.
Sample Databases
The Samples directory located in the \Chem &
BioOffice\samples folder contains several small
databases, forms, and sample scripts.
Chem & BioOffice 2006 /ChemFinder
The Cs_Demo database contains about 300
structures covering a range of structural types. The
database contains two tables, both of which are
visible using the form Cs_Demo.cfw. This is the
form used in the following tutorials. Demo.cfw is a
simpler form which displays only the main table of
the same database.
CAUTION
We recommend you make a working copy of the database
before experimenting with it. If you make changes to the
data or structures in the database, the examples in the
tutorials may no longer give the documented results.
The following procedure creates a working copy of
the Cs_Demo.cfw database.
1. Open Windows Explorer.
2. Create a folder for the database copies.
3. Select all Cs_Demo.* files.
4. Right-click, and choose Copy.
5. Select the folder you created for the database
copies.
6. Right-click and choose Paste.
You can now experiment with adding, modifying,
and deleting data in the copies with no effect on the
Cs_Demo database.
Tutorial 1: Creating
Forms
Forms allow you to display your data in a
customized format, to browse and search through
your database, and to interact with other
applications, such as ChemDraw and Chem3D.
ChemFinder Tutorials 313
Tutorial 1: Creating Forms
 In this tutorial, you learn to create, edit, and save the 3. Click the Data Box tool .
following form: 4. In the form window, drag diagonally to create a
box.
Administrator

You create forms using the Form toolbar shown

below: 5. Draw two more boxes in the same way. You
edit them in later steps
NOTE: The Form toolbar docks on the left side of the
ChemFinder window by default, but can be docked anywhere
or torn off, as shown below.
.

Selection tool Frame Text Button Subform

A Frame, a Framed Box, and a Text Box are

Data box Framed box Picture Checkbox Grid
different types of boxes and require a label.
For detailed information about each tool, see
To draw a Framed Box:
Creating Forms Manually on page 340.
1. Click the Framed Box tool and drag
Creating Data Boxes diagonally to create a framed box.
Data and structures from a database are displayed in A box labeled Data is created.
boxes. You create boxes using the tools in the Form 2. Point to the word Data, right-click, and select
toolbar. The Form toolbar only appears when you Label.
select Layout mode.
The Box Text or Label dialog box appears.
To create a data box:
1. From the Main toolbar, click New .
A new, blank form appears in the ChemFinder
window.
2. If the Form toolbar is not visible, click the
Layout mode tool . 3. In the Box Text or Label dialog box, type
The Form toolbar appears. Frame Box and click OK.

314 ChemFinder Tutorials CambridgeSoft

Tutorial 1: Creating Forms
 The label appears above the Framed Box. The label appears above the box.

TIP: You can change the font of the label from the Box
tab of the Properties dialog box. Just click the button
labeled Font.

To place a picture in your form:

1. Click the Picture tool and drag in the

form.
The Open dialog box appears.
4. Click the Frame tool . 2. In the ChemFinder System directory, choose
Buttrfly.wmf, then click Open.
TIP: The Frame tool is useful if you want to draw a The picture appears in the area you dragged in
frame around two or more data boxes. the form.

5. Place the pointer at the corner of the upper

right data box and drag to create a border
around the group of three data boxes.

The Enter the Label dialog box appears.

Editing Data Boxes

Edit the data boxes using the Selection tool:

1. Click the Selection tool .

6. In the Enter the Label dialog box, type Frame 2. Select the upper left box by clicking anywhere
and click OK. in it.

Chem & BioOffice 2006 /ChemFinder ChemFinder Tutorials 315

Tutorial 1: Creating Forms
 A selected data box is designated by four black
squares at its corners.
Administrator
3. Click an empty space in the form with the
Selection tool to deselect the box.
To select multiple boxes:
Press the Shift key and click in each box.
TIP: You can also select multiple boxes by dragging.
You can select all the boxes on the form by choosing
Select All from the Edit menu.
The frame and the box work as one object when
you select, move, resize, or delete. To separate them
into two objects:
1. Click inside the Framed box to select it.
2. From the Edit menu, choose Bring to Front.
To resize a box:
Select a single box, and resize it by dragging a
side or corner.
To reposition a box:
316 ChemFinder Tutorials
Select a box, point within the selection, and
drag the box.
If you select multiple boxes, dragging the center of
a selected boxes moves all of them at once.
To edit with the Clipboard:
1. Select a box.
2. Try each of the following:
From the Edit menu, choose Cut.
From the Edit menu, choose Paste.
From the Edit menu, choose Undo (Paste).
From the Edit menu, choose Redo (Paste).
NOTE: Undo and Redo work over multiple levels. You can
use Undo and Redo repeatedly to reverse multi-step
operations.
Deleting Data Boxes
To delete a data box:, do one of the following:
Select a box and press the Delete or Backspace
key.
From the Edit menu, choose Cut.
To clear the entire form:
From the Edit menu, choose Select All, and
press the Backspace key to remove the contents
of the form.
Creating and Saving a Form
To create and save a new form:
CambridgeSoft
Tutorial 1: Creating Forms
 1. Draw the form shown below, using the Framed The Box Properties dialog box appears with
box tool. the Database tab displayed.

NOTE: The Data Source option is only available in

Layout mode. Make sure the Layout mode toggle
button is depressed before performing this step.

2. From the File menu, choose Save As.

3. In the Save As dialog box, save the form as

tut1.cfw in the directory of your choice.

4. From the File menu, chose Close.

Tutorial 2: Opening a
Database 4. Click Open Database.

After you create a form, you can use it to connect

NOTE: The Open and Create Database buttons
to a database that actually stores information. In
work with ChemFinder databases only. To access data
this tutorial, you use the form you saved as
in other types of databases, use the Attach Table or the
tut3.cfw in the previous tutorial to access and
Oracle button (if available). For more information
retrieve information from an existing database.
about data sources, see Attaching Tables from Other
Applications on page 373.
Connecting a Database to a
Form The Open dialog box appears.

To connect a database to your form:

1. From the File menu, choose Open.

The Open dialog box appears.

2. Select tut1.cfw and click Open.

The form you created in the previous tutorial

appears, but all of its fields are blank You can
use this form to display the demonstration
database.
3. Right-click the Structure box and choose Data
Source. 5. Select CS_demo.mdb and click Open.

Chem & BioOffice 2006 /ChemFinder ChemFinder Tutorials 317

Tutorial 2: Opening a Database
 The database opens, and the Box Properties To assign fields to the other data boxes:
dialog box appears displaying the Database tab.
1. Right-click in the Name box and choose
6. Select a table. Molname.
Administrator

A list of the tables in the database and the fields

in each table are shown. The field you select NOTE: Once you have opened a database and table,
determines what type of data appears in the the shortcut menu displays the fields in the database.
box you selected in step 3.

The Molname field in the database is linked to

the Name box, and the data item for the first
record appears in the Name box.

2. Right-click in the Formula box and choose

Assigning Fields to Data Formula.
Boxes 3. Right-click in the ID box and choose MOL_ID.

To display structures from the CS_Demo database

in a Structure box on your form:

From the list of fields in the Box Properties

dialog box, click Structure, then click OK.

The Structure field is linked to the Structure

box. In the Structure data box, you can see the
contents of the Structure field for the first
record in the CS_Demo database. 4. From the File menu, choose Save As.

5. In the Save As dialog box, save the form as

tut2.cfw in the directory of your choice.

6. From the File menu, choose Close.

Congratulations! You have created your own

customized form for viewing the CS_Demo
database.

318 ChemFinder Tutorials CambridgeSoft

Tutorial 2: Opening a Database
Tutorial 3: Creating Your 6. Click Create Field.

Own Database The Create Field dialog box appears.

In this tutorial you will create a new database using

a different techniqueautomatic form generation.
1. Open a new blank form.
2. Right-click in the form and choose Data Source
from the context menu.
The Properties dialog box appears with the
Database tab displayed.
3. Click Create Database.
7. Type MolName in the text box, change the
The Save As dialog box appears. width to 254, and click OK.
4. Type mydb and click Save.
The name of the database appears in the NOTE: The maximum number of characters you can
Properties box. enter in any text field is 254 characters. If you want a
text field to contain more than 254 characters, choose
Memo/Rich Text from the Type drop-down list.

8. Click Create Field again. Type Boiling Point in

the text box, change the type to Double, and
click OK.

Database name NOTE: Use the field type Double to create a field
containing real numbers (such as -123.7 and 43.242) .

The data table tree display should reflect your

changes immediately.
ChemFinder creates one data table (MolTable)
containing four fields: Structure, Formula,
MolWeight, and MOL_ID.
5. Click the Field tab.
You are now going to add two new fields to the
data table.

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Tutorial 3: Creating Your Own Database
 9. Click the Form tab.
Administrator
Generate form
checkbox
Style button
10. Click the checkbox next to Generate form. Click
the Style button. In the Form Generation
dialog box, make sure the checkbox for
Structure in upper left of form is checked.
11. Click OK in the Form Generation dialog box
and again in the Properties dialog box.
The Mydb form is generated.
Check the field assignments in the data boxes.
1. Right-click in the structure data box.
There should be a check next to Structure
indicating that the Structure field is linked to
the structure data box.
2. Right-click in the Boiling Point data box.
320 ChemFinder Tutorials
There should be a check next to Boiling Point.
TIP: You can edit the form to suit your purposes. Notice in
the next section that the form has been rearranged to save
space.
Adding Records
Now that you created new fields and assigned them
to data boxes, you can add data to your database.
This tutorial was written to demonstrate use of the
ChemDraw ActiveX control (the default structure
mode). Before you begin to add structures, you
might want to check if ChemFinder is set
appropriately.
1. Right-click in the Structure data box, and select
Properties.
2. In the Box Style section of the Box Properties
dialog box, select ChemDraw style.
When ChemDraw style is selected, ChemFinder
defaults to the ChemDraw ActiveX control.
This allows you to edit structures directly in the
Structure data box in ChemFinder. ChemFinder
style opens ChemDraw in its own window for
editing.
Now you are ready to begin adding records to your
database.
1. Deselect the Layout tool to hide the Form
toolbar.
2. Double-click in the Structure box.
The ChemDraw ActiveX toolbar appears.
TIP: Even if your default is ChemDraw style, you can
open ChemDraw by right-clicking in the structure box
and selecting Edit in ChemDraw.
CambridgeSoft
Tutorial 3: Creating Your Own Database
 3. Draw benzene.
4. Click somewhere outside the Structure data
box to enter the structure in the data box.
The benzene molecule appears in the Structure
Data box on the form. ChemFinder calculates
the molecular formula, and assigns an ID
number of 1.
5. Click the MolName box and type Benzene.
6. Click the Boiling Point box and type 80.1.
To commit your new record:
Choose Commit Changes from the Record
menu.
You entered the first record in your database. The
size of your database is indicated in the Status Bar.
Chem & BioOffice 2006 /ChemFinder
Enter two more records:
1. From the Record menu, choose Add New
Record.
2. Add a record for n-Pentane (shown below),
with a bp = 36.1.
3. Repeat step 1 then add a record for Cyclo-
hexane (shown below), with a bp = 80.7.
NOTE: After you have two or more records in your
database, you can commit changes by moving to a
different record using the Record tools.
4. From the File menu, choose Save.
NOTE: Choosing Save saves any changes made to
your form. Clicking Commit Changes saves the data
into your database.
Tutorial 4: Searching a
Database
NOTE: The following examples require you to search the
entire database. This is the default search, unless the Over
Current List command is activated on the Search menu.
Please take a moment to make sure this command is NOT
activated before beginning this tutorial.
ChemFinder helps you organize and find
information. One way to find information is to
browse through the database one record at a time,
like turning the pages in a book. This is a good way
ChemFinder Tutorials 321
Tutorial 4: Searching a Database
 to see some of the information available. However,
(

because databases can be very big, browsing is often

inefficient.
Searching a database is like using the index of a
Administrator

book. With an index, you can quickly focus on the

few pages you are interested in. When you search a
database, you find only those few records that have
the information you look for. After you have this
smaller collection (a hit list), you can then browse it
much more efficiently than you could the whole
database.
ChemFinder performs the following types of
searches: 3. In the Samples directory, select CS_demo.cfw
Text and structure searches, demonstrated in and click Open.
Tutorial 4. The CS_Demo database opens in
Reaction searches, demonstrated in Tutorial 5. ChemFinder.
In this tutorial, you will learn how to search
substructures and text in the CS_Demo Database.
This database is included with ChemFinder as a
sample database of approximately 300 organic and
inorganic compounds.
TableFormView 225 dpi
Opening the Demo Data-
base
To open the CS_Demo database:
1. Open ChemFinder and in the Open dialog Before you begin searching, open the Explorer
box, click the Existing tab. window, if it is not already open.
2. Navigate to the...\Chem & BioOffice 2006\
ChemFinder\samples folder. (Normally, this is
in C:\Program files\.)

322 ChemFinder Tutorials CambridgeSoft

Tutorial 4: Searching a Database
 1. Choose Explorer Window from the View Formula Searching
menu.
To find compounds in the CS_demo database with
six carbons and one or two nitrogen atoms:
1. In the CS_demo database, choose Enter Query
from the Search menu, .
The form is cleared so that you can enter a new
query.
2. Click in the Formula box and type C6N1-2.

NOTE: This entry specifies a molecular formula

having six carbon atoms and one or two nitrogen atoms.

3. Press the Enter key.

The Status Bar indicates that 12 hits were
The Explorer Window appears. retrieved from the 285 records in the database.

The Queries tree in the Explorer window now

displays one query as a child of the full list.
Queries are saved with the form and can be
reviewed at any time. For more information on
queries in the Explorer window, see Managing
Queries on page 421
There are three methods for browsing the hits:
2. Click the Queries tab, and you are ready to start In the Form ViewUse the Record menu
your first search. commands or toolbar to navigate through
records.
TIP: The default, set in the Preferences dialog box, is to In the Data Table ViewBrowse the table to
save all queries listed in the Queries tree. If you dont want to view the records.
save a particular query, delete it before closing the form. In the Continuous Forms Viewview
multiple records in their own forms.

Text Searching Use Switch Views from the View menu to toggle
between the different methods.
In this exercise, you perform a molecular formula To browse the hit list, use the Record menu as
search then a name search. follows:

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Tutorial 4: Searching a Database
 From the Record menu, choose First Record, The molecular weight field is sorted in
Previous Record, Next Record, Last Record, or Go increasing order.
to Record. Try it.
Administrator

NOTE: As you change records, counters in the Status bar

indicate the current record, the current list size, and the total
size of the database.

To view the database in a table that shows the

records in a list:
From the View menu, point to Data Table, and
choose In Current Window. To change the column widths of your table:
NOTE: Switch to Table is a toggle. Selecting it again will Position the pointer over a table header divider
return you to the Form view. and drag to the width you want.
Pointer
The Table view appears and displays all the
records of the current list (in this case, the 12
records that were hit by the search) in a table.

TableListView 225 dpi

To use continuous forms to browse your records:

1. On the View menu choose Continuous Forms.
You can sort the records for a specific field in Table The Continuous Forms view appears. By
View. default, the Continuous Forms view shows the
same form as the Form view.
To sort records in Table view by the MolWeight
field:
Double-click on the MolWeight table header.

Adjust the height of any form by dragging the bar

divider on the left to view the forms clearly.

324 ChemFinder Tutorials CambridgeSoft

Tutorial 4: Searching a Database
Return to the Form view: Numerical Searching
Choose Form View on the View menu.
To search in the CS_Demo Database for
To retrieve all the records in your database:
compounds with molecular weights between 90 and
Double-click Full List in the Explorer window. 100:

Name Searching 1. Switch to the Form View, if you are not already
in it.
To find all compounds in the CS_Demo Database
with molecular names starting with benz: 2. From the Search menu, choose Enter Query.

1. Switch to the Form View, if you are not already The form is cleared so that you can enter a new
in it. query.
The Form view appears. 3. Click the Molecular Weight box and type
90-100.
2. From the Search menu, choose Enter Query.

TIP: Although the Tutorials describe the use of the

Search menu, you may find using the Search toolbar
more convenient. The icons on the toolbar match those
you have already seen on the Search menu. Clicking the
Find icon is equivalent to pressing the Enter key when
you are ready to begin your search. See Chapter 20,
Searching on page 403 for information on more
advanced use of the Search toolbar.

The form is cleared so that you can enter a new

query.
4. Press the Enter key.
3. Click the Molecule Name box, and type benz*.
You get 11 hits with molecular weights
4. Press the Enter key.
between 90 and 100.
You get 12 hits with names starting with
benz.

5. From the View menu, point to Data Table, then

choose In Current Window.
The Table view appears. Browse to verify that
the molecular names are correct.
NOTE: Notice that this search gave you benzene but not
bromobenzene. The query you entered above is an
anchored substring and only gives you strings starting with
the indicated substring. For more information on how to
specify text searches, see Text Searches on page 403.
5. From the View menu, point to Data Table, and
choose In Current Window.
The Table view appears. Browse to verify that
the molecular weights are correct.
NOTE: A molecular weight query is a decimal value or
range. The precision of the search depends on the number of
significant digits entered. For more information on molecular
weight searching, see Numeric Searches on page 404.

Chem & BioOffice 2006 /ChemFinder ChemFinder Tutorials 325

Tutorial 4: Searching a Database
 Substructure Searching The Search menu should appear as follows:

To enter a query and search for a substructure:

Administrator

1. From the Search menu, choose Enter Query.

The form is cleared to allow you to enter your

search terms. The status indicator in the status
bar is changed to remind you that you are in
query mode and the color of the form may
change.

2. Double-click in the Structure box.

A blue box is displayed around the Structure

box and the ChemDraw ActiveX toolbar
appears.
3. Draw benzene.
3. From the Search menu, choose Find.
ChemFinder begins searching. The progress of
the search is indicated by counters in the status
bar at the bottom of the window.
When the search is complete, the number of
hits is displayed in the Current List Size
window of the Status Bar, and the form
displays the first hit.

In this search you get 123 hits of structures that

To set the correct options for a substructure search: contain an aromatic six-membered ring. The
list you can browse is limited to the hits found
1. From the Search menu, select Substructure if it
in the search.
is not already selected.
2. From the Search menu, deselect Similarity if it
is selected.

NOTE: You can also set search preferences on the

Search tab of the Preferences dialog box. For more
information, see Chapter 21, Customizing
ChemFinder on page 429

326 ChemFinder Tutorials CambridgeSoft

Tutorial 4: Searching a Database
 In a substructure search, the matched portion
of each molecule is highlighted in red.
TIP: Some users prefer not to see red highlighting
because it masks the atom colors. You can change the
highlight color on the Color tab of the Preferences dialog
box. Selecting black will effectively cancel highlight-
ing, leaving atoms to display in their normal colors.
NOTE: If a search gets no hits, an alert appears and you
are returned to the query mode with the query on display.
Combined Searching
In some cases, you may want to combine structure
searching with text searching to find a specific class
of compounds. For example, you may want to find
all compounds in the database that have a benzene
substructure and that have a molecular weight
greater than 400.
To perform a combined search:
1. From the Search menu, choose Enter Query.
The form is cleared so that you can enter a new
query.
2. Double-click in the Structure box.
The ChemDraw ActiveX toolbar appears.
3. Draw benzene.
4. Click the Molecular Weight box and type >400.
5. Press the Enter key.
You get 8 hits from the 285 records in the
database.
6. From the View menu, point to Data Table, and
choose In Current Window.
Chem & BioOffice 2006 /ChemFinder
The Table view appears. Browse to verify that
the molecular weights are correct.
Congratulations! You have completed the tutorial
on searching a database using ChemFinder. You
may now close the CS_Demo database.
Tutorial 5: Reaction
Queries
In addition to helping you organize information
about individual substances, ChemFinder also
allows you to store and search chemical reactions.
There are many ways to search reactions, depending
on what sort of information you are interested in.
In this set of exercises, you learn some general
methods to search for different parts of reactions
using a sample from the ISICCR database. This
database is included with ChemFinder as a sample
database of approximately 250 reactions extracted
from the ISIs ChemPrep database of Current
Chemical Reactions.
Opening A Specific Data-
base
To open the ISICCR database:
1. From the File menu, choose Open.
The Open dialog box appears.
2. In the Samples directory, select Isiccr.cfw, and
click Open.
NOTE: The ISICCR.cfw form is formatted for a large
screen (1024 X 768). If you have a smaller screen, open
ISICCRsm.cfw for a simpler form.
ChemFinder Tutorials 327
Tutorial 5: Reaction Queries
 The ISICCR database opens in ChemFinder. The Search menu should appear as follows:
Administrator

O
O O
H
O
+

O O O
O O
H
OO

TableFormISICCR 275 dpi

Searching for Reactants

Searching for reactants is useful if you have a
known starting material and you are interested in
learning more about what substances it can
produce.
6. From the Search menu, choose Find.
For example, to search for Grignard reactions, or
ChemFinder searches. The progress of the search is
reactants:
indicated by counters in the status bar at the bottom
of the window.
1. From the Search menu, choose Enter Query.

The form clears.
2. Double-click in the Structure box.
The ChemDraw ActiveX toolbar appears.
3. Draw the following:
When the search is complete, the number of hits is
displayed in the Current List Size window of the
Status Bar, and the form displays the first hit. In a
substructure search, the matched portion of each
molecule is highlighted in red.

M
g nO
R
x
MgXHit 40%
+B
r
R
x
n
O
M
g N
+
N
+
O
X
R
x
n -

O
-

This structure represents a carbon atom
bonded to a magnesium atom, which is bonded
to any type of halogen. The arrow at the right
indicates that you are looking for this
substructure as a reactant.
4. From the Search menu, select Substructure if it
is not already selected.
5. From the Search menu, deselect Similarity if it
is already selected.
You get 3 hitsreactions in which an alkyl
magnesium halide is consumed. Browse the list of
three hits as in previous tutorials.
Searching for Products
In the next exercise, you search for information on
a particular reaction product. Searching for
products of reactions is very common in syntheses,
where you know what you are aiming for but you do

328 ChemFinder Tutorials CambridgeSoft

Tutorial 5: Reaction Queries
not know how to produce it. In this example, we
look for reactions that close a ring alpha to a
carbonyl.
8. Press the Enter key.
You get 3 hits containing a product with a
carbonyl ring that was formed during the
course of the reaction.

O
H H
O
H
O O

H H

H C
l H C
l
C
l

O O

To perform a reaction product search:

1. From the Search menu, choose Enter Query.

The form is cleared so that you can enter a new
query.
2. Double-click on the Structure data box.
The ChemDraw ActiveX toolbar appears.
3. Draw the following:
O
Searching by Reaction Type
In many cases, you have some idea of both your
starting materials and your products, but are
looking for some information on how to get from
one to the other.
For example, to search for reactions that reduce a
carbonyl to an alcohol:
1. Click Enter Query in the Search menu.

The form is cleared.

4. Switch to either selection tool (Lasso or
Marquee) and select the single bond next to the 2. Double-click in the Structure box.
double bond.
3. Draw the following:
5. Right-click, point to Topology, and choose Ring. .

6. Select the remaining single bond. O

O
H
7. Right-click, point to Topology, and choose Ring.
Right-click again, point to Reaction Center, and
4. Press the Enter key.
choose Make/Break. Your structure should
now look like this: Browse through the 23 hits. Each of the
reactions found shows the transformation of a
R
n
g
Rx
nRgO
n carbon-oxygen double bond to a carbon-
oxygen single bond.
The arrow at the left indicates that you are This hit list includes reductions of aldehydes,
looking for this substructure as a product. acids, and ketones.

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Tutorial 5: Reaction Queries
 Search Over List
In this example, you start with the previous list and
search again to get only ketone reduction reactions.
Administrator
To search over a list:
1. If you are not continuing directly from the last
example, double-click the previous query in the
Query Tree to make sure it is the active hitlist.
2. Select Over Current List from the Search menu.
3. Double-click in the Structure box.
4. Draw the following:
Rxn
[NOTO,H] [NOTO,H]
a. Using a Selection tool, right-click and set
Reaction Center bond properties to Change.
b. Using the Text tool, select one of the atoms
where the label is shown. Type [NOT O,H]
(all uppercase) and press the Enter key.
c. Still using the Text tool, select the label,
right-click and choose Repeat Last Label.
d. Double-click on the other atom to repro-
duce the label.
You specified a search for ketones by adding
the restriction that the atoms adjacent to the
carbon must not be oxygen atoms or hydrogen
atoms. You also specified that the double bond
had to change, not be broken.
5. Press the Enter key.
330 ChemFinder Tutorials
You get 13 hits. Each reaction shows the
reduction of a ketone to an alcohol. In the
Queries Tree, this search is shown as a child
of the first query.
TIP: If you plan to do several searches over a hitlist, use the
Set Domain to Current List command rather than Search
Over Current List. Setting a domain eliminates the need to
keep restoring the original hitlist.
Congratulations! You have completed the tutorial
on searching for reactions using ChemFinder.You
may now close the ISICCR database.
Tutorial 6: Using BioViz
BioViz is the ChemFinder visualization facility. In
this tutorial, you will be introduced to the basic
concepts of data visualization by producing a
simple one-variable chart. You can create multiple
plots and store them with the form. You can create
plots of the full list and of queries. In this tutorial,
you will create a plot of a query created in a previous
tutorial.
Reopen the CS_Demo database. If you
remembered to save the form, you have five
queries, ranging from eight to 123 hits. In the
examples below, the queries have been renamed to
indicate the search criteria.
Before you start, go to the View menu and activate
the Structure window. The Structure window gives
you a way to display structures without taking up
room on the form.
CambridgeSoft
Tutorial 6: Using BioViz
To create a plot of a hitlist:
1. Select the first query, Formula: C6N1-2 . Right-
click and choose Restore Query.
2. On the View menu, point to Plots and choose
New.
The Plot Properties dialog box appears.
3. Select the One Variable radio button.
The X-coordinate is grayed out and the Scatter
Plot style is selected by default.
4. Select MolWeight from the drop-down menu
for the Y-coordinate.
5. Click the OK button.
The Plot appears in a new window.
Chem & BioOffice 2006 /ChemFinder
Experiment with pointing to the data points on the
graph. Note that as you hover over a data point, its
structure appears in the Structure window.
Likewise, if you browse through the database, the
corresponding point is highlighted in red on the
plot.
To select a database record from the plot:
Click a data point.
The database display jumps to the data record
selected.
Return to the database form to view the result. To
plot another query:
1. Double-click the first structure query from the
list in the Explorer window. This is the query
with 123 hits.
The plot changes to display the new data set.
2. This plot is a bit cluttered. Select the Zoom
radio button at the bottom of the plot and drag
over the first twenty data points.
ChemFinder Tutorials 331
Tutorial 6: Using BioViz
 When you release the mouse button, the plot
expands to show the points selected.
Administrator
To restore the original scale:
Click the icons at the ends of the scroll bars.
Tutorial 7: Working with
Subforms
Subforms allow you to display relational data. If you
have a database containing two or more data tables,
and these data tables share a common, linking field,
then you can display data from both tables.
Whenever the value of the linking field changes in
the main form, the subform only displays those
records from its table which have the same value in
the linking field. You can also use subforms to
display data from different databases.
In this tutorial, you open the CS_Demo database
and display the MolTable in the main form. Then
you display the Synonyms table of the CS_Demo
database in a subform. By defining the MOL_ID
field as the linking field, you display the two sets of
data relationally.
Creating a Subform
1. Open your ChemFinder form tut1.cfw.
Opening this form connects you to the
CS_Demo.mdb database.
332 ChemFinder Tutorials
2. Make some space on the right side of the form
by rearranging the data boxes and making them
smaller.
3. Click the Subform tool .
4. In the form, drag to create a large subform.
TIP: If you cannot make room on the right side of your
form, you can put the subform at the bottom of the form.
When you release the mouse button the
Subform Properties dialog box appears.
5. Select Synonyms from the hierarchical tree
display.
6. Click the Form tab.
7. Click the Generate form checkbox, and click the
Style button.
8. Select the Plain form, and deselect all of the
fields to be included except Synonym. Click OK.
You are returned to the Subform Properties
dialog box.
9. Click the Subform tab.
10. SYN_ID already appears as the default in the
Link to Synonyms field section. Using the drop-
down menu, choose MOL_ID for the Link from
MolTable field.
11. Click OK.
You have just selected the data source for your
subform and linked it to the main form.
The MOL_ID field links the main form and
subform. Clicking in either form activates it.
CambridgeSoft
Tutorial 7: Working with Subforms
To test this:
1. Click anywhere outside the subform box, and
browse your database using the Record tools.
As each molecule record of the MolTable is
displayed, the subform shows the first
matching ID from the Synonyms table.
To display all of the synonyms:
1. Toggle out of Layout mode .
2. Double-click in the subform box to switch to
Table view.

2. Click inside the subform box.

Now when you browse, you are browsing only
the entries in the subform.

Save and close the file:

1. From the File menu, choose Save.
2. From the File menu, choose Close.
Congratulations! You have completed the
ChemFinder Tutorials.

Chem & BioOffice 2006 /ChemFinder ChemFinder Tutorials 333

Tutorial 7: Working with Subforms
Administrator

334 ChemFinder Tutorials CambridgeSoft

Tutorial 7: Working with Subforms
Chapter 15: Creating and Editing
Forms
Overview
You use forms to interact with information in a
database. A ChemFinder form is composed of data
boxes for viewing or modifying data items, such as
structures, numbers, text, or pictures. A form can
also contain subforms for relational access to
different data tables and different databases.
You can create a form in the following ways:
Automatically, using the Form Generator
dialog box.
Manually, using the Form tools.
With the Database Tree.
The example below shows a form displaying a
single record of information from a database.
Creating a form consists of creating a layout (see
Creating Forms Manually on page 340), and
setting box properties (see Creating and Editing
Tabs on page 344), tabs (see Editing Forms on
page 352), and security (see Securing Forms on
page 356).
You can edit your form at any time (see Editing
Forms on page 352 and Changing the Layout of
an Existing Form on page 354).
Chem & BioOffice 2006 /ChemFinder
The first step in designing a form is selecting the
database and deciding which fields to include.
Selecting a Database
A ChemFinder form does not store data directly,
but is simply the window through which you look at
data. When creating a form, you need to specify the
source of the data to display. A form displays data
from a single table in a database. To specify the data
source for a form, you must open or create a
database, then select a table.
If you want to view data from more than one table,
you must create a form for each table. Typically, you
create a main form for one main table and a
subform for each other table. For more
information, see Chapter 16, Relational Data and
Subforms on page 361.
You can connect a database to the form before
creating boxes, or any time after. If the form is
already connected to a database, you can change the
database or the data source. If the form has boxes
with fields connected to them, then the boxes
automatically connect to fields of the same name in
the newly-opened database.
Opening an Existing Chem-
ical Database
To open a database to associate with a form:
1. Right-click on the form and select Data Source.
The Form Properties dialog box appears.
2. Click Open Database.
Creating and Editing Forms 335
Selecting a Database
 The Open dialog box appears. To choose the data box to display:

1. Right-click in a box or frame, then click Field.

The Field properties appears.

Administrator

2. From the data source tree, select the field to

display.

3. In the Open dialog box, choose a database

with an .mdb file extension, then click Open.
The Form Properties dialog box reappears.
The CS_Demo database is shown below.

3. Click OK.

The field data is displayed in the box.

If you use this method with a framed box, the box

label will remain unchanged. If you want to use the
field name as the box label, you can do it in one step
as follows:

1. Right-click in a framed box.

A data source tree appears in the left side of the
Form Properties dialog box, displaying the
fields and their tables.
4. Click OK.
The database is associated with the form.
2. Select the field name from the list at the
bottom of the context menu.
The frame receives the field name and the data
is displayed in the box.

Selecting the Data to Display

You indicated the source of the data to display on
the form, but the form is still blank. To see the data,
you need to indicate what data to show in each box.
You can use the Box Properties dialog box, as
described in Setting Box Properties on page 44.

336 Creating and Editing Forms CambridgeSoft

Selecting a Database
Opening a Secured MS 3. Select the Users or Groups radio button to
assign permissions to individuals or groups.
Access Database
4. Select an Object Type from the drop-down
To open a secured Microsoft Access database in menu.
ChemFinder, you need to set the appropriate 5. Select the permissions you want to assign for
permissions in Access. that object type to each user or group.
6. Click Apply.
NOTE: If your database was created in MS Access 97 (as, 7. When you have finished assigning permissions,
for example, were some of the ChemFinder sample click OK.
databases), and you are using a newer version of Access, you 8. Open the database in ChemFinder.
must convert the database before you can edit it. These
instructions assume a database created in Creating a Database
Access 2002.Other versions may differ slightly as to options
and procedures. You can create a new, empty database and associate
it with a form.

To set the permissions: To create a database:

1. Open an existing form, or create a new one.
1. Open the desired database in MS Access.
2. Right-click in the form and select Properties.
2. On the Tools menu, point to Security, then
The Box Properties dialog box appears.
choose User and Group Permissions.
3. On the Box Properties Database tab, click
Create Database.
The Save As dialog box appears.

4. In the File Name box, type a name for your

database, then click Save.

Chem & BioOffice 2006 /ChemFinder Creating and Editing Forms 337
Selecting a Database
 A data source tree appears, containing the
database and its tables and fields.
Administrator

4. Click the Generate form checkbox, then click

Style.
5. Click OK. The Form Generation dialog box appears.
The Box Properties dialog box closes.

Creating Forms Auto-

matically
ChemFinder provides a Form Generation dialog
box from which you can automatically create a
form. You choose the form style and properties
from pre-defined options.
To begin creating a new form:
1. Open an existing database. 5. In the Choose Fields to be included section,
click the field names to include.
2. Right-click on a blank area of the current form
and choose Data Source. 6. To have a Structure box created in the upper
The Form Properties dialog box appears. left corner of the form, click the Structure in
upper left of form checkbox.
3. In the Form Properties dialog box, select the
Form tab. If you do not select this option, the boxes are
generated in the order they appear in the list.
7. Select the form style:

If you want the Then, in the

boxes to Form style
section, click

be surrounded by a Framed.
frame

338 Creating and Editing Forms CambridgeSoft

Creating Forms Automatically
 Saving a Form
If you want the Then, in the
boxes to Form style In most non-database applicationsincluding
section, click ChemDraw and Chem3Dyou edit data on the
screen, but your changes are not made permanent
be labeled above Titled. until you choose Save from the File menu.
In database programs such as ChemFinder, your
be labeled to the left Labeled. changes are automatically and permanently saved to
the database when you switch records. This is
not be labeled Plain. committing the changes. You then have the
opportunity to revert to the original data by
8. Choose the number of columns, between one choosing Undo Changes from the Record menu.
and four.
The Save command in the File menu refers only to
9. Choose the size and spacing of the boxes and changes made on the form itself, such as the position of
grid: boxes. Choosing the Save command from the File
menu has no effect on changes you make to data
If you want the Then, for Grid stored in the database. Saving a form also saves
boxes to be Size, choose subforms and changes that you make to subforms.
After you create a form, you can save it. When you
larger and spaced further Large.
retrieve the saved form, it automatically opens a
apart
connection to the database defined in the forms.

medium, relative to the Medium. To save a form:

Large and Small settings
1. From the File menu, choose Save. To save the
form under a new file name, choose Save As.
smaller and spaced closer Small.
The Save dialog box appears.
together

10. Click OK.

Your form settings are saved.
11. Click OK.
A Warning dialog box appears allowing you to
create a new form or replace the existing form.
Click No to create a new form.

2. Choose the directory in which you want to save

The generated form appears in the window. the form, type a filename, and click Save.

Chem & BioOffice 2006 /ChemFinder Creating and Editing Forms 339
Creating Forms Automatically
 ChemFinder saves the form with a .cfw A blank form, Form1, appears.
extension

Creating Forms Manu-

Administrator

ally
You create a form and define it by using the Form
tools to create objects and the Box Properties
dialog box to set the form properties. Using the Grid
In a new form, the snap grid is turned on by default.
Using the Form Tools This grid helps you align boxes on the form.
Turning on the grid forces objects to snap to the
You must use the Form Tools toolbar to design a grid as they are drawn.
form. Box creation commands are not available
from the menu. To toggle the grid on or off, do one of the
following:
To display the Form tools, do one of the following:
Click the Grid tool on the Form toolbar.
Click the Layout icon on the Main toolbar. From the View menu, choose Grid.

From the View menu, point to Toolbars, and NOTE: You can change the grid spacing using the
click Form. Preferences dialog box. See Setting Preferences on page
429.
The Form toolbar appears providing tools for
you to create and edit a form.
Creating Boxes
Selection tool Frame Text Button Checkbox
A ChemFinder form is composed of a collection of
boxes that display data. Each box displays one data
item of the current record. To create a data box, use
one of the tools on the Form toolbar.

NOTE: The Form toolbar is not visible unless the Layout

Data box Framed box Picture Subform Grid
button is selected.

Creating a New Form The Data Box displays a data item or structure. You
can use it to display any data from a database,
To create a new form:
including text, numbers, dates, molecules, reactions,
or pictures. It is the only box that allows you to edit
From the File menu select New, or click . data in the database. Data boxes do not have labels,

340 Creating and Editing Forms CambridgeSoft

Creating Forms Manually
but you can label them by adding a Frame or Plain
Text. You can also use the Data Box to display static
data not from a database.
To draw a Data Box:
1. Click the Data Box tool .
2. On the form, press and drag diagonally to
create a box.
To specify what type of data is displayed in the box,
see Creating and Editing Tabs on page 344. If the
form already has a database open, you can right-
click in the data box, select Field... and choose from
a list of the available fields.
Creating Frames
The Frame tool allows you to create a label
surrounding a data box or group of boxes. When
you draw a new frame, you are automatically
prompted for a text label to be attached to it.
To create a frame:
1. Click the Frame tool .
2. On the form, press and drag diagonally to
create a frame.
A framed box appears with the label Data. To
change the label:
3. Right-click on the label and choose Label from
the drop-down menu.
Chem & BioOffice 2006 /ChemFinder
The Enter the label dialog box appears.
4. Type the label you want to attach to the frame.
5. Click OK.
A fixed label appears on the frame.
To change a label:
1. Right-click on the edge of a frame and choose
Label.
2. Enter the new label as above.
Another way to change a frame's label is in the Box
Properties dialog. For more information, see
Creating and Editing Tabs on page 344.
You can use a frame to show live data from the
database. If a frame is connected to a database field,
it is updated automatically as you browse or search.
For example, you might place a frame around a
structure field, where the label on the frame
represents the name of the current structure. The
label changes every time the structure does. You
must use Box Properties to set up a live data
connection for a frame.
Creating Boxes with Frames
The Framed Box tool allows you to create a data
box and a frame simultaneously. You name the
frame in the Enter the Label dialog box.
When you create a data box and frame with the
Framed Box tool, these two items are connected.
To manipulate them separately:
Select the Framed box and from the Edit
menu, choose Bring to Front.
Creating and Editing Forms 341
Creating Forms Manually
 To create a framed data box:
1. Click the Framed Box tool . 1. Right-click the frame label and select Properties.
2. On the form, click and drag to create a box.
Administrator
3. In the Enter the Label dialog box, type the
label you want to attach to the frame, and click
OK.
The framed data box is labeled.
To edit the label of a framed data box:
1. Select the frame by carefully right-clicking near
the edge of the framed box and select Label.
2. In the Enter Box Label dialog box, type the
new label. The label does not have to match the
name of the field displayed in the box.
3. Click OK.
Automatic Labels
You can let ChemFinder automatically label your
framed box with the name of the field from the data
tree. This works slightly differently depending on
whether you created a box and added a frame, or
created a framed box.
To automatically label a framed box:
Right-click inside the data box and select the
field from the drop down list.
The data appears in the data box and the frame
label changes to match the field name.
342 Creating and Editing Forms
To automatically label a frame:
2. On the Box Properties tab, select a field from
the data tree. The field name will appear in the
text box under Data Source.
NOTE: If the text box is grayed out, you have not
clicked on the frame label.
3. Click OK.
The frame label changes to match the field
name selected.
4. Right-click in the data box and select the field
from the drop down list that corresponds with
the new label.
NOTE: When you change a label from the Box Properties
dialog box, the label and the data box are treated separately.
You must update the data box manually to match the label.
Adding Plain Text
The Plain Text tool allows you to display text
without a box or a frame. You can use it to place a
static label on the form. But, like a frame, you can
use it to display live data if desired.
To use the Plain Text tool:
1. Click the Plain Text tool .
2. On the form, click and drag to create an area to
specify where the text will appear.
CambridgeSoft
Creating Forms Manually
 The Enter the Text dialog box appears.
3. Type the text you want to display.
4. Click OK.
To change the font or color of the text, select it with
the Form toolbar Selection tool . Use the text
formatting toolbar to customize the text.
Adding a Button
To place a button on a form:
1. Write a script using the ChemFinder
Automation Language (CAL).
2. Click the Button tool on the Form toolbar.
3. On the form, click and drag to draw a button.
The Enter the Label dialog box appears.
4. Enter a label. The text can be descriptive
(Click to browse) and does not have to corre-
spond to the name of the script. Click OK.
For more information about using a button to run
a script, see Using Scripts on page 437.
Chem & BioOffice 2006 /ChemFinder
Adding a Checkbox
The Checkbox tool allows you to add checkboxes
to your form. A Checkbox can be assigned to either
a Boolean or an Integer field.
To add a checkbox:
1. Click the Checkbox tool.
2. On the form, drag an area large enough for the
text next to the checkbox.
The Enter the Label dialog box appears.
3. Type in the text and click OK.
4. Right-click, and assign the box to a field.
Adding Pictures
The Picture tool allows you to create a Picture Box
to display a Windows metafile. It can display a static
metafile stored in a.WMF file, or a live one stored in
a picture column of a database.
To create a Picture Box:
1. Click the Picture tool .
2. On the form, drag to create an area for the
picture to occupy.
The Open dialog appears.
3. In the Open dialog box, select the Windows
metafile (.wmf) you want to display, then click
Open.
The picture appears in your form.
NOTE: The metafile is not actually embedded in the form.
Only its filename is saved with the form. If you move or
rename the metafile, the form will not display the
Creating and Editing Forms 343
Creating Forms Manually
 corresponding picture. However, if you make changes to the
picture and keep its filename the same, the picture in the form
will be updated.
Tabs
Administrator

To read in a picture file or to replace a picture in a

Picture Data Box:
To rename a tab:
1. Right-click a picture and choose Read File.

The Open dialog box appears. 1. Right-click the tab and choose Rename Tab.

2. In the Open dialog box, select the metafile you The Tab Name dialog box appears.
want to display in the Picture Data Box, and
click the Open button.
The new metafile replaces the picture in the
Picture Data Box.

To save a metafile from a Picture Data Box:

2. Type a name for the tab and click OK.
1. Right-click on the Picture Box and choose Save
The new name appears on the tab.
File.
To remove a tab:
2. In the Save As dialog box, type a file name then
click Save. Right-click the tab and choose Delete Tab.
The picture is saved to a file in Windows The tab is removed.
metafile (.wmf) format.
Creating Forms with the
Creating and Editing Tabs Database Tree
If you have a large number of fields in a database,
The Database Tree is the same familiar tree as in the
you can access information more easily, and make
Database Properties dialog, showing the tables
the form less cluttered, by using tabs to divide a
(or views) and columns of the currently-open
long form into smaller parts contained on separate
database. When you open or activate a form or
tabs.
subform, or change databases, the tree updates to
display the current database, and expands to show
To create tabs on a form:
the columns of the currently-selected table.
1. Right-click an empty part of a form and choose
To view the Database Tree (if it is not visible):
Add Tab.
1. Choose Explorer Window from the View
Two tabs appear in the lower left corner of the
menu.
form. Clicking on the second tab will present
you with a new empty form. 2. Click the Database tab.

344 Creating and Editing Forms CambridgeSoft

Creating Forms with the Database Tree
To use the Database Tree to build a form:
1. Open a new form.
2. Right-click in the form, and choose Data
Source.
3. Click the Open Database button on the Data-
base tab.
4. Select a database, and click Open.
5. Click OK in the Form Properties dialog box.
The Database Tree displays the database.
6. Double-click the Structure field.
A structure box appears in the upper left of the
form.
7. Continue double-clicking the other fields.
8. Use the Selection tool to move the data boxes
to where you want them in the form.
Setting Box Properties
Use the Box Properties dialog box to set
ChemFinder form attributes, including: data
source, display type, font, and box style.
To open the Box Properties dialog box:
Right-click on a data box and choose Properties.
Chem & BioOffice 2006 /ChemFinder
The Box Properties dialog box appears.
NOTE: The Properties option is only available in
Layout mode.
Setting Data Box Styles
You can use the Box Properties dialog box to
change the style of a data box on a form. For
example, you can change a data box to a frame or
picture.
The Box Style menu only shows applicable styles
for each field. For example, you cannot show a real
number in a Picture.
For information about field types, see Creating
Fields on page 374.
You can choose from the following styles:
Data Boxdisplays alphanumeric data. Can
display multiple lines of data.
Framedisplays alphanumeric data. Can
display a single line of data.
Plain Textdisplays alphanumeric data. Text
data can be displayed in multiple lines. (Use
Ctrl+Enter to start a new line.) You set the
field size when you create the field, up to a
maximum of 254 characters.
Picturedisplays Windows metafile data.
Pictures are scaled to fit within picture boxes,
with fixed height to width ratios.
Creating and Editing Forms 345
Setting Box Properties
 Formuladisplays any kind of text but
numbers are subscripted. Formulas are
presented in modified Hill order, as follows: If
a substance contains both carbon and
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To set the box style:
1. Right-click in the data box to change and
choose Properties.
The Box Properties dialog box appears.

hydrogen, the carbons are listed first, followed

by the hydrogen atoms, followed by other
elements alphabetically by element symbol. If a
substance contains carbon, the carbons are
listed first, followed by other elements alpha-
betically by element symbol. Otherwise, all
elements are listed alphabetically by element
symbol.

Buttonused to create buttons to actuate

scripts. Buttons display button labels.
Rich Textdisplays styled data in multiple
lines. (Use Ctrl+Enter to start a new line.) You
can format text with the Text Format toolbar.
If the data in a field contains rich text, markup
characters are displayed.
Structure (ChemDraw style)displays chem-
ical structures or reactions. Reactions are laid
out for best fit with the box and the layout may
change if the box is reshaped. The box defaults
to using the ChemDraw ActiveX control to
create and edit structures, but you can reset the
preference. For more information, see Setting
Preferences on page 429.
Structure (ChemFinder style)as above, but
defaults to opening ChemDraw to create and
edit structures.
Structure (Chem3D style)as above, but
defaults to display 3D structures.
2. From the Box Style menu, choose the box
style.
3. Click OK.
Viewing Structures
You can display structures in a structure box in
ChemFinder, ChemDraw, or Chem3D styles. The
Chem3D style is a display only format that allows
you to rotate and analyze structures within a
ChemFinder structure window. See the Chem3D
Users Manual for information on using the
Chem3D ActiveX control.
If you choose ChemFinder style, ChemDraw will
open when you want to edit structures or create a
query. If you choose ChemDraw style, editing is
done in the structure box using the ChemDraw
ActiveX control.
The ChemDraw format displays more graphically-
rich drawings than the ChemFinder format.
However, ChemFinder does not use all of the
Chemdraw drawing features when searching.

346 Creating and Editing Forms CambridgeSoft

Setting Box Properties
For example, textual annotations are ignored, control. When you point inside the Structure Box,
R-group tables are not recognized. Certain the cursor becomes a hand that lets you grab and
graphics, such as rectangles and orbitals, are not rotate the structure.
transferred. and ChemFinder does not consider
their chemical implications.
To choose how to view structures:
1. Right-click in a structure data box and choose
Properties.
The Box Properties dialog box appears.
2. On the Box tab, in the Box Style section, select
the structure format to view from the menu:

If you want to Then choose Dragging within the structure allows you to freely
rotate the structure.
edit in the Structure Structure (ChemDraw
box using the Chem- style).
Draw ActiveX
toolbar

edit in ChemDraw Structure (ChemFinder

style).
Dragging the cursor across or up and down rotates
insert 3D images Structure (Chem3D the structure around the X and Y axes . To rotate
style). around the Z axis, drag outside the structure.

Right clicking displays a menu that allows you to

Viewing Structures in Chem3D Format modify the display.
Unlike the ChemDraw and ChemFinder styles,
Chem3D style is view only. You cannot edit the
structures in Chem3D style. Double clicking in the
Structure Box activates the Chem3D ActiveX

For more information on the Chem3D ActiveX

control, see the Chem3D Users Manual.

Chem & BioOffice 2006 /ChemFinder Creating and Editing Forms 347
Setting Box Properties
 Setting Fixed and Live Data The Choices tab appears.

In the Box Properties dialog box, you can

designate whether the data source is fixed or from a
Administrator

field. Fixed data is attached to the form and does

not change as you browse. Data from a field is
stored in the database and is different for each
record. As you browse, the record display updates
according to the contents of the field.

To specify live data for a data box:

1. In the Box tab, select the field to associate, then

click Field. 3. Take the appropriate action:
2. Click OK.
If you want to Then click
The box display updates as you change records.

To specify fixed data for a data box: use a list from a data- From table and follow
base table as the data the instructions at the
1. In the Box tab, select the field to associate, and box menu bottom of the dialog
click Fixed. box.

2. Type a label. If you choose a structure or

create your own list Fixed list of choices
picture field, click to browse to the file to
for the data box and follow the
display.
menu instructions at the
3. Click OK. bottom of the dialog
box.
The box display is fixed.
use a list from a data- a. From table. A
Adding a Data Box Menu base table and add list appears.
your own items to the
You can add a menu containing a list of choices to b. Click Fixed list of
data box menu
a data box so you can choose an item from it to choices, and edit
appear in the data box. the list.

To add a menu: 4. Click OK to close the dialog box, then click in

the data box.
1. Right-click on a data box and choose Properties. A button appears in the lower right corner of
The Box Properties dialog box appears. the box when you click in the box.

2. On the Box tab, click the With drop-down

choices checkbox.

348 Creating and Editing Forms CambridgeSoft

Setting Box Properties
 5. Click the button to display the menu.
6. Select any item on the menuthe text appears
in the top left corner of the box and the button
disappears.
Click within the data box to make the button
reappear.
Adding Scroll Bars
You can add scroll bars to a data box so you can
scroll through any additional data that is not visible
within a data box.
To add a scroll bar:
1. Right-click a data box and choose Properties.
The Box Properties dialog box appears.
2. In the Box style section, select With scroll bars.
3. Click OK.
The scroll bar appears on the bottom right in
the data box.
need a graphic here of a data box with scroll bar.
Hiding Data Boxes
You can show or hide boxes when switching
between query and browse mode. For example,
hide data boxes when you want hide non-searchable
boxes during query entry. Show data boxes to
display information useful for query entry.
When you are in form layout mode, all boxes are
visible, regardless of the setting.
Chem & BioOffice 2006 /ChemFinder
To set when boxes are hidden:
1. Right-click on the box and choose Properties.
2. In the Box Style area, select Hidden in Browse
Mode or Hidden in Query Mode.
3. Click OK.
4. Deselect the Layout Mode button to view the
results.
Customizing Text
You can customize text fonts, sizes, styles, colors,
and alignment in form boxes using the Text Format
toolbar. All of the standard text formatting options
are available.
To display the Text Format toolbar:
From the View menu, point to Toolbars, then
select Text Format.
The Text Format toolbar appears.
NOTE: Text copied from a word processor such as
Microsoft Word retains its styles when pasted into a Rich
Text box.
The text format toolbar is active:
When you are editing a memo field in a rich
text box. In this case, font changes apply only
to the current selection within the text.
When you are editing in a regular data (or struc-
ture) box. Font changes apply to the entire
contents of the box.
When you are in form edit mode, with the
selector tool active, and one or more boxes are
selected. Font changes apply to all selected
boxes (except frames around data boxes).
Customizing Fonts
All the labels on ChemFinder objects can be edited
to your specifications. You can edit any labels font,
font style, size, and color.
Creating and Editing Forms 349
Setting Box Properties
 To set the font for a label: To specify the numeric format:
1. Click Font. 1. Right-click on a data box containing numeric
The Font dialog box appears. data and choose Properties.
Administrator

The Box Properties dialog box appears.

2. Set the text font, style, size, and color.

The sample area previews the font.
3. Click OK to commit the changes.
2. Click Format.

NOTE: To change the color of the atom labels in the The Numeric Format dialog box appears.
structure box, you must use the Periodic Table. See Using
the Periodic Table on page 434

Customizing Numbers
Using the Box Properties dialog box, you can
specify how numeric data is displayed in forms you
can customize the following properties:
Currency symbol
Decimal position
Scientific notation 3. Select the appropriate option:

If you want to Then click

display

a varying number of Unformatted.

decimal places

a currency symbol Currency and select

the symbol from the
drop-down menu.

350 Creating and Editing Forms CambridgeSoft

Setting Box Properties
 The Form properties appear.
If you want to Then click
display

the currency symbol Symbol on right when

to the right of the a currency symbol is
number selected.

a standard Fixed point and select

floating-point value the number of
with a selected decimal places.
number of decimal
places
3. Take the appropriate action:

the numbers Scientific and select

displayed in scientific the number of To set the Click
notation decimal places. background
color of the
An example of the format you select is shown
in the Sample area of the dialog box. form Form Background.
4. Click OK.
The format is applied to the current data box. form in query mode Query Background.

Setting Color The Color dialog box appears.

You can set the following color options:
The form background color
The color of the form in query mode
The default background for all forms
To set the form background and form query colors:
1. Right-click on a data box and choose Properties.
The Box Properties dialog box appears.
2. Click the Form tab.

4. Select a color.
5. Click OK.
The Form or Query Background button
changes to reflect the color you choose.

Chem & BioOffice 2006 /ChemFinder Creating and Editing Forms 351
Setting Box Properties
 To set the default background color:
1. From the File menu, choose Preferences.
2. In the Preferences dialog box, click Color.
Administrator
3. On the Color tab, click Form Background.
4. In the Color dialog box, select a color and click
OK.
The color you chose becomes the default form
background color.
Editing Forms
You can move or resize boxes and other objects on
your form with the Selection tool and the items in
the Edit menu.
Selecting Objects on a Form
You can use the Selection tool to choose data boxes
and other objects on a form so you can move,
resize, or delete them.
When the selection tool is active, the Edit menu
commands apply to the boxes themselves. When
the selection tool is not active, the Edit Menu
commands apply to the contents of the active data
box.
To select an object on a form:
On the Form toolbar, click the Selection
tool , then click an object on the form to
select it.
A highlight appears around the object
indicating that it is selected.
Selection Marks
To select multiple objects on a form:
1. On the Form toolbar, click the Selection
tool .
2. Do one of the following:
352 Creating and Editing Forms
Press the Shift key and click on the multiple
objects.
Drag the Selection tool around the boxes
you want to select.
To select all the objects in the form:
From the Edit menu, choose Select All.
Moving Objects
You can move data boxes or any other object to a
different place on a form with the Selection tool.
To move objects on a form:
1. On the Form toolbar, click the Selection
tool .
2. Select the objects to move.
3. Drag the objects to a different place.
NOTE: To move a subform, you must click- drag the title
bar of the subform, not its contents.
To move objects one pixel at a time:
1. Select the objects you want to move.
2. Press an arrow key in the direction you want to
move the objects.
The objects move one pixel in the direction of
the arrow key.
Resizing Objects
You can resize a data box or any other object by
stretching it with the Selection tool.
NOTE: You cannot resize more than one object at a time
or simultaneously resize a box and its frame, unless you
create a framed box using the Framed Box tool. For more
information, see Creating Boxes with Frames on page
341.
CambridgeSoft
Editing Forms
To resize objects on a form: From the Edit menu, take the appropriate
action:
1. On the Form toolbar, click the Selection
tool .
If you want to Then choose
2. Position the pointer over an edge or corner of
the object until the pointer is a double-headed
arrow. reverse the effect of Undo.
the last change you
made to the form or
object

3. Drag in the direction you want to resize.

reverse the effect of Redo.
Undo
To resize objects one pixel at a time:
1. Select the object you want to resize. NOTE: Undo and Redo work over multiple changes.
2. Place the mouse pointer over an edge or corner Either command can be used repeatedly to reverse multi-step
of the object until it is a double-headed arrow. operations.
3. Press an arrow key in the direction you want to
resize the object. Ordering Objects
The edge of the object moves one pixel in the
direction of the arrow key. You can use the Bring to Front and Send to Back
commands to place data boxes in a specific
Deleting Objects sequence as follows:

You can remove data boxes and other objects from
a form with the Selection tool or items on the Edit
menu.
To remove objects from a form completely:
1. On the Form toolbar, click the Selection
tool . 2. From the Edit menu, choose Bring to Front to
2. Select the objects you want to delete.
3. From the Edit menu, choose Clear.
The object is removed from the form.
Reversing and Restoring
Changes
Select which overlapping data box is on top.
Set the order in which the cursor moves when
you press the Tab key.
To put a box on top or bottom:
1. Select the box.
put it on top, or choose Send to Back to put it
on the bottom.
The order in which data boxes are created is the
order in which the cursor moves as you press Tab.
You can set to which data box the cursor moves
first or last.

You can use the items on the Edit menu to reverse To set the cursor to move to a data box first:
or restore changes you made to a form. 1. Select a data box.
To reverse or restore changes: 2. From the Edit menu, choose Send to Back.

Chem & BioOffice 2006 /ChemFinder Creating and Editing Forms 353
Editing Forms
 3. Press the Tab key.
If you want to Then choose
The cursor moves to the box you set.
Administrator

line up along the

To set the cursor to move to a data box last:
middle of an object in Horizontal Center.
1. Select a data box.
a horizontal line
2. From the Edit menu, choose Bring to Front.
The box you set is the last box the cursor right edge of an Right.
moves to when you press Tab repeatedly. object

Aligning and Distributing The form objects line up according to your

choice.
Objects
You can line up objects relative to each other by To evenly space objects on a form:
aligning them and space objects at an equal distance
1. Press the Shift key and click the objects to
apart by distributing them.
distribute.

NOTE: In framed dialog boxes, the inner data box is 2. From the Edit menu, point to Distribute, then
aligned, not the frame. take the appropriate action:

To line up objects on a form:

If you want to Then choose
1. Press the Shift key and click the objects to align. space objects
evenly between
2. From the Edit menu, point to Align, then take
the
the appropriate action:

outer boxes of the Vertically.

If you want to Then choose
form
line up along the

left and right of the Horizontally.

top edge of the first Top.
form
object you place on
the form
The form objects are spaced according to your
choice.
middle of an object in Vertical Center.
a vertical line
Changing the Layout of
bottom edge of an Bottom. an Existing Form
object
You can use the Form Generation dialog box to
left edge of an object Left. automatically change the overall layout of an
existing form.
354 Creating and Editing Forms CambridgeSoft
Changing the Layout of an Existing Form
To change the layout of an existing form: 6. In the Form style section, select the form style:

1. In a form, right-click the background, then

choose Data Source. If you want the Then, in the
boxes to Form style
2. In the Form Properties dialog box, click the
section, click
Form tab.

be surrounded by a Framed.
frame

be labeled above Titled.

be labeled to the left Labeled.

not be labeled Plain.

7. In the Columns list, choose the number of

3. Click Generate new form, then click Style. columns, between one and four.
The Form Generation dialog box appears. 8. In the Grid size list, choose the size and
spacing of the boxes and grid:

If you want the boxes Then

to be choose

larger and spaced further Large.

apart

medium, relative to the Large Medium.

and Small settings
4. In Choose Fields to be included section, click
the field names to include.
smaller and spaced closer Small.
5. To have a Structure box in the upper left corner
together
of the form, click Structure in upper left of form.
9. Click OK.
A message box appears.

Chem & BioOffice 2006 /ChemFinder Creating and Editing Forms 355
Changing the Layout of an Existing Form
 10. Take the appropriate action: Setting Security Options
If you want to Then click
To set what ChemFinder form options are available
to users:
Administrator

change the overall layout for Yes. 1. Right-click in the form you want to secure, and
the current form choose Properties.
The Form tab of the Box Properties dialog
create a new form based on No. box appears.
the existing form

Securing Forms
You can control the options available to users of
your forms by setting the security options.
You can also provide the database connection
information used to log on to an MS Access
database. MS Access provides a security system that
allows the creation and management of usernames
and passwords, and the assignment of permissions
to those usernames. MS username password 2. Click Security.
account information is stored in the Workgroup
NOTE: The Security button does not appear if the
Information file (.mdw, .mda). For more
security on your form has been set to not allow access to
information about securing an MS Access database,
the Security options.
see Opening a Secured MS Access Database on
page 337. The Form Security dialog box appears.

The lower left corner of the dialog box

indicates whether security is defined.
3. Type the user name to use for logon in the
Username box.
The Enable button becomes available.

356 Creating and Editing Forms CambridgeSoft

Securing Forms
 4. Type the password to use for logon in the Pass-
word box. If you want users Then click
to
Use of a password is optional.
To enforce Workgroup Security in an MS Access
use a username pass- Logon to MS Access
Workgroup Administrator database: database
word to log on to the
Take the appropriate action: MS Access database
(.mdb files)
If you want to Then
be prompted to log on Prompt for database
to a database with a logon
enter a work- Type the name of the MS
group file name Access Workgroup data- username password
base in the Workgroup when the form is open
Information file box.
use a username pass- Protect molecule
word to open the database
browse for the Click File and select the
workgroup file file. molecule database
(.mst files)

NOTE: Enforcing workgroup security is optional. be able to access the Security dialog avail-
Form Security dialog able.
To select the Database Security options you want box
enabled:
Take the appropriate action: encounter all of the Database security.
above options
If you want users Then click
to To select the Forms options you want enabled:

be prompted to log on Password to open

with a username pass- Form
word to open a form

Chem & BioOffice 2006 /ChemFinder Creating and Editing Forms 357
Securing Forms
 Take the appropriate action:
If you want users Then click
to
If you want users Then click
to
Administrator

use scripts Can use scripts menu

open or create data- Open/create data-

bases base edit scripts Edit scripts

create forms Create new forms use all of the above Automation
options
open forms Open other forms
To select the Edit options you want enabled:
Take the appropriate action:
edit forms Save changed forms

If you want users Then click

change the layout of a Change form layout
to
form

clear forms Clear

use all of the above Forms
options
delete relational and Cut
structural data
NOTE: The behavior of Forms permissions has changed
from earlier versions of ChemFinder. If you disable Forms copy relational and Copy
permissions you cannot open the Properties dialog box by structural data and
right clicking on the form. You must go to the File menu and multiple table rows to
select Database to open the Properties dialog box. the clipboard

To select the Automation options you want paste relational and Paste
enabled: structural data from
Take the appropriate action: the clipboard

If you want users Then click Perform all of the Cut/copy/paste

to above functions

To select the Browse options you want enabled:

access OLE automa- Allow CAL/OLE
tion writing and Automation access
programming
NOTE: Must be
checked to enable
export to Excel

358 Creating and Editing Forms CambridgeSoft

Securing Forms
 Take the appropriate action
If you want users to Then click

If you want users Then click

to search exact structure Full structure
only
browse databases Browse database
records search substructures Substructure
only
view data in forms in a View form as table
table search similar struc- Similarity
tures only
view data in contin- View in continuous
uous view forms view use all of the above Searching
options
edit and view struc- Edit/view structures
tures in ChemDraw in ChemDraw To select the Update records options you want
enabled:
view structures in View structures in Take the appropriate action:
Chem3D Chem3D
If you want users to Then click
perform all of the Browse be able to
above options
update database Update records
To select the Search options you want enabled: records
Take the appropriate action:
add database records Add new records

If you want users to Then click

delete database records Delete records

submit queries Query database

To allow users to import data SDFiles or RDFiles:
records
Click Import data.
use current hit list for Search over current To allow users to export data, including delimited
searching list text files:
Click Export data.
search the entire data- Search over full data-
base To select the Print options:
base

save and manipulate hit Enable hit list tools

lists

Chem & BioOffice 2006 /ChemFinder Creating and Editing Forms 359
Securing Forms
 Take the appropriate action: 2. Enter your password, then click OK.

Security is disabled and the defaults are reset.

If you want users to Then click
Security Disabled appears in the lower left
Administrator

corner of the Form Security dialog box.

print a single record only Single record

Print several records Several records

Overriding Security
You can temporarily remove security in order to
Use print preview mode Print preview
edit the security options.

perform all of the above Print To temporarily disable security:

functions
1. In the Form Security dialog box, click
To finish selecting options: Override Security.

1. Click Enable. The Validate Security dialog box appears.

2. Click OK.
NOTE: This form only appears if you entered a password
The options you choose are applied to the when you enabled security. SeeSetting Security Options on
form.
page 356

Disabling Security
You can disable security and reset the defaults.

To disable security and reset defaults:

1. In the Form Security dialog box, click Disable.

The Validate Security dialog box appears.

2. Enter your password, then click OK.
NOTE: This form only appears if you entered a password
when you enabled security. SeeSetting Security Options on You are allowed to edit the security options.
page 356 Security Overridden appears in the lower left
corner of the Form Security dialog box.

To turn the security back on:

In the Form Security dialog box, click Over-

ride Security to toggle security back on. Secu-
rity Enabled appears in the lower left corner
of the Form Security dialog box.

360 Creating and Editing Forms CambridgeSoft

Securing Forms
Chapter 16: Relational Data and
Subforms
Overview
Subforms allow you to work with multiple data
tables in a relational database. You should be
familiar with working with ChemFinder forms and
databases before proceeding to subforms.
Accessing Relational
Data Using Subforms
A subform is a special box within a form that
behaves like a separate form file. A subform is used
to display information stored within a database, but
it usually displays data from a different database (or
different table within the same database) than the
main form. A subform is usually linked to the main
form, so that retrieval of data in the main form also
retrieves related records in the subform.
Like other types of boxes, you can move select and
resize a subform on the main form. However, you
cannot select it by clicking inside it. You must click
the title bar. When you click inside a subform, you
you activate the miniature form inside the box and
can work within it.
Below are examples of subform use:
You have data that is associated in a
one-to-many relationship. For example, you
want to view a chemical structure together with
its physical properties, stored in a separate
table.
Chem & BioOffice 2006 /ChemFinder
You are running a stockroom and you want to
store package sizes and prices in the same place
because they are related. Each chemical may be
available in lots of package sizes, and you
wouldnt want to re-draw the structure every
time you added a new package. You can use a
subform so the physical property information
is entered once in the main form and the
package sizes and prices are entered many
times in the subform.
By linking these two data tables with a linking
field you can make these tables relational; one
table can interact with the other. The contents
of a linking field are not important, as long as
they are different for each record in the main
form. Various forms of ID numbers are often
used as linking fields. As you browse through
the main form, corresponding records in the
subform appear.
Creating a Subform
You create a subform, place form objects on it, and
connect the subform to a database just as you do a
regular form. For detailed information on these
procedures, see Chapter 15, Creating and Editing
Forms on page 335.
Subform Generator
New in ChemFinder 10: The Automatic Subform
Generation feature enhances the Form Generation
feature introduced in ChemFinder 7, making it
possible to create subforms along with standard
data boxes.
Relational Data and Subforms 361
Creating a Subform
 Generating Subforms Automatically
Automatic subform generation is part of automatic
form generation (see Creating Forms Automati-
cally on page 338).
Administrator
1. Open the Box Properties dialog box and
select the Form tab.
2. Check the Generate Form checkbox, then click
the Style button.
Form generation
The Form Generation dialog box appears.
3. Click the Subforms button.
subforms button
362 Relational Data and Subforms
The Subform Generation dialog box appears.
link to field
link from field
Add button
4. For each subform you want to include:
a. Choose a field in the Link from box to specify
the linking field of the parent form.
b. Expand the table you want to display in the
subform in the Link to box, and select the
linking field of the subform.
c. Click the Add button to append the selected
subform to the list being generated.
5. When you have added all subform links, click
the OK button to close the dialog box and
return to the Form Generation dialog.
Subform Changes in Chem-
Finder 9
Creating and linking subforms in ChemFinder has
been simplified, beginning with version 8.5. Users
of previous versions should note the following
changes:
There is now a single dialog box which sets
properties of both the subform box and its
subform. You set all of the details in one place,
in a single operation.
In the new dialog box, the Database, Table, and
Field tabs reflect the data source of the
subform, not the parent form. The database
tree control in the dialog box also shows
subform data source. You can use the Explorer
window to display the tree control of the
parent data source, if they are different.
CambridgeSoft
Creating a Subform
 As before, the Form tab shows properties of the By default, newly created subforms are associated
subform, while the Subform tab shows with the same database as the main form.
properties of the box and the linkage between
the subform and its parent. To use a different database as the data source for
the subform:
When creating a new subform, you get the
same dialog box by clicking within the subform 1. Click the Open Database button.
as by clicking on the box header.
The Open dialog box appears.
For convenience, the dialog box comes up
automatically whenever you create a new
subform box.
After you have created a subform, the subform
tool is deselected. This prevents the frequent
mistake of drawing a subform box, then trying
to draw a data box within it and getting another
subform.

To create a subform:

1. Start ChemFinder and open or create a form.

The form should have at least one data box,
and be linked to an existing database.
2. Click the Subform button on the Form
toolbar.
2. Choose a database and click Open.
The Database table appears in the tree control.
The following illustration shows the CS_Demo
database.

3. Click somewhere in the form and drag to create

a data box.
When you release the mouse button the
Subform Properties dialog box appears.

3. Select the table to be linked (in this case,

Synonyms).

4. Click the Form tab. Check Generate form. Set

the style if you like.

Chem & BioOffice 2006 /ChemFinder Relational Data and Subforms 363
Creating a Subform
 5. Click the Subform tab. The tab should contain Changing the Layout of
reasonable data (Link To SYNONYMS (subform)
= SYN_ID, Title = Synonyms) based on the an Existing Subform
choices made so far. You can use the Form Generator to automatically
Administrator

change the overall layout of an existing subform.

To change the layout of an existing subform:
6. Choose Mol_ID from the Link from MOLTABLE
(main form) drop-down menu.
NOTE: To use the subform relationally to the main
form, the two forms must have one field in common.
This Linking Field must share the same data type
(text, integer, real) as a field in the main form. The
fields do not need to have the same name.
1. Right-click on the title bar of the subform data
box and choose Properties.
2. Click the Form tab.
3. Select the Generate New Form checkbox, then
click the Style button.
4. In the Form Generation dialog box, click the
checkboxes of fields you do not want to
include. (The default is all fields selected.)
5. In the Form style section, select the form
options you want. For a detailed description of
the options, see Changing the Layout of an
Existing Form on page 354.
6. Click OK.
7. In the Properties dialog box, click OK.
An alert box appears.

7. Modify box properties as desired. You may

want to change the box title, font, presence of
scrollbars, etc.

8. Click OK. The new subform appears showing

8. Take the appropriate action:
one synonym.

9. Optional: double-click in the subform to If you want to Then click

switch it to table view.
change the overall Yes.
The Subform is connected to the database you
layout for the current
chose.
subform
In this example, when a record is retrieved in the
main form, its Molname is used to search the create a new subform No.
Synonym field of the Synonyms table of CS_Demo.
The subform displays the hits from this search. The subform is automatically changed.

364 Relational Data and Subforms CambridgeSoft

Changing the Layout of an Existing Subform
By default, the table name of the subform is
displayed in bold, 8 point Arial font.
Working with Subforms
You must select a subform to work with it. The
subform title bar is highlighted when the subform
is selected. After a subform is selected, the toolbars
affect the subform. You can use the Record tools to
browse the subform and add records.
To select a subform:
Click anywhere in the subform.
To return to the main form:
Click the main form.
To select a subform box:
With the selection tool, click in the title bar.
Searching a Subform
You search a subform the same way you search the
main form. You can search a subform and the main
form simultaneously.
To search:
1. From the Search menu, choose Enter Query to
clear the subform and main form.
2. Enter a query in the data boxes you want.
3. From the Search menu, choose Find.
If the subform is linked to the main form, a
cleared form appears. The search is executed,
and ChemFinder returns you to the main form
where it displays a hit list containing records
related to those that match in the subform
search. You can browse and save this hit list
just as you would a hit list from a main form
search.
Chem & BioOffice 2006 /ChemFinder
If the subform is not linked to the main form, it
behaves independently of the main form and is
searched separately.
Viewing Subform Data
in a Table
If you have more than one record in the subform
associated with a single record in the main form, it
may be more convenient to view the subform as a
table while you browse through the main form. The
table view shows you the complete list of related
records for each entry in the main form.
To display a subform in Table view:
Select the subform and do one of the
following:
Double-click on a record in the table.
From the View menu, point to Data Table,
and choose In Current Window.
A table view of the records in the subform
appears.
To return to the Form view, repeat the above action.
Using Scripts in Subforms
You can specify a CAL script to be executed when
you click an item in a subform in table view. The
subform can then be used as a list selection box.
The script can use CAL commands to retrieve the
clicked item, and perform an action on it. For more
information about CAL, see Appendix M: CAL
Commands.
To specify a CAL script:
1. Right-click on the subform header and choose
Properties.
The Subform Properties dialog box appears.
Relational Data and Subforms 365
Working with Subforms
 In Table view, the entries are blue and
underlined indicating that they are hot linked to
a script.
4. Click any of the hot links to run the script.
Administrator

2. In the Table script box, type the name of a CAL

script or click and select a script.
3. Click OK.

366 Relational Data and Subforms CambridgeSoft

Viewing Subform Data in a Table
Chapter 17: Working with Data
Overview Secured accessyou must open the database
with a user name and password. You are
Working with data includes: subject to the security restrictions applied to
the database.
Opening Databases
Browsing Databases NOTE: Earlier versions of ChemFinder cannot read
Creating a Database ChemFinder 7.0 .cfw files.
Creating a Portal Database
Entering Data into a Database Read-Only Access
Editing Data Any of the following conditions determine whether
Changing the Database Scheme a database opens in read-only mode:
You work with data within ChemFinder by entering If the component files (extensions .cfw, .mdb,
it into a database, editing it, and interfacing with .ldb, .mst, .msi) have read-only attributes.
ChemDraw and Chem3D.
If the files are on read-only media, such as
You can perform all of these functions on data CD-ROM.
using the commands in the menus, or you can use
If you select Read-only in the File Open dialog
the buttons in the Record toolbar for most of these
box when you open a form or database.
functions.
When you open a read-only database, the following
Add Commit Omit conditions apply:
Record Changes Record
READ appears in the status line.
You can not modify data in text or structure
boxes.

Delete
Undo
Changes Record
Opening Databases
When you open a database in ChemFinder, you can
access the data in any of three ways:
Normal accessyou can read and write data.
Read-Only accessyou can read but not
write data. The database is write-protected.
NOTE: If only the form (.cfw) file is set to read-only
READ does not appear on the status line and the database
can be modified.
Multi-user Access
If a database resides on a network, more than one
ChemFinder user may access it at the same time.
Each user can view, print, or modify records
independently of the others.

Chem & BioOffice 2006 /ChemFinder Working with Data 367

Opening Databases
 The following table shows how the type of user Microsoft Jet Relational Database
affects the other users in the group. Enginethe database engine that underlies
Microsoft Access enforces security. The user
User type Affect on other users names and passwords are stored in an MS
Administrator

Access Workgroup Administrator database.

Multiple readers in User actions do not affect each
read-only access other.
Multiple writers in All users can read and write. A
normal access user may see another users edits.
If two users try to edit the same
area at the same time, one is
alerted that the database is tempo-
rarily locked.
One writer, The writer, in normal access, is not
multiple readers affected by the readers. The
readers, in read-only access, may
see the writers edits.
If two people are viewing the same record within a
database, and one person changes the data in that
record, the second person will not see the changes
immediately. The changes will be visible when the
second user switches to another record, then back
to it.
For more information on Form access, see
Securing Forms on page 356. For more
information on MS Access security, see Opening a
Secured MS Access Database on page 337.
When you open a form or database that has security
options applied to it, you are prompted to enter a
username and password to log on.
When you open a secured MS Access database
from within ChemFinder, a username, password,
and workgroup information file is required.
Contact your Access Database Administrator for
this information.
To open a secured form:
1. In the Validate Form Security dialog box,
type your Username and Password, then click
OK.

Secured Access
ChemFinder supports the following types of If the form you access includes a secured
security: molecule database, the Database Logon
dialog box appears.
Form accessChemFinder enforces form
access security by requiring a user name and
password, which are stored in the form (.cfw)
file.

Molecule file accessChemFinder enforces

molecule file access security by requiring a user
name and password, which are stored in the
databases .mst file.

368 Working with Data CambridgeSoft

Opening Databases
 2. Type your Username, Password, and Workgroup
Information File name (if applicable), then click
OK.
The form opens.
Browsing Databases
You can browse a database using the buttons on the
Record toolbar.
First Record Go to Record Last Record
Previous Record Next Record
To Browse:
Click First Record to display the first record in
the database.
Click Previous Record to display the record
before the currently shown record.
Click Next Record to display the record after the
currently shown record.
Click Last Record to display the last record in
the database.
You can go directly to a specific record as follows:
1. From the Record menu, choose Go To Record.
The Record Number dialog box appears.
NOTE: The current record number is displayed in the
Status Bar.
2. Type the number of the record (within the
current list) to display, and click OK.
Chem & BioOffice 2006 /ChemFinder
The specified record is displayed.
NOTE: Record numbers are temporary, referring only to
positions within the current list in its current sort order. For
example, if you have done a search that found ten hits, then
the only valid record numbers are 110. If you want to move
to a specific absolute location in a database, you must run a
search for a value in a field that identifies that location.
The Data Table
Sometimes browsing through a data record set is
more convenient if the data is presented in tabular
format.
NOTE: You cannot add or modify records while viewing
data in a table.
To display data in a table:
On the View menu, point Data Table, then
choose In Separate Window.
A list window containing the fields and records
in the form appears.
To display a particular record in the form:
Click that records entry in the list window.
By default, the fields in the Data Table are displayed
in the order in which they were created.
To reorder the columns in the Data Table:
Working with Data 369
Browsing Databases
 1. Click one of the column headers to select the
column.
Column selection indicator
Administrator
2. Drag that header to a new position.
The cursor changes to the icon shown below.
The new position is indicated with a dashed
vertical line.
To resize the column widths in the Data Table:
1. Place the cursor on the dividers in the top
header.
The cursor changes to the icon shown below.
370 Working with Data
2. Click-drag to adjust the column width.
NOTE: To hide the column, right-click and choose
Hide Column from the context menu.
To resize the row heights in the Data Table:
1. Place the cursor on the dividers in the left
header.
The cursor changes to the icon shown below.
2. Click-drag to adjust the row height.
NOTE: To resize all rows, right-click in a column
header and choose Resize Rows to Fit from the context
menu.
R-Group Tables
In Data Table display, you can display a
substructure search as table of R-group
substituents.
1. Run a substructure search. You cannot prepare
a table from a full structure or similarity search.
NH
CambridgeSoft
Browsing Databases
 2. Switch to Data Table view.
3. Right-click in the Structure column, and
choose R-Group Table from the context menu.
The following changes occur:
the topmost structure is replaced with the
template not exactly the same as the query
you used, but one with Rs attached at all
positions which found substituents.
new columns are generated for all the Rs.
the other rows are populated with the Rs hi.t
NOTE: The data in this table is just for display. It is not
saved anywhere, nor can it be exported or sorted.
Chem & BioOffice 2006 /ChemFinder
Creating a Database
Instead of opening an existing database, you may
want to create a new, empty one. This procedure
results in a simple database with one table for
storing structures.
To create a database:
1. Right-click and choose Properties.
2. Click Create Database.
The Save As dialog box appears.
3. Choose the directory to which you want to save
the database.
4. Specify a name for the database, and click Save.
ChemFinder creates the database containing one
table (called MolTable) with four fields:
Structure
Formula
Molecular weight
Mol_ID
The Mol_ID field corresponds to a column in the
table where a numeric ID is automatically entered
as each structure is registered. The other fields
represent information stored in the structural
portion of the database, linked to the assigned ID.
Molecular formulas and molecular weights are
automatically calculated from a structure. These
internal fields cannot be edited or deleted.
After creating a database, you can create fields for
storing other types of data. It is not necessary to
create the entire set of fields before working with
the database. You may add more fields later.
Working with Data 371
Creating a Database
 Creating Tables The Create Table dialog box appears.

There is no limit to the number of tables a database

can contain. You may want multiple tables in a
Administrator

database in order to manage relational data, or

simply to organize different collections of
information in the same place.

A table must contain at least one column. When

you create a new table, ChemFinder creates a 4. Type a name for the new table, then click OK.
numeric column called ID. You can use this column The table appears in the Data Source tree.
to store integer data, or delete it and replace it with
your own columns.

Table names must:

Begin with a letter

Not contain punctuation characters

Not be the same as a table already on display

To create a new, empty table:

1. Right-click and choose Properties.

The Box Properties dialog box appears.

Deleting Tables
2. Click the Table tab. To delete a table from the database:

The Table tab appears: 1. In the data source tree, select the table to
delete.
2. Click the Delete Table button.

3. Click Yes.

The table and all data it contains are

immediately deleted from the database.

CAUTION
You cannot undo a deleted table. Before you delete a table,
create a backup copy of the database to prevent accidental
loss of data. For more information, see Backing up
Databases on page 377.
3. Click Create Table.

372 Working with Data CambridgeSoft

Creating a Database
Attaching Tables from Other
Applications
You can use ChemFinder to add chemical
structures to a database you have already developed.
If your database was developed in Microsoft
Access, you can open it directly in ChemFinder.
If you are using another database system such as
FoxPro, dBASE, Btrieve, Paradox, or Oracle, you
cannot open the database directly. You must open
or create a ChemFinder database, and use Attach
Table to link to tables in the data source. After you
attach a table, it appears and functions as if it were
part of your local ChemFinder database.
The procedure you use depends on whether the
tables you want to attach are from a file-based
(Access, FoxPro, dBASE) or non file-based
(Oracle) database system.
Attaching Files from a File-Based Data-
base
To attach a file-based database table:
1. Right-click and choose Properties.
2. Click the Table tab, then click Attach Table.
The Attach Table dialog box appears.
3. Click Open MS Access Database.
Chem & BioOffice 2006 /ChemFinder
4. From the Files of Type drop-down menu,
choose the type of database you want to access.
NOTE: The list of file types available in the Attach
Table Open dialog varies from one computer to another.
The files for which you have drivers installed shown. For
example, if the Paradox is not installed, you may not
have Paradox drivers on your system or in the
drop-down list.
NOTE: If the database type you wish to access is not
on the list, it may not be a file-based system, and you
need to connect using ODBC. For detailed instructions,
see Attaching Files from a Non File-Based
Database on page 373.
5. Choose the database to access, then click OK.
6. In the tree diagram, click the name of the table
you want to attach, then click OK.
The Database dialog box appears, showing the
newly-attached table along with the original
MolTable. The database is ready to use.
Attaching Files from a Non File-Based
Database
If the database you want to attach is not file-based,
such as Oracle, you can attach it using Microsoft's
Open Database Connectivity (ODBC).
To attach a non-file-based database table:
1. Right-click and choose Properties.
2. Click the Table tab, then click Attach Table.
The Attach Table dialog box appears.
3. In the Attach Table dialog box, click Open
Oracle/ODBC Data Source.
The Select Data Source dialog box appears.
Working with Data 373
Creating a Database

Administrator
4. From the Machine Data Source tab, select the
ODBC data source to access, then click OK.
NOTE: The ODBC data source dialog box shows all
data sources known to ODBC, including ChemFinder,
Access, and other file-based data sources. If you attempt
to open one of these through the ODBC dialog, you get
an error message. File-based data sources must be
opened using Open Database, as described above.
NOTE: If the ODBC data source dialog does not
show the database you seek, you may need to create a
new data source. You can do this using the New button.
For details, click the Help button in the ODBC dialog
box.
5. If you are prompted for a user name and pass-
word, enter it. If you don't know what name
and password to use, see your System Admin-
istrator.
6. Click on the name of the table you want to
attach, then click OK.
The source of the data to display on the form is
indicated, but the form is still blank. To access the
data, you need to draw some data boxes, and
indicate what data to show in each of those boxes.
374 Working with Data
Creating Fields
Whether you created a new database or are working
in an existing one, you can add or remove fields in
the selected table.
You can choose from the following types of fields:
Text fieldAllows you to enter text such as
names, comments, and references. A text field is
fixed in length, and requires that you choose a
maximum length (width) for any data item to be
stored in the field. If you enter a width of 50, then
you cant store any item with more than 50
characters in that field.
You can specify widths of text fields as large as 254
characters. If this is insufficient, you need to create
a Memo/Rich Text field instead.
Because the text field width cannot be modified
after a field is created, it is often wise to err on the
side of caution and make it longer than you need
initially. On the other hand, larger field widths also
create larger files and slower search times.
NOTE: Non-ASCII characters will not display correctly
in a data table text field.
Integer fieldUsed for whole numbers such
as ID's. All integers in ChemFinder are long, so can
accommodate billions of values (232 of them).
Double fieldUsed for real numbers such as
physical constants and unit prices. Real numbers in
ChemFinder are double-precision.
CambridgeSoft
Creating a Database
 Picture fieldAllows you to store a Windows
metafile, such as a spectrum or experimental setup,
as a data item in a database.
NOTE: A Picture box on a form may be used to display a
static, decorative picture attached to the form, or it may be
used to show pictures stored in the database which change as
you move from record to record.
Memo/Rich Text fieldUsed to display text.
Memo fields can be of any length. Because memo
fields are less structured, searching them can be
slower than searching a text field. Additionally,
memo fields cannot be sorted.
To search for text:
1. Right-click in a memo or plain text field.
2. Select Find Text.
The Find Text dialog box appears.
3. Enter the text and the match conditions.
4. Click Forward or Backward to search.
5. Click Find Next on the context menu, or use F3
to search for the next occurrence.
Memo fields can store Styled Text. For more
information, see Styled Text on page 383.
Date fieldAllows you to store dates. The
dates are displayed according to the settings in the
Windows Regional Settings control panel.
Chem & BioOffice 2006 /ChemFinder
Structure fieldConsists of four fields: a
numeric ID stored in the relational database, plus
three fields (Structure, Formula, MolWeight) that
take data from the ChemFinder structure database
files.
BooleanUsed with checkboxes. When searching
Boolean fields, you can only search for ON. This is
because ChemFinder automatically clears all fields
when activating the Queries form.
You can create more than one set of structure fields
in a table. Each is assigned a unique set of names,
and each refers to its own ID column in the table,
although all structural data is taken from the same
structure database files.
To create a field:
1. Right-click on a data box and choose Properties.
The Box Properties dialog box appears.
2. Click the Field tab.
The Field properties appear.
3. Click Create Field.
Working with Data 375
Creating a Database
 The Create Field dialog box appears. The structure displayed as a diagram.
The Molecule ID, which connects the structure
to a record in a relational table.
The formula derived from the structure.
Administrator

The molecular weight derived from the struc-

ture.
To create multiple structure columns in a table:
1. From the File menu, choose Database.
The Form Properties dialog box appears.
4. In the Name box, type a name.
5. In the Type box, choose a data type.
6. For text fields only, in the Width box, choose a
width.
7. Click OK.
The name of the new field appears in the data
source tree.

Deleting Fields
Just as you can create any field and assign it to a data
box at any time, you can modify the database by
deleting fields from the selected table. 2. Create or open a database.
To delete a field: 3. Click the Field tab.

1. In the field list, select the field to be deleted. 4. Select the Table in which you want to create
new structure columns.
2. Click Delete Field.
5. Click Create Field.
3. When prompted whether you want to delete
the selected field, click OK to delete it or click The Create Field dialog box appears.
Cancel to leave it unmodified.

CAUTION
When you delete a field, all data contained in the field is
also deleted. You are not warned explicitly about this.

Adding Multiple Structures

You can include more than one structure on the
same form by creating multiple structure columns
in a table. Each structure column you create
represents four types of data:
6. Select Structure from the Type drop-down list.
An uneditable name is assigned to the field.
7. Click OK.

376 Working with Data CambridgeSoft

Creating a Database
 Four new fields appear in the list and are
named to belong to the same set of structure
columns.
8. Connect the new fields to boxes by
right-clicking on the appropriate data box and
choosing the field.
Adding Structures to
Non-Chemical Databases
If you opened a database that you created using a
program other than ChemFinder and you want to
add structures to it, you can create structure fields
in any modifiable (non-attached) table.
To create a structure field:
1. Open a database.
2. Right click, choose Properties.
3. Click the table to which you want to add struc-
tures.
4. Click the Field tab.
5. Click Create Field.
The Create Field dialog box appears.
6. From the Type drop-down list, choose Struc-
ture, then click OK.
You do not provide a name or other details when
you create Structure columns. ChemFinder
automatically creates four columns and names
them. These columns contain no data until you
enter structures into the database.
Backing up Databases
To back up the current ChemFinder database:
1. Choose Copy Database from the File menu.
A Save As dialog box appears. By default, your
copy is named YourDatabase_copy.cfw.
2. Rename your copy (if you wish), select a loca-
tion, and click OK.
Chem & BioOffice 2006 /ChemFinder
A complete set of ChemFinder database files is
created in the selected location.
Moving Databases
ChemFinder saves only the definition of the form
and information for connecting to the database.
The actual data are stored in files with .msi and .mst
extensions for structure data and in files with an
.mdb extension for non-structural data. If you want
to move a database to another computer, you must
move (for a default ChemFinder database) at least
four separate files. This number might be greater if
you have several forms that access the same
database.
NOTE: The .msi, .mst, and .mdb files all have the same
file name, but the name of the .cfw files might be different
depending on how you saved them.
After you move the database to its new location,
open your forms to make sure the data source links
have been retained. If ChemFinder cannot locate
the data source and displays an empty form, you
need to use the Database command on the File
menu to reconnect to the data source.
If the form is connected to a remote data source on
a network, you have fewer files to move. The data
source can remain on the remote machine, and you
only move the .cfw file that contains your form for
accessing the data. You may need to reconnect it to
the data source if it is not done automatically. This
situation is common in large organizations where
several people access the same central data source.
Creating a Portal Data-
base
To carry out certain operations, such as sorting
structural data, ChemFinder needs to create
temporary tables in a database. This cannot be done
in a read-only source such as a data CD.
Working with Data 377
Creating a Portal Database
 Instead of accessing the read-only source directly,
you can create a portal databasea local, writable
database with attachments to the external tables of
interest. The portal looks and behaves just like the
Administrator
target database, but without the limitations.
ChemFinder creates a portal database when
needed. For example, if you are using a database
CD, perform a search, and attempt to sort by
formula, a message appears that offers to create a
local database, attach the current table, save the
form, and proceed with the sort. If you create the
local database, you can use the new form to get the
data with full functionality and performance.
When you are using a read-only database,
ChemFinder offers to create a portal database.
ChemFinder does not automatically create a portal
database during searching because it would destroy
the hit list. When this happens, ChemFinder
displays a message. You can manually create a portal
database or sort to automatically create one, then
repeat the search.
Entering Data into a
Database
You enter data into a database by adding a new
record. Adding a new record consists of three steps:
378 Working with Data
Clearing the form
Adding new data
Committing the new entries
Clearing the Form
To begin adding a new record:
1. Create a form and link it to a database. For
more information, see Creating Forms Manu-
ally on page 340.
The form should contain all the data boxes you
want to view and edit. The boxes should be
assigned to their appropriate fields.
2. From the Record menu, choose Add New
Record.
3. All of the boxes in the form are cleared to
prepare for entering new data. The Status Bar
is updated to show that you are in record addi-
tion mode:
Adding New Data
To add alphanumeric data:
Click in a box with an alphanumeric field and
type the data.
CambridgeSoft
Entering Data into a Database
To add a structure: The new record is added to the database.

1. Right-click in a box with a structure field.

NOTE: Selecting Commit Changes (or moving to another
2. Do one of the following: record if you have two or more records) saves the data to the
database. You do not need to select Save from the File menu;
If you want Then right-click and choosing Save saves any changes to the form layout, not
to choose changes to data in a database.

draw a structure a. Edit Structure.

ChemDraw opens.
b. Draw the new structure
in the From ChemFinder
window.
c. From the File menu,
select Exit and Return to...
to insert the structure
into the form.
import a struc- a. Read Structure.
ture
b. Select the file to insert
and click Open.
Duplicating Records
You can create a new record by modifying an
existing one. To duplicate a record:
From the Record menu, choose Duplicate
Record.
You are in Add Mode and the form fills with
data from the previously displayed record.
When you select Commit Changes, you create
a new record whose fields contain the data on
displayed. Before committing the duplicate,
you can modify fields or structure and commit
changes just as you would with any other new
record.

The file is inserted into NOTE: When duplicating records, only those fields that
ChemFinder. are visible on the form are duplicated. Data in fields present
in the database but not visible on the form are not copied into
the new record. The new record has a new Molecule ID.
NOTE: See the ChemDraw Users Guide for information
about using ChemDraw.
Undoing Data Entry
Committing the New Data Before committing a new data entry, you can revert
the contents of the form to its previous unmodified
When you finish entering all of the data items, do
state.
one of the following:
Perform another action such as moving to
To undo your changes:
another record or printing. From the Record menu, choose Undo
The record is automatically committed. Changes.

From the Record menu, choose Commit After you commit the changes, they cannot be
Changes. undone.

Chem & BioOffice 2006 /ChemFinder Working with Data 379

Entering Data into a Database
 Editing Data
Modifying the data in a database is performed by
directly changing the data items on the form and
Administrator
(for compounds containing carbon) followed
alphabetically by any other elements. Formulas for
compounds without carbon are sorted in
alphabetical order. Sorting text fields such as

committing those changes. molecular name sorts the records alphabetically.

After sorting, the database must be reset to its

NOTE: The Formula and MolWeight fields are
automatically calculated by ChemFinder from the Structure
field and cannot be edited by the user. The MOL_ID field
is also set automatically by ChemFinder and cannot be
edited.
Editing Data
original state before you can update it.
NOTE: You cannot edit records sorted by formula or
molecular weight. However, if you attempt to sort one of these
fields, ChemFinder offers to set up a database (a portal
database) which allows the operation. For details, see
Attaching Tables from Other Applications on page 373.

To edit data:
Sorting Fields
Click the data box whose data item you want to
edit. To sort a field:

If you click on a Structure data or a picture box it is
highlighted. If you click on a data box containing
alphanumeric data, a cursor appears in the data box.
To edit alphanumeric data:
1. Replace it with the text or number you want.
Right-click in the field you want to sort, point
to Sort, then choose Ascending or Descending.
Sorting from the Data Table
To sort directly from the Data Table:

2. From the Record menu, choose Commit 1. From the View menu, choose Data Table.
Changes, or move to a different record.
2. In the Data Table, double-click on the table
header of the field you want to sort.
NOTE: Moving to a different record always commits
changes first.

Sorting Data
You can sort most types of data in a form. Sorting
the Mol_ID field, the molecular weight field, or any
other numeric field arranges the current list in
increasing or decreasing order. Sorting the structure
field arranges that field by increasing number of
atoms contained in the structure. Implicit Sorting in Reverse Order
hydrogens are not counted. Sorting the formula
field orders the records by increasing C-H-N count To sort a column in reverse order:

380 Working with Data CambridgeSoft

Editing Data
 Double-click on the table header again.
NOTE: There is also a context menu option for sorting in
Data Table view. Right-click in a column and choose Sort
Column.
Sorting Languages Other Than English
Text that you sort must be in the same language as
default language of the system on which the
database was created, or an incorrect sort order can
occur.
The ChemFinder sample databases, created in
English, can be sorted correctly using the following
languages:
English
German
French
Portuguese
Italian
Modern Spanish
If you want to sort text in a different language than
the one in which the database was created, perform
the following procedure:
1. On a computer using the same language as the
text you want to sort, open MS Access.
2. Open the .mdb file you want to sort.
3. Compact the database: on the Tools menu,
point to Database Utilities, and click Compact
Database.
4. After the database is compacted, close MS
Access.
The correct sort information is written into the
database. When you perform a sort in
ChemFinder, the sort order will be correct.
Resetting the Database
To reset the database to its original state:
Chem & BioOffice 2006 /ChemFinder
From the Search menu, choose Retrieve All.
Editing Structures
You can edit structures by using the ChemDraw
drawing tools. You can also neaten the appearance
of a structure by cleaning it up.The Clean Structure
command is used to neaten the appearance of
molecules by regularizing bond lengths and angles.
Since the degree of change required cannot be
determined a priori, the Clean Structure command
begins gently. You may need to repeat the
command to get the changes you wish. For more
details about how the command works, see Using
Structure CleanUp in Chapter 7: Advanced
Drawing Techniques of the ChemDraw Users Guide.
Before committing a data entry, you can revert to
the previous unmodified record by choosing Undo
Changes from the Record menu.
To edit structural data:
1. Do one of the following:
Right-click in the structure box and choose
Edit Structure.
Double-click the structure box.
ChemDraw opens and the structure appears in
the From ChemFinder window.
2. Edit the structure using ChemDraw.
3. Click in the ChemFinder window or close the
ChemDraw window when you are finished.
4. From the Record menu, choose Commit
Changes, or move to a different record.
The changes are stored.
To clean up a structure:
1. Right-click in the box containing the structure
to neaten.
2. Choose Clean Structure.
3. To save the cleaned up structure, choose
Commit Changes, from the Record menu.
Working with Data 381
Editing Data
 Working with Structures Using Chem-
Draw
You can enter or edit ChemDraw structures within
Administrator
Data Boxes that are of the Structure field type. You
can work in ChemDraw directly, or work in the
Structure data box using the ChemDraw ActiveX
toolbar. You choose the default in the Structure
data box Box Properties dialog box.
To set the preference:
1. Right-click in the Structure box.
2. Choose Properties from the context menu.
3. Use the drop-down menu in the Box Style
section to choose your default:
a. ChemDraw style to use the ActiveX toolbar
b. ChemFinder style to edit in ChemDraw.
TIP: When ChemDraw style is the default, you still
have the option of editing directly in ChemDraw. Just
right-click in the Structure box and choose Edit in
ChemDraw.
To edit a structure:
Double-click in the structure data box.
ChemDraw opens or the ActiveX toolbar
appears, depending on your default.
If you already have a structure in a data box, that
structure appears in the edit window. You can
modify and manipulate the structure just like any
other ChemDraw structure.
If there is no structure in the Structure data box, the
edit window is blank. You can draw a structure to
store in the ChemFinder database. When you have
finished, do one of the following:
If you are editing in ChemDraw, choose Exit
and Return to Structure from the File menu.
If you are editing with the ActiveX toolbar,
click outside the Structure box.
382 Working with Data
The new or edited structure is now displayed, but
has not yet been added to the database.
From the Record menu, choose Commit
Changes, or move to a different record.
The changes are stored.
With a few exceptions, ChemFinder can store any
chemically meaningful structure or reaction that
can be drawn in ChemDraw. Within ChemDraw,
you can confirm that a structure is chemically
meaningful by selecting it and choosing Check
Structure from the Structure menu. For more
information, see the ChemDraw Users Guide.
Two exceptions are:
ChemFinder does not support importing
molecules with multiple or variable points of
attachment such as ferrocene.
ChemFinder does not recognize bare
heteroatoms. For example, if you draw the
following structure:
N
ChemDraw reports an illegal valence when you
choose the Check Structure command.
ChemFinder automatically infers hydrogen atoms
to main-group elements as necessary to fill their
lowest acceptable valence. The structure above is
registered in ChemFinder as methylamine,
CH3NH2.
Structures and reactions drawn with query
properties are generally meaningful only in the
context of a query. Query structures can be stored
in a ChemFinder database, but they are not treated
as Markush structures and are not guaranteed to be
hit by all valid search queries. For more
information, see Appendix J: Structural Query
Features.
CambridgeSoft
Editing Data
ChemDraw allows you to draw many objects that
have no chemical meaning. These include boxes,
circles, arrows, orbitals, and others. It also allows
you to assign non-chemical styles (color) to objects
that have chemical meaning. ChemFinder ignores
these properties, and stores only objects with
chemical meaning in structure fields.
To store a ChemDraw drawing exactly as drawn,
store it as a picture. You can copy and paste a
ChemDraw drawing into a Picture field.
NOTE: Objects stored in a Picture field have no chemical
significance and cannot be searched.
Viewing Models using Chem3D
ChemFinder also provides access to Chem3D; a
Structure data box can be designated as Chem3D
style.
To view the molecular model for a structure:
1. In the Database pane of the Explorer window,
double-click the Structure field to add another
Structure field to the form.
2. Right-click in the field to display the Box
Properties dialog box.
3. In the Box Style section, select Structure
(Chem3D style) from the drop-down menu.
Chem & BioOffice 2006 /ChemFinder
The Structure field displays a 3D structure.
To rotate the model or modify the display, double-
click in the field. If you then right-click in the field,
the context menu displayed is the Chem3D control
context menu, giving you access to Chem3D
commands.
See the Chem3D Users Guide for more
information about using Chem3D.
NOTE: Unlike interaction with ChemDraw, changes you
make to a model within Chem3D are not transmitted back
to ChemFinder, and thus are not saved. You can put a
picture of the Chem3D model into a database by saving the
Chem3D model as a metafile and inserting it into a Picture
field. The picture does not retain a connection table and
cannot be edited.
Styled Text
You make changes to text fonts, sizes, styles, colors,
and alignment with the tools on the Text menu or
the Text Format toolbar shown below.
To display the Text Format toolbar if it is not
visible:
On the View menu, point to Toolbars, and
choose Text Format.
Working with Data 383
Editing Data
 The Text Format Tool appears. To delete an entire record:
1. Move to the record that you want to delete
.

Subscript
Font Bold Bullets
using the Record commands or tools.
Align
Administrator

Left 2. From the Record menu, choose Delete Record.

The record is permanently removed.

Font Size Superscript Center NOTE: You can delete multiple records if you use the Table
Right view.

You can format text in plain text or Memo/Rich

Text data fields. Changing the Database
Scheme
Undoing Changes
You can create or remove tables or fields in an
Before committing your changes, you can revert to existing or new database as long as the database is
the previous unmodified state. not read-only and you have permission to modify it.
You may also attach, or link, tables from external
To undo your changes: data sources.

From the Edit menu, choose Undo.
After you commit the changes, they cannot be
undone.
Redoing Changes
When you undo an action, the Redo command
becomes active. You can reverse the effect of the
Undo command by choosing the Redo command.
To redo the last action performed:
From the Edit menu, choose Redo.
The last action undone is reinstated.
Deleting Data
You can delete the contents of individual fields by
using the Delete or Backspace keys. You cannot
delete a structure, formula, molecular weight or
Mol_ID.
You use the Box Properties dialog box to perform
the following procedures.
To access the Box Properties dialog box:
1. Create or open a form and link it to a database.
For detailed instructions, see Creating a Data-
base on page 371.
2. Do one of the following:
From the File menu, choose Database.
Right-click any empty space in the form
window and choose Data Source.
The Box Properties:Database dialog box
appears.
If the database contains more than one table, only
one is selected at any given time. The contents of
the Field tab of the dialog box, and of the form,
reflect the selected table.
To select a table:
Click the table name.

384 Working with Data CambridgeSoft

Changing the Database Scheme
Chapter 18: Visualizing Data
With BioViz
ChemFinder 10 extends and improves the BioViz (pointed at) are displayed as red solid with a black
charting tool to make it even more useful, most circle. Mousing over a selected point displays a
importantly by adding Statistical Analysis. double hollow red circle surrounded by a black
circle. Points belonging to queries are displayed as
With BioViz, you can identify trends and solid colored points without circles.
correlations in your data, and within subsets of your
data, without the extra step of exporting to another Figure 18-1Point Selection
application. You can have as many plot windows as
you like, each showing a different visualization of
moused-over point
data from the current form.
BioViz is designed to be used with the Structure query point
Window and the Queries Tree. While not necessary
selected point
to creating visualizations, they offer considerable
convenience when working with plots. Before
working with BioViz, go to the View menu and More plotting flexibility
activate the Structure and Explorer windows. The
Structure window gives you a way to display You can now change the field plotted on the X or Y
structures without taking up room on the form. axis with the context menu.
The Queries Tree in the Explorer Window gives
1. Point in the area of the numbers just below or
you an easy way to track multiple hitlists.
to the left of an axis.
To create a new plot, view an existing plot, or delete 2. Right-click. The context menu displays a list of
a plot, use the BioViz Plots submenu of the View plottable fields.
menu. Plots are saved with the form and will come
back when it is opened, though they may be hidden. 3. Select a different field to plot on that axis.
Figure 18-2Changing Fields with the Context Menu
Improvements in Version
10
Better Selecting And Mouse-
overs
To facilitate viewing selected points when queries NOTE: You can only change fields when the chart is not
are displayed, the selected point is displayed as a locked.
double hollow red circle. Points being moused-over

Chem & BioOffice 2006 /ChemFinder Visualizing Data With BioViz 385
Improvements in Version 10
 Details Window
In ChemFinder 10 a new Details Window displays
field values (other than Structure) when viewing a
BioViz plot. To display the Details window, select it
Administrator
from the View menu.
Figure 18-3: View menu New Toolbar Options
The window floats by default, but can be docked
with other windows.
Figure 18-4: Details Window
To add new fields to the Details Window:
1. Right click in the Details Window.
2. Select the field to be displayed.
A check mark appears next to the selected field.
Fields display in the order you select them.
3. To remove a field from the Details Window,
right-click and deselect it.
386 Visualizing Data With BioViz
Removal of Empty Points
In version 9, a point which has an X value, but not
a Y value, is represented as a so-called empty
point on the plot with a distinctive marker. If there
is a Y value, but no X value, the point is simply
omitted (though noted). Version 10 omits both
empty X and empty Y points. All omitted
points are noted, and may be reviewed by clicking
the Notes button at the bottom of the chart.
Figure 18-5: Notes
Histogram Improvements
In ChemFinder 10, each bin in a histogram is
labeled with its high-low cutoff points.Note also
that the data for the selected bin is displayed at the
bottom of the screen.
Figure 18-6Histogram Labeling
data for selected bin
Also, histogram plots now respond to filtering.
CambridgeSoft
Improvements in Version 10
Figure 18-7Histogram Filtering The BioViz Plot Properties dialog box
appears.

Creating a Plot
To begin working with BioViz, select a set of data
to work with. You can plot an entire database or the
results of database queries. You can filter the plot to
limit the data range within a given dataset.
To create a new plot:
1. From the View menu, point to BioViz Plots and
select New.
2. Select a Dimension (one or two variables) and a
Style (line, scatter, or histogram).
3. Select the variable(s) from the drop-down
list(s).
4. Optional: select other options, change the
name.
5. Click OK to view the plot.

The plot appears in a separate window.

In a 2D plot, you may plot any numeric field on the

X axis and any other on the Y. For a 1D plot, you
choose only the value to be plotted on the Y axis,

Chem & BioOffice 2006 /ChemFinder Visualizing Data With BioViz 387
Creating a Plot
 where the X axis represents record number. For a
histogram, choose a single value to be plotted on Dialog Option Description
the X axis, with the frequency plotted on Y.
Another way to select a field to be a variable, or Bin By number: Sets up n bins
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create a 1-D plot is to right-click in a property field evenly spread across the
and select BioViz Plot from the context menu. whole range of values.

By size: Sets up bins of size n.

The number of bins will be
as many as are necessary to
cover the range.

Log scale Select this checkbox to

display a log scale.

When you right-click in a numeric data box, you Base Base of the log scale. You
may choose that value to be plotted on either axis, must enter a number, thus
or as a 1D plot against record number. In the latter for a base e log scale, you
case, the plot appears immediately when you release must enter 2.718281828
the mouse button. For a 2D plot, you must first
select a data box for the other axis. Use the Reset
X,Y command to clear both X and Y settings and
Locked Locks the display. When the
start again. display is locked, the
following have no effect:
BioViz Options filters
BioViz options are available from the Properties
changes in the current
dialog box and from the context (right-click) menu.
Some of the context menu commands repeat list
options in the Properties dialog box. These are not list coloring
repeated in the following tables.
Properties dialog box
Dialog Option Description options (except Name) are
blocked.
Dimension Number of variables plotted. Selection and mouse-overs
One and two dimensional are not affected.
plots are currently
supported.

Style Currently supported plot

styles are Line, Scatter, and
Histogram.

388 Visualizing Data With BioViz CambridgeSoft

Creating a Plot
Dialog Option Description
Name BioViz automatically names
plots with sequential
numbers (BioViz1, etc.) Edit
this field if you want to give
your plot a different name.
Context menu Description
options
Zoom on Drag A toggle which selects the
mode of operation when you
drag a rectangle on the plot.
If Zoom On Drag is checked,
the rectangle defines the area
you want to examine, and
releasing the drag will cause
the plot to zoom in on that
area. When unchecked, drag-
ging a rectangle selects the
points within it without
changing the scale. You can
use zoom to reset the scale
even on locked displays.
Unzoom Resets the scale after a zoom,
or a series of zooms.
Rescale to All Scales the plot so that the
Points visible points fill the plot
window.
Autoscale Automatically rescales every
time you change the list (that
is, perform a search, restore a
list, etc.).
Chem & BioOffice 2006 /ChemFinder
Context menu Description
options
Copy Image Copies the plot to the Clip-
board, allowing it to be
pasted into other documents.
Selection to List Creates a hitlist from selected
data points. The list is
displayed in the Queries Tree
and is treated and saved like
any other search query.
You cannot use Restore
Query on a list selected this
way, but you can use Restore
List to retrieve the records.
Statistical Analysis
You can now perform statistical analysis of BioViz
plots. When you specify two variables, a second tab
appears on the BioViz Plot Properties dialog box.
Figure 18-8BioViz General Properties
analysis tab appears when
2 variables are specified
For descriptive statistics, minimum, maximum,
mean, median, and standard deviation can be
calculated for both X and Y variables. R-Squared is
available only when curve fitting is chosen.
Visualizing Data With BioViz 389
Statistical Analysis
 Figure 18-9BioViz Analysis
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R2 is available when curve fitting is
selected
Results of descriptive statistics are displayed at the
bottom of the plot.
Figure 18-10Displaying Statistical Analysis Results
descriptive statistics display
You may choose from linear, quadratic, or cubic
curve fitting. A confidence interval of one to three
standard deviations may also be displayed. Both
descriptive statistics and the curve fit update
dynamically when the recordset changes or filters
are applied.
390 Visualizing Data With BioViz
Cleaning Up the Plot
Sorting and Filtering
Once you have created a plot, you might want to
clean up the display. There are two ways to do this:
sorting the data on a field, and using filters.
The standard ChemFinder sort feature is the first
step in cleaning up a graph. You may sort into
ascending or descending order. There are two ways
to sort a dataset on a given field:
Right-click in the field box and select Sort from
the context menu.
Display the Data table view, and double-click
on the table header of the field you want to
sort.
For more information on sorting, see .
Filtering
BioViz filters limit the display of a variable by
trimming either end of the range, that is, you can
eliminate high points, low points, or both from the
display. Filters can be set for either or both plotted
variables. You may also filter the dataset on other
variables, up to a total of 31 filters per chart.
Filters are set in the filter window, which, by default,
is displayed below the Queries window. When a
filter is set:
All plots associated with a given form are
affected, unless the plot is locked before
applying the filter.
Points missing a value for a given field are
hidden whenever the filter for that field is
visible.
To display the Filter window:
CambridgeSoft
Cleaning Up the PlotSorting and Filtering
 Check the box next to Filter Window on the
View menu.
Filter window
To activate a filter:
Right-click in the Filter window, and select a
variable from the list. When you view the
context menu again, the variable will appear
with a check mark next to it.
To remove a filter:
Right-click in the Filter window to display the
context menu, then click the variable to
deselect it.
Chem & BioOffice 2006 /ChemFinder
The following bio-assay example shows two plots
of the octanol/water partition coefficient (CLogP)
plotted against an activity measure called
Fold_Above_Control. The second is filtered on
molar refractivity. Note that the upper chart has
been locked to prevent the filter from affecting it.
lock
To apply the filter:
Press the thumb at one end of the slider and
drag along the slider.
In the bottom diagram, the plot is limited to
Molar_Refractivity from 10 to 33.
Filter Slider Adjustment
In ChemFinder 10, filter sliders can be adjusted in a
new way. Once the top and/or bottom of the range
has been set, you can move the entire range. For
example, in Figure 18-11A, the Boiling Point filter
has been set to display a range of about 250
from 501.3K to 753K.
Figure 18-11Filter Slider Adjustments
A
B
Visualizing Data With BioViz 391
Cleaning Up the PlotSorting and Filtering
 By dragging the blue part of the slider, you can view
any 250 range of the chart that you want. In Figure
18-11B, the range being displayed has been moved
to 651.5K903.2K. The size of the range hasnt
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changed, just its location.
Plotting Searches
When you perform queries (see Chapter 20,
Searching on page 403), and have one or more
hitlists attached to your form, the BioViz plot
displays the results of the current hitlist. You can
display overlays by selecting hitlists rather than
making them current.
For example, the following plot shows results of a
screening test relative to a control.
To remove outliers more than 2.5SD from the
control:
Search for <2.5 and >-2.5 in the SDs Above
Control field.
The plot displays the results for the hitlist.
NOTE: By default, the hits are shown on the same
scale as the original list, which may cause them to cluster
in one sector of the window. If this happens, right-click
the plot and choose Rescale to All Points or
Auto-scale. Rescale to All Points operates on the
current datapoints only; Auto-scale sets a switch so that
all subsequent searches and list operations will
automatically rescale the plot.
392 Visualizing Data With BioViz
To display the results of an overlay on the full list:
1. Open the Queries pane of the Explorer
Window.
2. Double-click on the Full List to make it the
current list.
3. Click the query to select it for display, over the
current list.
:
Selected query shows a check mark ( b )
Selecting a list by single-clicking in the queries tree
(or choosing Color On Plot from the tree context
menu) causes points on the plot to be recolored.
The recolored points are those which are on both
the selected list and the plotted one. You may color
more than one list at a time. When a list is colored
on the plot, its item in the queries tree is shown with
a check mark; clicking it a second time uncolors it
and removes the check mark.
Synchronization of Plots
Multiple plots attached to a form are synchronized.
If you select (mouse over) a point in one plot, the
same point is highlighted in all other plots (and the
related structure is displayed in the Structure
Window).
This behavior is slightly modified if one of the plots
is a histogram. Selecting a histogram bar does not
highlight points in other plots, but selecting a point
in a line or scatter plot will highlight the corre-
sponding histogram bar.
CambridgeSoft
Plotting Searches
Changing the Display This time, when you release the mouse
button, the plot display zooms in to show
Once you have selected data points and produced a only the points selected. When the plot is
plot, there are several options for modifying the zoomed, scrollbars appear. Use these to
display. reposition your view of the zoomed plot.
Click the circled-point icon on a scrollbar
Changing Colorsto change the color of a
to restore that axis to the previous zoom
plot:
a. Open the Queries pane of the Explorer win-
dow.
circle-point icons
b. Right-click a list and choose Change Color.
Selection and Zoomingto select a part of
the plot and zoom in:
To select part of the plot:
a. Drag a rectangle across a portion of the plot.
The portion of the plot is displayed in red.
b. To select more than one section, use Right-click and choose Unzoom to restore to
Shift+drag or Ctrl+drag. the full view.
To zoom-in on part of the plot: Changing the Styleyou can change the style of
an existing plot. For example, you can turn a
a. Right-click in the plot and choose Zoom on
scatter plot into a histogram.
Drag. This is a toggle switchchoose it again
to deselect. a. Right-click in the plot and select Properties.
b. Drag a rectangle across a portion of the plot. b. In the properties dialog box, select the style
and click OK.
The plot displays in the new style.

Chem & BioOffice 2006 /ChemFinder Visualizing Data With BioViz 393
Changing the Display
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394 Visualizing Data With BioViz CambridgeSoft

Changing the Display
Chapter 19: Importing and Exporting
Data
Overview Supported formats for output files only:

Bitmap (bmp)
You can move data into and out of a database if the
data is in a supported file format. You can import ChemFinder XML (cfxml)
single files, import or export databases, or add data
to an existing database. Encapsulated Postscript (eps)

GIF (gif)
Supported File Formats
Microsoft Word (doc)
ChemFinder allows you work with individual
chemical structures and reactions in various file TIFF (tif)
formats. The supported formats are:
Windows metafile (wmf)
ChemDraw (cdx) For information on the .cdx, .ct, and .cdxml file
ChemDraw XML (cdxml) formats, see the ChemDraw Users Guide. For
information on the .c3d file format, see the Chem3D
Chem3D (c3d) Users Guide. For information on MDL file formats,
see http://www.mdli.com/ (A document describing
Connection Table (ct)
the file formats is available in PDF format.)
Delimited text (csv, txt)

MDL Molfile (mol)

Importing Data
MDL RXNfile (rxn) ChemFinder allows you to import ChemDraw
structures, Structure Data files (SDFiles) and
MDL RDFile (rdf)
Reaction Data files (RDFiles) directly into a
MDL SDFile (sdf) database. In addition, you can import text files that
are comma or tab delimited.
MDL Sketch (skc)

MDL Graphic (tgf) Importing Structures

Questel F1D (f1d) ChemFinder imports structure files directly into a
Questel F1Q (f1q) database. You can choose to replace the existing
records, append new records, or merge the data,
SMD 4.2 (smd) eliminating duplicates.

Chem & BioOffice 2006 /ChemFinder Importing and Exporting Data 395
Importing Data
 The general procedure for importing structures is: The Data Import dialog box appears.
1. From the File menu, point to Import and
choose type of structure file to import.
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The Open Chemical Structures dialog box

appears. 4. Click the File button, and select a database to
import into.

TIP: You can also type in a name to create a new

database file.

5. Choose the type of import: Overwrite,

Append, or Merge.
a. If you have selected Merge, click the Merge
tab and choose the matching field, match
options, and logging options.
6. Select the fields to be imported with the check-
boxes.
b. Optional: Double-click the field name to
2. Browse to a folder containing structures.
change the name of the field, field type, and
width in the Data Field Import dialog box.
3. Select a file or files (using Ctrl+click or
Shift+click) and Click Open.

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Importing Data
 7. Optional: Click the Logging tab to change To import structure and reaction data files:
details of the log file.
1. From the File menu, point to Import, and
8. Optional: Click the Form Style tab to select the
choose the type of file you want to import
style of boxes that will be created for new
import.
fields.
9. Optional: Click the Advanced tab to set the The Open dialog box appears.
Advanced options.
2. Choose the file to import and click Open.
10. When you have finished selecting your options,
click Import. The Data Import dialog box appears.

The structures are imported to the specified The Data Import dialog box scans the file to
database. determine what data fields are present and how
much space to allow for them in the database. The
Importing Structure Data number of records scanned is shown in the status
bar. If the input file is large, the scan may take a
and Reaction Data Files while.
ChemFinder allows you to import Structure Data
files (SDFiles) and Reaction Data files (RDFiles)
directly into a database. Because these files contain
both structures and data, ChemFinder creates fields
in the database to accommodate the incoming data.

In RDFiles, incoming data may be hierarchical and

complex. When loading RDFiles, ChemFinder
converts the data to a relational form, creating new
tables as necessary and generating linking data.

NOTE: When importing RDFiles, boxes are

automatically created on the form only for fields in the root
table of the RDFile. Subforms must be created and
positioned manually.

If you have a blank form when you import,

ChemFinder creates boxes on the main form. If you
To interrupt the scan:
have a form with boxes when you import, new
boxes are created on tabbed forms. Press the Esc key.
You can import with a form linked to a database, a A message box appears to confirm that you
blank form, or no form. If you import with no really want to stop. The scan continues until
form, ChemFinder creates a new form. Selections you click Yes.
you make on the Form Style tab of the Data Import
dialog box determine what the form will look like. To abort the scan:

Chem & BioOffice 2006 /ChemFinder Importing and Exporting Data 397
Importing Data
 Click Stop scanning.

NOTE: You should let the scan go to completion so that all

needed fields are created in the database before loading.
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Using Log Files

During the import, ChemFinder creates a log file of
the actions taken. The log file (.log) is a text file that
is created alongside the input file and overwrites any
previous log file. The log records data of your
choice form the following options during the
import.
Errorserrors and warnings
General datainformation about the input
file and import process
Records processedlogs an entry for each 2. Select the appropriate options.
record of the input file
Structures registeredlogs an entry for each To start from Click
structure stored in the database
Data registeredshows each data item the beginning of the beginning.
stored in the database SDFile or RDFile
Database schemashows input fields found
and columns generated a specified line line and type the
number line number.
The log file for an RDFile import additionally
presents an overview of the data table hierarchy
within the RDFile. a specified byte byte and type the
number byte number.
You can choose whether to create the log file or
not. If you choose to create the log file, you can save
a specified record record and type
it with a different name or append to an existing log
the record
file.
number.
Importing from a Specified Location
You can start an import from an arbitrary location 3. Click Import.
in an SDFile or RDFile, such as a byte or line
number. Reading a Structure
To set the location from which to import:
In addition to importing, ChemFinder can read files
1. Click the Advanced tab of the Date Import of any of the supported structural formats. For
dialog box. example, if you have structures stored in

398 Importing and Exporting Data CambridgeSoft

Importing Data
ChemDraw format, you can open them directly Multiple files can be dropped at once, but you
from ChemFinder without having to import or cannot mix types (as defined in column 1 of the
redraw them. table). If several structure or graphic files are
dropped at once, they are loaded into successive
To read a structure from a file into a structure box: ChemFinder records. If only one is dropped, you
1. In the structure box, right-click and choose are asked if you wish to append the
Read Structure. structure/graphic in a new record or overwrite the
existing record. If more than five
The Open dialog box appears. structures/graphics are dropped, an alert will ask
2. Choose the file to read. you if you wish to proceed.
3. Click Open. Dropping one or more form files opens the forms,
The structure is read into the structure box. without affecting the current form and database.
The database is not affected by this operation
until you choose Commit Changes or move off Importing Text Files
of the record. You can import comma or tab delimited text files.
The Import Delimited Text command uses the
Drag and Drop same dialog and has most of the same features as
You can drag certain types of files from the Import SDFile. Delimited text (DT) differs from
Windows Explorer or Desktop onto ChemFinder. SD files in that:
The following table summarizes the ChemFinder DT files cannot contain structures.
Drag and Drop options.
DT files are not as well defined, and require
interpretation in order to determine field
type of supporte comments names and delimiter type.
file d file
types To import text records into a new database:
4. Open a new, blank form.
Structure CDX Must be dropped into 5. On the File menu, point to File Import and
a structure box. choose Delimited Text.
SKC
6. In the File Open dialog, browse to select the
MOL input file.
The input file is scanned to determine the field
MST
delimiter. If the file extension is .csv, the
delimiter is taken to be comma. If the
Graphic WMF Must be dropped into extension is .txt, the first few lines of the file
a picture box. are examined for the presence of commas or
EMF tabs. If one or the other is found, it is taken as
the delimiter. If not, an alert is presented.
Form CFW Does not need to be This alert will appear in two cases:
dropped onto an
existing form. c. The input file contains only a single column.
The alert can be ignored (click OK).

Chem & BioOffice 2006 /ChemFinder Importing and Exporting Data 399
Importing Data
 d. The input file has some delimiter between
fields other than tab or comma.
In this case you must specify the delimiter
using the File Export dialog box.
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(*.txt) format, or in the Comma Separated Value
(*.csv) format readable by most spreadsheets.
When you export a file, all records in the current
hit list are exported. You can include or exclude

fields to be exported from a checklist.

To specify the delimiter using the Role Export
dialog box: To export a file:
1. Click Cancel to dismiss the alert and abort the 1. From the File menu, point to Export, and select
import. the output file type.
2. Open a form containing data, and retrieve a
small hit list.
3. On the File menu, point to File Export and
choose Other.
The File Export dialog box appears.
4. Click the Text Options tab.
5. Choose the Other radio button, and specify a
delimiter.
6. click Export to save the choice (and carry out an
export)
7. Go back to step 1 of the import procedure to
begin the import again.

TIP: Once you have specified a delimiter, it will be

remembered and you will not have to repeat this
The Data Export dialog box appears.
operation.

The input file scan also determines the names and

types of the data fields in the input file. Field names
must appear in the first line of the file, in the correct
order, separated by the same delimiter as the data
items. Field types are determined by examining all
the data in each column, using the same rules as for
SD import: if all items in one column are integers,
then the field type is set to integer, and so on.
Widths of text fields are set to accommodate the
largest item in the file.

Exporting Data Files

You can create a new SDFile, RDFile, ASCII text,
or MS Word file by exporting records from an
existing database. Text files can be saved in text

400 Importing and Exporting Data CambridgeSoft

Exporting Data Files
The Data Export dialog box is similar to the Data
Import dialog box. It gives you options for file
naming and file type selection, and lets you select
which fields will be exported. If you save to an
existing file, you have the option to replace or
append the records.
2. Type a name and path for the file, or click File
and browse to an existing file.
3. For delimited text exports, click the Text
Options tab and choose appropriate options.
NOTE: Choosing Comma delimited does not
automatically set the file type. Text files (*.txt) may be
either tab delimited or comma delimited. If you want to
export in the Comma Separated Value (*.csv) format,
you must name your file accordinglyeither by typing the
name or selecting the file type from the Save As dialog
box.
4. Click Export.
The file is exported.
Saving Structures
Saving structures is similar to exporting them,
without the fuss.
To save the structure on display:
1. Right-click in the structure data box, and
choose Save Structure.
The Save As dialog box appears.
2. Choose the destination directory.
3. Type the file name and choose a file format.
4. Click Save.
The structure is saved to the indicated file. You can
read these files with any application that supports
the specified file format.
NOTE: To save most of the file types listed above, you must
have ChemDraw Pro installed.
Chem & BioOffice 2006 /ChemFinder
Exporting an ASCII File
Delimited text files may be the most universal file
format used by non-chemical applications. In a
delimited text file, each line represents a record, and
all fields in the record are listed in order from left to
right, separated by some character such as a tab or
a comma. Individual records are separated by
carriage returns. ChemFinder allows you to include
a header line at the start of the file that lists the
names of all of the fields. It also allows you to
append to, or overwrite, existing text files.
You can import a delimited text file saved by
ChemFinder into many other applications,
including spreadsheets and external database
systems. Choose the .csv file format to export to
spreadsheets, and the .txt format for general export.
NOTE: In delimited text files, structures are automatically
exported as SMILES strings.
Exporting a Word file
The export to MS Word option is similar to the
other export options, however a couple of points
are worth noting:
Export to Word is much slower than to other
formats. For this reason, you should probably
limit the use of this option to relatively short
hitlists.
You can speed up the export by not exporting
the structure field.
Structures are exported as OLE objects, and
can be edited in Word with the ChemDraw
ActiveX toolbar.
If you should, by accident, begin exporting a
large database, you can terminate the export by
bringing ChemFinder to the front and pressing
the Esc key.
Importing and Exporting Data 401
Exporting Data Files
 Export to SDFile field name. Deselect any subform fields you do
not wish to export (and select those main form
When you export to SDFile, you are allowed to
fields you do wish to export).
export subform fields. Each subform field is
exported to a separate record in the SDFile, but
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4. Click the Export button.

separate subform records are concatenated into a
single multi-line text block.
NOTE: Re-importing a file of this type will not regenerate
To export subforms: the original database! It will bring back the data, but not in
1. Point to Export on the File menu, and choose the subtables and subforms you started with. To do this,
SDFile. export to cfxml.
The Data Export dialog box appears.
2. Click the Text Options tab, and select the Export When exporting to SDFile, you may append to, or
subform data checkbox. overwrite, existing SD files. This option is only
3. Return to the Export tab. In the Field column of available for SD files and delimited text exports.
the Data Fields table, all subform fields now
appear with checks in the checkbox next to the

402 Importing and Exporting Data CambridgeSoft

Exporting Data Files
Chapter 20: Searching
Overview
You can search a ChemFinder database by querying
any field or combination of fields. You can specify
a chemical structure and/or text as the query. When
searching text or numbers, you can use wildcards or
specify a numerical range. When structure
searching, you can search by sub- or full structure,
search for an exact match, similarity, or
tautomerism, and specify how stereochemistry will
be matched. You can also combine structure
searching with text or numerical searching. A new
Find Structure command performs duplicate,
error, isotopic label, and other special structure
searches.
The chapter describes the different types of
searches and how to set up and manage searches. It
concludes with some examples of advanced
techniques.
Text Searches
ChemFinder, like all databases, supports text
searching. You can search any alphanumeric field
for strings of text. You could use text searching, for
example, to find chemical names, or comments in a
reference field.
For text searches, ChemFinder interprets the query,
then passes it as Structured Query Language (SQL)
to the relational database. The following rules apply
to these queries:
When searching a normal text field, a plain
text string is taken as an anchored substring,
which hits any string starting with the indicated
substring.
Chem & BioOffice 2006 /ChemFinder
When searching a memo field, a plain text
string is unanchored, and hits any string which
contains it anywhere.
When searching a normal text field, if the text
query starts with = (for example =toluene) then
the search requires an exact text match.
Text strings may contain wild cards or Boolean
operators. Standard wild cards are % or *.
These characters are equivalent and hit any
string. Other wild cards are also possible. If
wildcards are present, they override the above
defaults.
NOTE: Using wildcards or a = in memo fields may
lead to unexpected results. This is because a memo field
may contain formatting information surrounding the
text you see, so a search like benz* may give no hits.
Using *benz*, however, will give the same results in a
memo field as in a plain text field.
A checkbox in the Search Preferences dialog
allows you to request a full-word match. When
this box is checked, a hit must contain the
query as a complete word, not embedded
within a larger string.
Boolean operators are NOT, OR, and AND.
They may be used to combine search terms
within one field.
TIP: Use NOT* to search for empty fields.
Examples of queries:
Entry Possible Hits Will Not Hit
benz Benzene, Bromobenzene
Benzoic acid
Searching 403
Text Searches
 benz OR Benzene, Azobenzene
Molecular Formula
*bromo* Benzoic acid, Searches
Bromobenzene,
Dibromobenzene
Administrator

Formula searching allows you to search molecular

compositions. Searches can be inclusive, exact
=benzene Benzene Benzoic acid, (designated with an equals sign) or with the element
Benzene-d6, range you specify.
Bromobenzene
The following table shows query examples.
Numeric Searches
Entry Possible hits
Searching numerical data allows you to find
information such as boiling points and molecular C6H6 compounds with 6 carbons and
weights. 6 hydrogen atoms, plus any
number of other elements.
Ranges are specified using a hyphen between the
values at either end of the range. =C6H6 compounds with 6 carbons and
For numerical searching, the query is a decimal 6 hydrogen atoms and no other
value or range. If a single value is given, the number elements.
of significant digits determines the precision of the
search. A hit is any value that rounds off to the C6N0 compounds with 6 carbons, no
query. nitrogens, plus any number of
other elements.
Examples of queries:
C6 N1-3 compounds with 6 carbons and
Entry Possible hits one to three nitrogen atoms,
plus any number of other
90 values from 89.5 to 90.5 elements.

90.1 values from 90.05 to 90.15 Formula queries consist of element symbols and
element counts or ranges. The following rules
90100 values from 90 through 100, apply:
inclusive
Symbols may be one or two letters. Symbols
may be in upper or lower case; if there are
>=90 and <=100 values from 90 through 100, ambiguities, the program resolves them
inclusive according to rules described in Appendix K,
Formula Input Rules..
>90 and <100 values from 90 through 100,
exclusive Capitalize the symbols properly and insert
spaces between elements.

404 Searching CambridgeSoft

Numeric Searches
 Use the Periodic Table to enter formulas. For
more information, see Using the Periodic
Table on page 434 and Appendix K,
Formula Input Rules.
Element counts are single integers or ranges
(two integers separated by a hyphen). If a count
is omitted, it is assumed to be 1.
If the formula query is preceded by = (for
example =C6H6) then the search requires an
exact formula match, containing no elements
other than those indicated. If there is no =, then
the search is a partial match: other elements
may be present in the hits.
Symbols may be repeated. For example,
CH3CH3 is interpreted as C2H6.
NOTE: Formula searches are completely non-
structural: CH3CH2OH matches both dimethyl ether
and ethyl alcohol because both compounds have the same
condensed formula: C2H6O.
Parentheses may be used to group elements
and apply a count to the entire group. For
example, (CH2)3 is interpreted as C3H6.
Spaces or non-alphanumeric characters other
than parentheses are ignored.
Date Searches
Dates might be used to track individual reaction
runs, purchasing histories, and so on. Searching
dates is very similar to searching numerical data.
Ranges are specified using a hyphen between the
values at either end of the range. Ranges may also
be indicated using inequality operators (<, >)
together with the AND operator.
Dates are always displayed according to the
preferences set in the operating systems
International control panel, but need not be input
in that format.
Chem & BioOffice 2006 /ChemFinder
The following table shows query examples.
Entry Possible hits
Apr 11, 1971 the exact date April 11, 1971
March 31, 1971 any date in the second
July 1, 1971 quarter of the year 1971
>4/ 11/71 any date after April 11, 1971
Find List
Use the Find List command to retrieve records
having specific values in any non-structure field.
Type parameters into the Find List box as follows:
If the column you search is an integer type, you
can use hyphens to indicate ranges.
If the column you search is a number or text
type, you cannot use hyphens to indicate
ranges; you must search for an exact match.
NOTE: To search for a list of records using partial
text (a wildcard search) or range of numbers, do a
search on the relevant field.
If the column you search is a text type, you
must use quotes around any item that contains
commas. For example, you must type 1,2-Pyran
as 1,2-Pyran.
You may save a list as a text file and retrieve it
later with the File button.
To find a list:
1. From the Search menu, choose Find List.
The Find List dialog box appears.
Searching 405
Date Searches

Administrator
2. From the Column menu, choose a field.
3. Paste or type a list of field parameters into the
Find List text box.
4. Click OK.
The list of matching records is retrieved.
Structure Searches
You can search a ChemFinder database by sub- or
full structure for similarity or exact matching. To
define your search more precisely, use the query
functions in ChemDraw. These are described in
Chapter 9 of the ChemDraw User Manual, and in
Appendix J: Structural Query Features. in this
manual.
ChemFinder matches structures in three ways:
Search type (Normal/Exact/Similar)
Structure mode (sub- or full structure)
Tautomerism
NOTE: Not all options for each type are compatible with
other types. For example, Tautomeric searches must be either
Exact or Normal.
406 Searching
Search Type
Normal Searching
A Normal search finds structures that either
contain (Substructure) or match (Full Structure) the
query. When drawing a structure query, you can
attach different features to a query, such as atom
lists and variable bond types, to perform a narrower
or broader search. You can also modify the results
of a Normal search by selecting options in the
Search Details tab of the Preferences dialog box.
The query structure is highlighted in red in the
hitlist structures to visualize the match.
Exact Searching
NOTE: The Exact search type was known as the Identity
search type in previous versions of ChemFinder.
The Exact search type is intended for use in
compound registration, when you must know if a
perfectly identical copy of your query compound is
already present in the database. It is similar to a
Normal Full Structure search, except that generic
atom and bond types such as R, A, and Double-or-
Aromatic in the query will match corresponding
atom and bond types in the target only if they are
CambridgeSoft
Structure Searches
also of the same generic type. Thus, an R hits only
another R atom. Moreover, stereochemistry must
match precisely between query and target. If the
stereochemistry of the query is unspecified, it will
only hit targets which do not specify
stereochemistry.
The Search Details tab in the Preferences dialog
box is unavailable for Exact searches.
Similarity Searching
A Similarity search finds structures that have
structural features that generally correspond to
those in the query. Similarity searches are by their
nature fuzzy. In a Full Structure similarity search,
toolbar, you can attach different features to a query,
such as atom lists and variable bond types, to
perform a narrower or broader search.
For more information about what query features
you may use and how these features affect a search,
see Appendix J, Structural Query Features..
An example of substructure searching of
Cyclopentane:
This substructure will hit
query
O

the results are guaranteed to include all hits you

would obtain from a substructure search with the
same query. Usually, they include additional hits.
For this reason, similarity searches are useful if you
have a general idea of the types of compounds you
are looking for, but dont have a precise conception HO

of the target compound.

Unlike exact searches, similarity searches do not

highlight matched portions of the target
compounds. Similarity searching matches general
structural features and not specific atoms and
bonds, so highlighting specific areas would not be O

and other molecules

appropriate.
You can adjust the degree of similarity by using the
slider on the Search Type tab of the Preferences NOTE: In searching substructures, ChemFinder finds the
dialog box. substructure query regardless of its orientation or drawing
presentation in the targeted molecules. Bonds shown in bold
For a detailed description of the similarity searching
above are actually highlighted in red in ChemFinder.
algorithms, see Appendix L, Similarity Rules..

Substructure Searching Fragment Searching

The default search type is Normal Substructure
searching. It finds structures that contain the query,
plus any additional attachments at the open
positions. The substructure is highlighted in red in
the hitlist structures. Using the ChemDraw ActiveX
You can draw more than one structure or structure
fragment in your substructure search query. In the
Search Details tab of the Preferences dialog box,
you may allow fragments to overlap in the target
structure.

Chem & BioOffice 2006 /ChemFinder Searching 407

Structure Searches
 For example, if you perform the following
substructure query with Query fragments may
overlap in target selected:
Administrator
OH
The hit list will include the following:
OH
The dot indicates an atom shared between the two
fragments. The hit list will not include this molecule
if the overlap option is deselected.
Full Structure Searching
Selecting the Full Structure radio button in the
Search Type Preferences finds structures that
completely match the query. You may get more than
one hit if there are duplicates in the database or if
there are stereoisomers in the database and you did
not specify a particular one to be matched. For
more information, see Stereochemistry on page
408.
Stereochemistry
You can specify whether or not you want a
structure search to consider stereochemistry. Given
a structure with one or more stereocenters, you can
store four different possibilities:
A given absolute configuration. To specify this,
centers must be drawn with stereo bonds, and
the entire structure marked Abs (CHIRAL).
A racemic mixture of the drawn configuration
and its mirror image. This is drawn as above,
but without the Abs (CHIRAL) mark.
An unmarked structure, representing unknown
stereochemistry, or a mixture of all possible
stereoisomers.
A given relationship between centers. That is, a
known orientation of the substituents with
respect to each other, rather than a known
408 Searching
absolute configuration. To specify this, centers
are drawn, not with the standard hashed and
wedged bonds, but with thick stereo bonds.
If these options are checked in the Search tab of the
Preferences dialog, then any stereochemistry
indicated on the query must be matched by the
target. For more information on changing searching
preferences, see Setting Search Details
Preferences on page 414.
3D Properties
3D queries are particularly useful in
pharmacophore searching where you are looking
for a particular 3D relationship among atoms and
bonds, for example in a series of potential receptor
ligands. You can create a 3D query in ChemDraw
Pro by adding geometries (lines, planes, etc.) and
constraints (specified as ranges) to a query
structure. For example, you might specify that two
atoms must be between 4 and 5 apart, or that
two planes must be separated by 80-100.
ChemFinder can then use these properties to refine
a search. See the ChemDraw Users Manual for
information on how to add 3D properties to
structures.
Searching with R-Groups
ChemFinder 10 supports queries using R-tables,
including multiple R-tables. Queries containing
large numbers of R-groups or large numbers of R-
values are not advisable however, because
ChemFinder pre-processing expands the query,
substituting all combinations from the R-group
table(s).
Alternative Groups
Instead of submitting multiple queries on structures
that share a common substructure, you can submit
a single query with the parent structure and variable
CambridgeSoft
Structure Searches
functional groups or substructures. The parent
structure is drawn with attachment point(s) that
refer to a list of alternative groups that you define.
Figure 20-12: Alternative groups, sometimes called R-
Groups or G-Groups (Generic Groups)
6. Type a title in the Alternative Group Title box.
The title must match the atom label in the
parent structure (R, in the example above).
Figure 20-13: Defining an R-Group: Step 4
Title box

F G
1

NH2
G

1 F

1 NH2
7. Draw the substructure fragments in the Alter-
1 OH
native Group box. Use the single bond tool to
OH
define a fragment, and the text tool, atom
HotKeys, or Nicknames to create atom labels
for each variable.
Figure 20-14: Defining an R-Group: Step 5
R

Defining an Alternative Group

1 Cl
R
To define an alternative group:
CH2OH
1. Click the query icon to begin the search.
2. You will need a bit more space than the struc- Ph
ture window provides, so right-click in the
structure window and click Edit in ChemDraw
8. Add the Attachment Points:
on the context menu.
a.Click the diamond shaped
ChemDraw opens to a new page.
Attachment Point tool on the Chemical
3. Draw the parent compound. Label the atom Symbols palette.
where the alternate groups will attach with a
b. Click the open atom position on each
generic label such as R.
substructure fragment.
4. Click the Alternative Group query tool .
5. Drag with the tool in an open part of the page
TIP: Alternatively, the HotKey .(period) can be
to create an area large enough to draw the alter- used to add attachment points.
native groups.

Chem & BioOffice 2006 /ChemFinder Searching 409

Structure Searches
 Figure 20-15: Completed R-Group
R as:
1
1 Cl
Administrator
1 CH2OH
1 Ph
NOTE: In the above procedure, the parent structure was
drawn, then the R-Group table was added. In fact, the order
doesnt matter. You may create the R-Group table first, then
draw the parent structure. In either case, as soon as a generic
atom label in the structure matches the group title in the R-
Group table, a hollow attachment point symbol appears next
to the label in the parent structure.
9. Type Ctrl+W to return to ChemFinder.
The structure and the R-Group table appear
in the structure window.
10. Continue the query as usual.
Reaction Searches
You can search and store reactions. In a reaction,
one or several compounds (reactants) are
transformed into other compounds (products).
Individual reactants (or products) are separated
from each other with plus signs. The reactants are
separated from the products with an arrow.
Reactions may have multiple steps, for example
(A) (B) (C) (D). Here, (A) is the
reactant and (D) is the product. (B) and (C) are
intermediates for the complete reaction.
A multi-step reaction is actually a shorthand
notation for many related reactions. In the example
above, (B) is an intermediate for the complete
reaction, but it is also a reactant relative to (C) or
(D). It is also a product relative to (A). The
410 Searching
complete reaction implies many subreactions, such
(B) (D) and (A) (B).
Reaction Centers
The most important part of a reaction is the part
that actually changes from the reactants to the
products. This part, which probably includes a
number of atoms and bonds, is called the reaction
center. For example, only the bold bond below (and
the two atoms on either side) is part of the reaction
center. The rest of the structure is unchanged from
the reactant to the product:
O OH
F Cl F Cl
By default, ChemFinder considers reaction centers
whenever you search for reactions. ChemFinder
assumes that any atoms and bonds that change in
the query must be part of the reaction center of the
target.
For example:
F Cl
does not hit
O OH
F Cl F Cl
when the Reaction query must hit reaction center
preference is selected. Even though there is a C-F
bond in the target reactant and a C-Cl bond in the
target product, these bonds do not participate in the
reaction, which really affects another part of the
CambridgeSoft
Reaction Searches
compound. If you deselect the Reaction query must of the data about a reaction. Maps are used during
hit reaction center preference, this query hits the searching to resolve certain types of structure
target above. search hits.

When creating reaction queries, it is important to Consider a simple esterification reaction:

consider what sort of information you are really
looking for. Suppose you want to convert n-decanal O O
OH
to n-decanol: H2O
OH O

O
Does the ester oxygen come from the acid or the
alcohol? You specify the fate of individual atoms
through an atom-to-atom map. In reality, the ester
oxygen in this reaction originates in the alcohol, so
OH
the atom-to-atom map looks like this:
Are you really interested only in these two 3 3
compounds? You might be interested in any O
6
O
OH
reaction that converts a straight-chain aldehyde to 2
Rxn
5 2
5 H2O 4

the alcohol: 1 OH 4 1 Rxn O

6

H H By matching numbers across the arrow, you can see

H
O
H
OH
where atoms move during the course of the
reaction. The other reaction (not observed
H H
experimentally), where the ester oxygen comes
from the acid, would be mapped like this:
Since the corresponding n-octanal n-octanol 3 3
O O
reaction would probably occur under very similar Rxn OH 6

conditions, it is a reasonable thing to look at. 2 5 2

5 H2O 6

OH 4 O
Generally, you want to use substructure queries that 1 1
4
Rxn

include little beyond the reaction center in question

when you are searching for reactions.
NOTE: ChemFinder supports several query properties to
allow you to specify exactly how a bond participates in a
reaction center. For more information about these properties,
see Setting Search Details Preferences on page 414.
ChemFinder uses atom-to-atom map information
to determine reacting centers for reactions. If only
some atoms are mapped, ChemFinder uses that
information and does not worry about the specific
fates of the other atoms. For example, if you dont
know (or dont care) about the mapping of some
atoms, you can leave them unspecified in the atom-
to-atom map.

Atom-to-Atom Mapping By default, atom-to-atom mapping is not displayed

within ChemFinder. To turn on this display, select
The second most important part of reaction Atom-to-Atom Map on the Structure sub-menu of the
searching is the atom-to-atom map. You can specify View menu. For more information, see Setting
maps in ChemDraw, where they are stored as part Preferences on page 429.

Chem & BioOffice 2006 /ChemFinder Searching 411

Reaction Searches
 NOTE: For information about specifying atom-to-atom
maps with ChemDraw, see the ChemDraw Users Guide.
Administrator
Searching for Reactants
If you know what starting materials you are
interested in but dont know their products, you
might perform a reactants query. A reactants query
is very similar to a reaction search, except that there
is nothing to the right of the arrow. For example,
consider the query:
O
O
If you are doing a substructure search, this finds any
reactions in which maleic anhydride or a compound
containing a maleic anhydride substructure is
consumed or transformed.
Searching for Products
If you know the desired end product but not how
to get there, you can do a products query. A
products query is similar to a reaction search,
except that there is nothing to the left of the arrow.
For example, consider the query:
If you are doing a substructure search, this finds any
reactions in which bicyclo[2.2.1]heptane or a
compound containing this substructure is
produced.
412 Searching
Searching for Intermediates
Rarely, you may be looking for reactions for which
you only know something about an intermediate.
An Intermediate Search is very similar to a normal
reaction search, except that there are arrows on
both sides of the target structure. For example,
consider the query:
R C C O
This finds any reactions containing the Ketene
structure shown as an intermediate.
NOTE: ChemFinder cannot predict products or
intermediates of reactions. It finds this information only if it
is already present in the database.
Combined Searches
You can combine structure searching with text
searching to find a specific class of compounds. For
example, you may want to find all compounds in the
database whose names end in mycin and whose
structures contain a phenyl ring. Because you are
entering multiple queries in different data boxes,
there is an implicit AND condition between data
items in different fields.
To perform a combined search:
1. From the Search menu, choose Enter Query to
clear the form.
2. Enter the structural query, if any.
3. Enter the text and/or numeric queries in the
appropriate boxes.
4. From the Search menu, choose Find.
An example of combined searching:
CambridgeSoft
Combined Searches
Suppose you want to find all molecules in the Searching Procedures
CS_Demo database that contain a benzene ring and
which have names related to penicillin. Searching includes the following steps:
1. From the Search menu, choose Enter Query to Setting the search type preferences (Structure
clear the form. searches only).
2. Draw a benzene ring.
Entering the query in the form.
3. Enter *penicillin* in the Molname field.
Submitting the query to the search engine.
4. With the Substructure option selected, choose
Find from the Search menu. To perform a search, use the Search menu or the
You get 2 hits of molecules whose names contain corresponding tools in the Search toolbar.
penicillin and whose structures have an aromatic
ring of six carbon atoms. Enter Retrieve Previous Restore Over
Query All Query List Current
List
NOTE: In a combined search, progress reports are given
only during the structure search part. When the counters at
the bottom of the screen are advancing, structures are being
searched. You can press Esc to end a search during the
structure searching. You cannot end a search during the SQL Find Find Current Save Restore Find
searching by pressing Esc. Molecule List Previous List
List

The following procedures describe searching with

SQL Searches the Search menu. You may use the Search toolbar
SQL (Structured Query Language) can be used to instead for most procedures.
create powerful searches. The details of the
language are not discussed here. Setting Search Type Prefer-
Queries beginning with a backslash (\) are taken as ences
straight SQL, and passed directly to the database as
You can set preferences for the type of structure for
the WHERE clause of the SQL query. These must
which you want to search.
contain column names and punctuation as dictated
by SQL. For example, a valid query might be To set Search Type preferences:
\[molname] like 'benz*' and [bpoint] > 200.
1. Right-click in the Structure box and choose
A straight SQL query may be entered in any box of
Preferences.
the form which contains non-structural data. The
SQL query is not associated with the box in which The Preferences dialog box appears, with the
it is entered. Search Type tab displayed.

Chem & BioOffice 2006 /ChemFinder Searching 413

SQL Searches
 If you want to Then click

find structures that are Tautomeric.

Administrator

tautomeric forms of the

query

match bonds as drawn, Non-tautomeric

without tautomeric forms

3. Click OK.

TIP: You dont always have to access the Preferences dialog

to change search preferences. Switches on the Search menu
allow you to toggle Substructure/Full Structure and
2. Take the appropriate action: Normal/Similarity.

If you want to Then click Setting Search Details Preferences

find structures containing a Substructure. You can set preferences for the details of each
common structural search.
component
To set Search Details preferences:

find a particular structure
search with variability in
the query
search for a precise match
Full Structure. 1. From the File menu, choose Preferences.
The Preferences dialog box appears.
Normal
2. Click the Search Details tab.
The Search Details tab appears.
Exact.

find structures having Similar and set

features similar to the query the degree of
similarity.

NOTE: The
higher the
value, the fewer
hits found.

414 Searching CambridgeSoft

Searching Procedures
 3. Take the appropriate action:
If you want to Then click
If you want to Then click
Require that any reac- Reaction query must
tion center present in hit reaction center.
Allow uncharged non- Hit any charge on
the query overlap with
carbon atoms in the heteroatom.
reaction centers in the
query to match charged
target. This preference
atoms in the target.
applies only to reaction
NOTE: Charged atoms searching.
in the query must always
match charged atoms in Prohibit generic struc- Generics hit only
the target, regardless of tures from hitting any generics.
this setting. other structures in a
query.
Allow uncharged Hit any charge on
carbon atoms in the carbon. Require full-word text Text: match full word
query to match charged matching. If you do not only
carbon atoms in the check this box, the
target. query will hit any
matching text fragment.
NOTE: Charged atoms
in the query must always
Require that the stere- Match stereochem-
match charged atoms in
ochemistry of the target istry and click How to
the target, regardless of
structure match that of set how the stere-
this setting.
the query structure. ochemistry is
matched.
Allow hits to contain Permit extraneous
molecular fragments in fragments in full struc-
addition to the structure ture searches. Setting Stereochemical Search Prefer-
hit by the query. ences

The Stereochemical Search Preferences dialog

Allow fragments in the Query fragments can
box is activated from the Search Details tab of the
query to overlap (share overlap in target.
Preferences dialog box.
one or more atoms) in
the target.
To set Stereochemical preferences:

1. Click the How button on the Search Details tab

of the Preferences dialog box.

The Stereochemical Search Preferences

dialog box appears.

Chem & BioOffice 2006 /ChemFinder Searching 415

Searching Procedures
 set to Same, a query marked with thick bonds will
only hit a target that has the same relative
relationship between centers.
3. Set the Double bond hits:
Administrator

If you want the Then in

configuration of a
double bond in
the query to

match the target struc- Double bond hits, click

ture exactly. Same.

2. Set the Tetrahedral stereo center hits: match any configura- Double bond hits, click
tion in the target. Any.
If you want a Then
tetrahedral 4. Click OK.
stereocenter in the
query to Entering Query Mode
To clear the form and enter Query Mode:
match the target exactly. in Tetrahedral stereo
From the Search menu, choose Enter Query.
center hits, click Same.
You are in Query mode.
match same or opposite in Tetrahedral stereo In Query mode:
configuration at the center hits, click Either.
The form background color changes.
center of the target.
QRY appears in the status bar.

match any target. in Tetrahedral stereo Form boxes which do not permit data entry
center hits, click Any. become editable for entry of queries.
Form boxes are displayed according to their
match a relative relation- click Thick bonds visibility properties. For more information, see
ship between centers represent relative Hiding Data Boxes on page 349.
stereochemistry.
Entering and Submitting a
When Thick bonds represent relative stereochemistry Query
box is cleared (default), thick bonds are
interchangeable with hash/wedge bonds. When the To enter the query:
box is checked, and Tetrahedral stereo center hits is 1. Position the cursor over the field you want to
search and click to select it.
2. Enter the query in the data boxes.

416 Searching CambridgeSoft

Searching Procedures
 3. From the Search menu, choose Find.
TIP: Press the ESC key to leave Query Mode without
searching.
ChemFinder searches. The number of hits is
shown in the Status Bar at the lower right
corner of the window.
NOTE: If a search gets no hits or an error occurs, an alert
appears and you are returned to Query mode to enter a
different query or modify the current one.
The hit list is a subset of the complete database.
You can browse it as you would any database using
the Record commands in the Record menu or
toolbar.
For example, to view the hits in tabular form:
From the View menu, choose Data Table.
Stopping a Search
To stop a structure search in progress, press the Esc
key. The query stops and you return to browse
mode.
NOTE: Only queries that involve structural data
(structure, molecular formula, and molecular weight searches)
can be stopped in this manner. SQL searches and searches
that involved non-structural data cannot be aborted.
Refining a Search
You can refine a hit list of one or more records by
entering a query that searches only the hit list, not
the entire database.
To refine a search:
1. On the Search menu, verify that Over Current
List is selected.
2. From the Search menu, choose Enter Query.
Chem & BioOffice 2006 /ChemFinder
ChemFinder searches over the previously
retrieved hit list. If no hits are found, a message
appears asking whether to search over the
entire database.
As long as the Over Current List switch is on, each
search further refines the current list. Use the
Retrieve All command to reset. You may also use the
Restore Previous List command, which acts like a
Back button. Restore Previous List goes back one in
the history, including any Retrieve Alls you might
have done.
Entering a Structural Query
To begin a structural query:
1. From the Search menu, choose Enter Query, to
clear the form.
2. Place a structure into a data box use any of the
following methods:
a. Double-click in the structure box and edit
with the ChemDraw ActiveX toolbar.
b. Right-click and select Edit in ChemDraw.
c. Right-click and use Read Structure... to open
an existing molecule file.
d. Use Paste from the Edit menu to insert a
structure from the clipboard.
3. Choose Preferences from the Search menu,
and click the Search Type tab.
4. Select the appropriate options. Optionally,
select options on the Search Details tab as well.
5. Choose Find from the Search menu.
The status bar counters indicate search progress.
When the search is complete, the form displays the
first hit. The list you can browse is limited to the
hits. For Normal or Exact searches, the hit portion
Searching 417
Searching Procedures
 of each molecule is highlighted in red. If a search
doesnt find any hits, you are returned to query
mode.
Administrator
TIP: You can change the highlight color in the preferences
dialog. For example, to show no highlighting, choose black as
the highlight color. See Color Preferences on page 430 for
more information.
Using the Current Molecule as a Query
As you browse through a database, you may submit
any structure on the screen as the structural query.
Often, you use similarity or substructure searches
(see above) with this type of query to find related
compounds.
To use the current molecule for a query:
1. Using the Record commands, go to the record
containing the structure that you want to use as
a query.
2. From the Search menu, choose Current Mol As
Query.
All boxes of the form are cleared except the
structure so that the molecule on display can be
used as part of the query. You can then
continue with the query as if you had drawn the
structure from scratch.
Finding the Current Molecule
The Find Current Molecule command, located in
the Search menu and on the Search toolbar, is
similar to the Current Mol as Query command
discussed above. As you browse through the
database you may find a molecule that interests you,
and want to find other related records.
The Find Current Molecule feature lets you
perform a quick structural search of the structure
currently being displayed on the form. However,
this feature does not allow you to enter other search
terms. The type of structure search (complete
418 Searching
structure, substructure, and/or similarity) is
determined by what you have selected in the
Search menu.
To find the current molecule:
1. Browse to the record containing the structure
of interest.
2. From the Search menu, choose the type of
structure search you want to perform.
3. From the Search menu, choose Find Current
Mol.
ChemFinder begins the search and displays the
search status on the lower right corner of the status
bar. When the search is complete, the form displays
the first hit, and the list you can browse is restricted
to the records hit by the query.
Entering a Reaction Query
The general procedure for creating a reaction query
is very similar to creating a structural query.
Clear the form:
From the Search menu, choose Enter Query.
The form clears.
Enter the query:
1. Double-click in the Structure box.
The ChemDraw ActiveX toolbar appears.
2. Draw the structure or substructure or reaction
in the From ChemFinder window.
3. Click somewhere in the form outside the Struc-
ture box.
Now you can enter more query terms in the other
data boxes for a combined search.
1. From the Search menu, select or deselect the
Substructure option.
NOTE: The Similarity option is not available for
reaction queries.
CambridgeSoft
Searching Procedures
 2. From the Search menu, choose Find.
The search proceeds as with simple structure
searching.
Special Structure
Searches
The Find Structures submenu on the Search menu
provides for several common types of searches that
would be awkward or arcane to conduct using
regular means. As with other searches, all of these
searches operate within the current record set if the
Over Current List option is in effect. Otherwise, the
whole list is searched, regardless of how many
records are currently displayed.
These are generic searches, made without entering
any query information. The options are:
Empty StructuresLocates records
containing no structure. It is equivalent to
specifying a molecular weight of zero in a
regular search. It is provided because the latter
method is a bit obscure.
ReactionsLocates structures that are reac-
tions. The same effect can be achieved by
entering a bare arrow as a structure query.
Chem & BioOffice 2006 /ChemFinder
With Stereo CentersFinds structures
containing tetrahedral stereochemistry.
With Isotopic LabelsRetrieves records
containing a structure with an atom that either
has a mass number, or has an Isotopic Abun-
dance attribute.
Query StructuresLocates structures with
any generic variability such as atom types (R, A,
M, Q, X, Alkyl, Aliphatic, EDG, EWG), bond
types (single-or-double, etc.), variable charge,
element lists ([C,N,O]), ring bond count, etc.
3DLocates structures that
could be targets in a 3D search. These are
structures scaled in Angstroms and having Z
coordinates. Both conditions must be met.
Structures that meet only one of these condi-
tions can be found by using the With Errors
search.
Fischer ProjectionsLocates structures
drawn as Fischer Projections.
DuplicatesLocates all records whose struc-
tures duplicate at least one other.
If Clustered is selected, the query will be a list of
duplicates only, clustered together (that is, a
sorted list). This makes duplicates easier to
compare, but you cannot edit records displayed
in a sorted list.
If Unique Structures Only is selected, the query
will be the same as the parent list, but with only
one unique copy of each duplicate structure.
NOTE: The Duplicate search must be performed in Full
Structure mode. If the Search type is set to Substructure, you
will get an error message reminding you to reset the search
type preference to Full Structure.
With ErrorsLocates records with possibly
faulty structures. Depending on the error,
and whether the database is read-only, it may be
possible to automatically re-register the struc-
Searching 419
Special Structure Searches
 ture with a corrected version. Unlike other
search operations, this scan begins at the
currently displayed record and proceeds to the
end of the record set, or until the scan is
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aborted.
The following categories of structural error are
treated:
Ambiguous stereochemistryFlags struc-
tures with ambiguously drawn tetrahedral or
double bond stereochemistry. Not correctable.
Valence/chargeFlags structures containing
an atom with an impossible valence or charge.
Sometimes correctable.
Net charge presentFlags structures
containing a net charge. This option is not
checked by default because it is not normally
useful. Not correctable.
Unrecognized atomsFlags structures
containing an atom that was not interpreted by
ChemFinder. Such atoms typically have atom
type R with a greyed text label containing ques-
tion marks. Not correctable.
Mass imbalanceFlags reactions in which
the molecular formulae of reactants is different
from products. Not correctable.
Doubly drawn atomsFlags structures in
which two atoms are very close together and at
least one of which lacks a label. (Also, to qualify
as a doubly drawn pair, the combined valence
420 Searching
of explicit bonds must not exceed the capacity
of either atom.) You get this sort of structure
when attempting to draw a bond from an
existing atom, but miss and accidentally create
a new atom. ChemDraw flags these cases with
a wavy red box.
3D not scaled in Angstroms
Flags structures with Z coordinates not scaled
in Angstroms. Such structures will not be
struck in a 3D search.
Outdated representationAs the MST data-
base format evolves, it becomes problematic to
correlate old stored information with the
current live data structures. Moreover, bugs
affecting stored data (e.g., molecular weights)
get fixed, making the stored data become grad-
ually less effective for searching. The best solu-
tion is to upgrade databases periodically. This
menu option lets you locate and repair faulty
data in an older database without upgrading the
database.
MiscellaneousPresently, this checks one
thing: that isotopic masses seem reasonable.
To perform a With Errors search:
1. Select the categories of interest.
2. Click the Scan button.
When a structure is flagged, its record is
displayed, the offending atom or bond (if any)
is flashed and an alert offers the user several
choices.
The options are:
if you want to... then click...
ignore the error and Continue
continue checking the
same structure.
CambridgeSoft
Special Structure Searches
if you want to...
rewrite the MST record,
thus correcting the
problem.
The Register (and like
buttons) will not appear if
the database is read-only or
if re-registering would not
correct the problem.
re-register other records
that exhibit the same type
of error automatically.
suppress all alerts and re- Reregister All
register all records that may
benefit from it.
leave the current record as Skip to Next Record
is (uncorrected) and
continue the scan from the
next record.
stop the scan.
This leaves you on the last
record that exhibited a
problem
flash the problematic Flash
atom or bond.
This button only appears
when the error revolves
around an atom or bond.
Clicking the button creates
a circle that moves toward
the atom/bond, drawing
the eye to it.
Chem & BioOffice 2006 /ChemFinder
then click...
Managing Queries
ChemFinder 9 has a new tool to manage queries.
Reregister The Queries Tree Control in the Explorer window
maintains a list of search queries from the current
and previous sessions. Queries are associated with
forms, and the query list is saved when you save the
form. When you open or activate an existing form,
the tree updates to show only the queries for that
form.
Each time you carry out a search or list operation, a
new query is generated in the tree. A name is
assigned to the query, and it is displayed in the tree
Rereg. Sim. Recs. along with the size of the list (number of hits) and a
(Re-register Similar brief description. The generated name is Q<n>*,
Records) where n is a sequential number, and * indicates that
the query has not been named or marked for saving.
CAUTION
Depending on your preference settings, unnamed queries
may be automatically discarded. See Saving and
Restoring Lists on page 423 for details.
To activate the Queries tree control:
1. Select Explorer Window from the View menu.
Stop Scanning 2. Click the Queries tab to display the Queries
tree.
Queries are listed as children of the database
(displayed as Full List). When you select Search Over
Current List from the Search menu before
performing a query, it is displayed as a child of the
previous list. (The current list is indicated with a
frame around the colored box.)
Searching 421
Managing Queries
 Database (Full List) if you want to... then
choose...
Current list (marked with
a frame)
Administrator

Search Over Current List choose a different query icon Change Color
query (child list) color from the Color Picker
dialog.

modify the query and/or rerun Restore Query

it.

To restore a query: Restore Query goes to Query

Double-click a query.
TIP: Double-clicking the root item, Full List, has the
same effect as choosing Retrieve All from the Search
menu.
mode and displays the structure.
You may modify the query, then
rerun it manually.
save the query to a separate file, Save Query...
with extension .cfq.

The Queries context menu mark the query so it will be Keep

When you right-click on a query, you display a menu
with commands to manage the query.
if you want to...
repeat the search using the Rerun
selected query. (This is the same
as double-clicking on the query.)
saved (as named) when the form
is saved.
This has no effect unless the
Query Saving preference has
then been set to Discard unnamed
choose... queries. See Saving and
Restoring Lists on page 423.
delete the selected query from Remove
the tree.

The next time you save the

merge the hits of the selected
query with the current list. See
Restoring a Hit List on page
424 for details.
Restore List
form, this query will be lost. If
you delete by mistake, you can
close and reopen the form
without saving.

apply the query's color to a plot Color On Plot

of the intersection of the
selected query with the current
list. (This is the same a single-
click on the query.)

422 Searching CambridgeSoft

Managing Queries

if you want to... then
choose...
rename the query. Rename
When the Query Saving prefer-
ence has been set to Discard
unnamed queries, this has the
same effect as Keep.
for all queries at the same depth Sort Folder
in the tree, sort alphabetically by
name.
You also use the context menu to display the Query
Properties dialog box. In this dialog box, you can
modify the query name, add a comment, or change
the color used in plots. Text entered in the
Comments box will replace the standard description
displayed along with the number of hits.
Domains
If you are browsing a list other than the full
database, you can make it seem that the database
consists only of the current child list.
On the Search menu, point to Domains and
select Set Domain to Current List.
Chem & BioOffice 2006 /ChemFinder
The current list acts like a full database. For
example, a Retrieve All command will retrieve
only this list; without selecting Search Over
Current List, searches will go over it only, etc.
To reset searches to the full database:
On the Search menu, point to Domains and
select Reset to Full Database.
NOTE: Set Domain to Current List remains in
effect until cancelled. If you save the form, it will be
saved with the form file and will still be in effect when
you open the form again.
Saving and Restoring Lists
You can save queries individually as .cfq files (as
with previous versions of ChemFinder) or
automatically when saving the form. The old
commands for saving and restoring lists (as .cfq
files) still appear on the Search menu, and on the
context menu displayed when you right-click on a
specific query. If you close a form without having
saved your queries (or other changes), you are
prompted to save or discard changes.
On the General tab of the Preferences dialog box,
there is an option to save all queries (the default), or
only those that have been renamed. If you select
this option, there are two ways to save a query with
the form:
Rename the query, either with the Rename
command in the context (right-click) menu, or
from the Query Properties dialog box (also
accessed from the context menu.)
Mark the query with the Keep command on the
context menu. Query saved in this way retain
their standard name.
Searching 423
Managing Queries
 To edit a saved hit list, open the text file with a text
editor such as Notepad and edit the values you want
changed.
Administrator

Restoring a Hit List

Once you have saved a hit list, you can perform
another search then integrate the results from the
second search with the results from the first. Thus,
you can perform Boolean operations on different
searches.

To integrate the results of two searches:

1. Perform a search and save the hit list.

Saving a Hit List 2. Perform another search.

3. From the Search menu, choose Restore List.
Create a query and perform the search.
The Open dialog appears for you to choose the
file that you want to integrate with the current
1. When you have received the hit list, choose
hit list.
Save List from the Search menu.
4. From the Open dialog box, open the text file
The Save As dialog appears for you to save the that you want to integrate with the current hit
hit list as a text file. list.
The Restore List dialog box appears.

5. Select the integration option and click OK.

Replace current listdiscards the current hit
list and displays the records from the hit list
2. In the Save As dialog, type a filename for the you chose to open.
hit list, and click Save.
Intersect with current listdisplays only
The file consists of a list of values of the primary those records that appear in both the current
key of each record in the hit list. If there is no hit list and in the saved hit list. This is a
primary key, the molecule ID is used. Boolean AND operation.

424 Searching CambridgeSoft

Managing Queries
 Subtract from current listdisplays only To create the hitlist for the first part of this search:
those records that are in the current hit list but
1. Open the CS_Demo database.
that are not in the saved hit list. For example, if
the current list contains records, 1, 2, 3, 4, and 2. Create the first query by drawing benzene in
5, and the restored list contains records 4, 5, 6, the Structure data box and entering 50-200 in
and 7, then only records 1, 2, and 3 will be the Molecular Weight Data Box.
displayed. This is a Boolean NOT operation; it 3. Search the query.
shows the records in the current list that are You get 75 hits.
not also in the restored list.
4. From the Search menu, choose Save List.
Union with current listdisplays all records 5. Save the hitlist as benz.txt.
in either the current list or the saved hit list.
This is a Boolean OR operation. To create another hitlist for the second part of the
search:
The hit lists are integrated. You can browse and
save this new hit list just as any other hit list. 1. Draw the query shown below in the Structure
Data Box.
NOTE: If you merge two lists and get an empty result, N
an alert appears and the list reverts to the previous list. C

2. Search the query.

Search Examples
The following are examples of searching options.
By specifying atom and bond properties, you see
how to use the query functions in ChemDraw to
search the database more effectively. All
substructure search query properties recognized by
ChemFinder are listed and described in Appendix J,
Structural Query Features..
Working with Multiple Hit Lists
A detailed example of how you can use hitlist
management to perform specific, sophisticated
searches follows.
You get 103 hits.
3. From the Search menu, choose Save List.
4. Save the hit list as c-n.txt.
Integrate the two hitlists:
1. From the Search menu, choose Restore List.
2. In the Open dialog box, open the benz.txt file.
3. In the Restore List dialog box, click Replace
current list,
4. then click OK.
You return to your first list of 75 hits
5. From the Search menu, choose Restore List.
6. In the Open dialog box, open the c-n.txt file.

Suppose you want to search for all compounds in
the CS_Demo database that contain a benzene
substructure and have molecular weights between
50 and 200. After you perform this combined
search, you want to find which of these compounds
do not contain a carbon-nitrogen bond. By
integrating hitlists, you can perform this search.
7. In the Restore List dialog, click Subtract from
current list, then click OK.
The hit list is reduced to the 60 records with
compounds containing a benzene
substructure, not containing a C-N
substructure, and having molecular weights
between 50 and 200.

Chem & BioOffice 2006 /ChemFinder Searching 425

Search Examples
 If you had chosen the Replace current list option in
the last step, then only the C-N records would be
displayed. Choosing Intersect with current list would
display those records in either list. Finally, choosing
Administrator
Union with current list would display all records from
both lists.
Using Atom Lists
Using the text tool in ChemDraw, you can enter in
a structural query a list of possible atom types, one
of which must match in the target compound.
If you want to search for molecules containing a
benzene ring with an ether, amine or phosphane
group, a query might look like the following:
[O,N,P]
Atom Types and Bond Types
To broaden or narrow a search query, you can
define the properties of the atoms and bonds in a
structural query. These properties are definable in
ChemDraw Pro using the Atom Properties and
Bond Properties dialogs accessible from the
Structure menu.
Suppose you want to find all molecules that contain
a non-oxygen chalcogenide bonded to another
atom, not necessarily carbon. You also want the
bond type between the chalcogen and the other
atom to be a single or double bond. The query,
drawn in ChemDraw Pro, may look like this:
This atom may be any non-hydrogen atom
A
S/D This bond may be single or double
[S,Se,Te]
This atom must be S, Se, or Te
426 Searching
The A label denotes that the atom may match any
atom except hydrogen. The indicator near the bond
indicates that the bond has been defined; in this
case, in the Bond Properties dialog of ChemDraw,
you specified that the bond type may be single or
double, S/D. Finally, by entering S,Se,Te enclosed
in brackets, you specified that one of these elements
must match in the target molecules.
Searching Fullerenes
A search of fullerenes can illustrate the restrictions
you can place on a formula search. Suppose you
want to find all fullerenes containing 20 to 80
carbon atoms, but you also do not want to include
large organic molecules.
The formula query could be:
C20-80 H0
By designating zero hydrogen atoms, you exclude
hydrocarbons from the hit list. By clearly
capitalizing the elements and spacing the query, you
avoid searching ambiguities, although there were no
ambiguities in this example.
Searching Link Nodes and Multivalent
Rs (MVRs)
ChemFinder versions 8 and later contain a new
atom type, the link node. A link node is a
placeholder for zero or more unspecified atoms. It
is especially useful when searching for targets with
any of several ring sizes, or chains substituted in
particular ways at either end. While link nodes are
traditionally divalent, ChemFinder places no
constraints on the upper limit of the range. Multi-
CambridgeSoft
Search Examples
valent R (and A) atoms are functionally similar to Using ChemDraw's Atom Properties menu to
link nodes. They may be thought of as higher apply either of these properties to the link node
valent link nodes. restricts the range of target atoms to the specified
topology. For example, specifying the link node to
O be aromatic would give the following results:
(C
H2)0
-200
B
r Br Query Results
(C
H2)1
-2

Hits cyclopropanones, Hits alpha, omega- Will hit

cyclobutanones, and dibromides and Br Br

-lactams bromine
(C
H)0-200 Br
C
l P
h C
l P
h B
r B r
A (L
N )1-999 Br Br

A multivalent A query Br

Will not hit

The traditional representation of a link node is CH2, Br Br

but this is misleading because any atom type can

substitute for the link node. For this reason,
ChemFinder represents link nodes as LN.

NOTE: ChemDraw recognizes link nodes, but does not

support an LN atom type. Use (R) instead of (LN) when
drawing the query in ChemDraw or with the ChemDraw
ActiveX control.
Although any atom type of a target atom matches a
link node, you can impose two restrictions the on
the link node:
Unsaturation
Ring topology.
Searching More Than One Substructure
A substructure search may contain more than one
substructure unit. Suppose you want to find all
compounds in the CS_Demo database which
contain a benzene substructure and another
substructure unit containing chlorine bonded to
any atom. A structure query, as drawn in
ChemDraw would look like this:
A Cl

You should get five hits. Browse the hits. By

specifying the query as above, you obtain hits such
as benzyl chloride, shown below, where the
substructure units are not connected.

Chem & BioOffice 2006 /ChemFinder Searching 427

Search Examples
 .
H Cl O Cl
O

H Cl
OH
O
Administrator

O
OH
The substructure units can overlap; they can share
a common atom. Examples of this overlap are
shown below
Cl

428 Searching CambridgeSoft

Search Examples
Chapter 21: Customizing ChemFinder
Overview
You may customize ChemFinder in the following
ways:
Customize display of your molecules, fonts,
pictures and forms.
Customize the Favorites tree
Design the toolbars to your specifications.
Perform automated tasks, such as interfacing
with Microsoft Excel, or by using CAL, the
ChemFinder Automated Scripting Language.
Structure Display
To display carbon atoms on methyl groups or on
interior aliphatic or aromatic chains, check the
relevant check boxes in the Carbon labels section.
To display hydrogen atoms on heteroatoms or on
terminal carbons:
Select the Fill valence radio button in the
Hydrogen Labels section.
Selecting None means these types are displayed
without implicit hydrogens.

Setting Preferences
The Preferences dialog box allows you to
customize the display of molecules, pictures, and
forms, and set options for searching and exporting.
1. Click the tab containing the preferences to set.
2. Select the preferences, and click OK.

Display Preferences
To set the Display preferences:
From the File menu, choose Preferences.
The Preferences dialog box appears with the
Display tab on top.
To display reaction centers:
On the View menu point to Structure, and
select Reaction Info.

Chem & BioOffice 2006 /ChemFinder Customizing ChemFinder 429

Setting Preferences
 With reaction centers shown, any bond that
changes in the course of a reaction is colored.
Additionally, any atoms that participate in
reaction centers are circled if none of their
Administrator
adjacent bonds participate in the reaction
center.
To display atom-to-atom maps:
On the View menu point to Structure, and
select Atom-to-Atom Map.
With atom-to-atom maps shown, equivalent
atoms in reactants and products are colored the
same.
These two preferences affect only the display
of reactions. Not checking the boxes means
these types are displayed as all other atoms and
bonds.
Using Keyboard Shortcuts
When using a form, you can use keyboard shortcuts
to show or hide atom-to-atom maps, reaction
centers, atom numbers, and bond numbers.
To use keyboard shortcuts select Enable keyboard
shortcuts on the Display tab of the Preferences
dialog box.
When keyboard shortcuts are enabled, the
following keys toggle these properties:
A: show/hide atom numbers
430 Customizing ChemFinder
B: show/hide bond numbers
M: show/hide atom-to-atom maps
R: show/hide reaction centers
S: show/hide stereochemistry
Scaling Structures
To scale each structure so that it is as large as
possible within its structure box:
Click Fit to box.
To display all structures with a constant bond
length:
1. Select Uniform bond length.
2. Select the bond length percentage.
With Uniform bond length selected, structures
may be reduced in size if they are too large to
fit within the structure box, but they will never
be enlarged.
Framing Pictures
To select whether the pictures in a form are
surrounded by a border:
Select Framed.
Grid Spacing
To set the grid spacing (in pixels) on a form:
Type in a number, or press the up and down
arrows to change the current value by one unit.
Choosing a small grid spacing allows you to place
objects more precisely by snapping to a tighter
matrix.
Color Preferences
To set the color preferences:
In the Preferences dialog box, click the Color
tab.
CambridgeSoft
Setting Preferences
 ASCII file export (see Exporting an ASCII
File on page 401)
Alerts
ChemFinder opening window
List of the last files used

To set the general preferences:

1. From the File menu, click Preferences.

The Preferences dialog box appears.

2. Click the General tab.

The General tab appears.

The color tab allows you to specify the color of
various interface elements.

To set a color:
3. Click the button corresponding to the interface
element you want to change.
The Color dialog box appears.

Structure Registration Options

To have ChemFinder present an alert when
attempting to enter a structure with an atom in a
non-standard valence state:
In the Registration section, click Check valences.
To have ChemFinder confirm when you are about
to modify data in the database:
In the Registration section, select Ask to commit
4. Select the new color. changes.

5. Click OK. ChemFinder Opening Options

General Preferences You can set ChemFinder to open with the

ChemFinder Opening dialog box or to open the
The general preferences are as follows: last form you were using.

Chem & BioOffice 2006 /ChemFinder Customizing ChemFinder 431

Setting Preferences
 To set the options for what ChemFinder displays
when it starts up:

1. On the General preferences tab, select one of

Administrator

the following:

If you want to Then click

set ChemFinder
to

You can open items in the Favorites Tree from

start with the Show opening dialog.
within ChemFinder by double-clicking them:
Opening dialog box

if the file is double-clicking

open the last form Open last form on
will
you used startup.

a ChemFinder form, open it.

2. Click OK.

a ChemFinder script, execute it.

Setting the Recent File List Size
You can set the number of files you opened recently an SD- or RDFile, load it.
that ChemFinder shows.
a ChemFinder query, restore it.
To set the list size for the most recent files opened:
any other type of open it in its source appli-
1. From the General preferences tab, choose the document, cation.
number of file names to display.
2. Click OK. There are two ways to add items to the Favorites
Tree:
Customizing the Favor- Drag one or more files from Windows
Explorer into the Favorites window.
ites Tree Use the context menu.
The Favorites Tree is a user-constructed collection To create a new folder in the Favorites Tree:
of file system objects. It may include folders,
1. Point to the parent folder. (The new folder
subfolders, ChemFinder forms, structure files, and
will be a subfolder of this folder.)
documents of all kinds. Its purpose is to allow you
to collect, organize, and access the data and 2. Right-click and choose New Folder.
documents you use regularly. 3. Type in a new name for the folder.

432 Customizing ChemFinder CambridgeSoft

Customizing the Favorites Tree
To add an item to a folder:
1. Point to a folder.
2. Right-click and choose New Item.
A File dialog box opens.
3. Browse to the file you want to add, select it, and
click Open.
The item is added to the folder.
To rearrange items or folders in the tree:
Drag the item to a new location.
To resort a folder or subfolder alphabetically:
Right-click on the folder and choose Sort
Folder.
Customizing Toolbars
ChemFinder lets you format your toolbars. You can
Customize the toolbars by dragging buttons on or
off.
To open the Customize dialog box:
From the View menu, point to Toolbars, and
choose Customize.
The Customize dialog box appears.
Chem & BioOffice 2006 /ChemFinder
To add an option to a toolbar that is already in the
ChemFinder window:
1. In the Customize dialog box, click the
Commands tab.
2. Locate the command and click+drag an option
from the Commands window to a toolbar in the
ChemFinder window.
The option appears where you drop it on a
toolbar.
You can delete a button by dragging it off the
toolbar.
To return a toolbar to the default settings:
1. In the Customize dialog box, click the Toolbars
tab.
The Toolbars tab appears and shows all of the
toolbars that currently appear in the
ChemFinder window.
2. Click the toolbar you want to return to default
settings, then click Reset.
The toolbar in the ChemFinder window
changes to the default settings.
Customizing ChemFinder 433
Customizing Toolbars
 To return all the toolbars to the default settings:
1. In the Customize dialog box, click the Toolbars
tab.
Administrator
The Toolbars tab appears and shows all of the
toolbars that currently appear in the
ChemFinder window.
2. Click Reset All.
Using the Periodic Table
ChemFinder features a periodic table for data
display and formula entry. Selecting an element
displays physical and historical data.
To display the Periodic Table window:
1. From the View menu, choose Periodic Table.
2. Click on an element to display its name, mass,
and other properties in the top box, and to
display its symbol in the bottom edit box.
By clicking on different elements and numbers
sequentially, you can create a molecular formula in
the bottom editable text box. You can then paste
this formula into the form for a formula query.
To copy a formula from the Periodic Table to the
form:
1. Drag the text to copy, then press Ctrl+C.
2. Click OK in the Periodic Table window to close
it.
434 Customizing ChemFinder
3. In the form, click the formula box into which
you want to paste the text and press Ctrl+V.
To display data about the selected element in the
Element Editor, do one of the following:
Display the desired element and click the
display box at the top of the Periodic Table
window.
Double-click the desired element button.
The Element Editor displays properties of the
selected element. The color of the element is shown
in the periodic table for that element and in any
structure data boxes in which that element is
present.
To change the color of an element:
Click Color.
To reset an elements color to the default:
In the Element Editor, click Revert to Default.
NOTE: The data of the Periodic Table is stored in a tab-
delimited ASCII file called CS ChemFinder Custom
Elements.txt located in your ChemFinder system directory. It
can be easily edited with a text editor or spreadsheet program
if you want to change default data values.
CambridgeSoft
Using the Periodic Table
ChemFinder Automation
Language (CAL)
ChemFinder is equipped with its own scripting
language, the ChemFinder Automation Language
(CAL). CAL is used to operate the program from
the keyboard, or to create custom scripts for
automating simple operations such as switching
between forms or sending data to Microsoft Excel.
CAL scripts are stored in text files, with their
pathnames stored in forms. In Chem & BioOffice
2006 you have the option of storing scripts directly
in formfiles. Scripts created in Chem & BioOffice
2006 are stored internally by default. When you
open a form which references external script files,
you will be prompted to store the script internally.
If you choose to convert the external script files to
internal, the scripts will be saved when the form is
saved, and the original script files may be deleted.
Scripts originally saved as internal may be also be
saved externally.
The Enter CAL Command dialog box appears.
You can type CAL commands and execute them
one at a time.
The Command drop-down list contains previously
entered commands.
To rerun a previously entered command:
1. Select the command from the list.
2. Click Execute.
For detailed information about the command
language, see Appendix M, CAL Commands.
Getting CAL Help
To display information about the CAL scripting
language:
In the Enter CAL Command dialog box, click
Help.
The CAL Scripting Help window appears
containing commands, variables, and syntax
notes.

TIP: You can save the form with a different name, and the
original will remain untouched (in which case deleting the
script files would not be a good idea).

If you choose to leave the form unmodified, the

alert will continue to show up every time the form
is opened. You can suppress the prompt with the
Check for external scripts checkbox in the General
tab of the Preferences dialog box.
To perform a CAL command: TIP: In Chem & BioOffice 2006 this window is resizable.
From the Scripts menu, choose Command
Line.
Creating a Script
To create a script:
1. Create a button on a form.
2. Label the button.
3. Right-click and choose Edit Script.

Chem & BioOffice 2006 /ChemFinder Customizing ChemFinder 435

ChemFinder Automation Language (CAL)
 The CAL editor appears. To execute a script not assigned to a button:

Choose the script from the Scripts menu.

Administrator

NOTE: To execute a script that does not appear on the

menu, use the Command line and enter Call <script
filename>.

Debugging a Script
You can step through a script line-by-line when
4. Type in your script commands, or use the debugging it.
Import button to import an existing script.
To view a script line-by-line:
5. Click OK to create a new file.
1. From the Scripts menu, choose Command
TIP: You can still create scripts in Notepad or another text Line.
editor if you wish. Save the file with extension .cfs in the The Enter CAL Command dialog box
\ChemFinder\System subdirectory if you want the name appears.
of the script to appear on the Scripts menu.
2. Type step on and click Execute. this turns on the
step mode, where each step is displayed.
The CAL editor is a simple, resizable text-entry
window. It accepts carriage returns and tabs. To 3. Run a CAL script by doing one of the
copy /paste, use Ctrl+C/Ctrl+V. To undo or redo following:
(last change only) use Ctrl+Z.
If your script Then
The Verify button runs the script through the CAL
command parser. The parser checks only that lines appears in the choose the appropriate
begin with recognized keywords, so just because a Scripts menu. script.
script is parsed without error does not mean it will
run correctly. does not appear in in the Enter Script
the Scripts menu. Command dialog box,
The Properties button displays a dialog box used to
type call and the name
specify whether the script is to be stored in an of your script, then
external file or internally, and to provide a file path click Execute.
or script name. You can assign a script any name
you like, but the name must be unique among
4. Press any key except Escape to execute the
scripts on the current form.
command and go to the next command.
The OK button saves the script. The Run button As each step is encountered, it is displayed in
saves the script and runs it. the status line.

436 Customizing ChemFinder CambridgeSoft

ChemFinder Automation Language (CAL)
 5. Press the Esc key to stop debugging the script.
CAUTION
In the Enter Script Command dialog box, type step off to
exit the debugging mode.
Trigger Scripts
Trigger scripts run in response to certain
predefined events. A trigger script can, for example,
automatically load a box with data calculated from
the contents of another box whenever you move to
a new record.
You access a trigger script from the Run script on
listbox in the Form tab of the Properties dialog box.
The listbox shows the available trigger events, and
allows you to create, edit, enable, or disable scripts
for each event.
Run script on...
To run a script on an event:
1. Click the checkbox of the desired event in the
listbox. If an event is not checked, no script will
run on that event, even if one is available.
2. Click the event name to highlight the row of
the listbox. (Clicking in a checkbox does not
select the row.)
3. Click the Edit button to write or edit the script
in the CAL Editor.
4. Click OK to return to the form.
Chem & BioOffice 2006 /ChemFinder
The script will automatically be executed at the
specified event.
5. Save the form if you wish to keep the changes.
Communicating with
Other Applications
There are two general methods of communicating
with other Windows applications such as Microsoft
Excel: by using a script within ChemFinder, or by
using a Visual Basic procedure within the other
application. The following is an overview of each
method.
Using Scripts
A ChemFinder (CAL) script can communicate with
other Windows applications using either of two
commands:
EXECto start an application and possibly pass
information on the command line.
DDEto communicate using Dynamic Data
Exchange with a DDE-ready application.
Using EXEC is straightforward, but limited. You
can start all Windows applications by this
command. Most can be passed a filename on the
command line, such that the specified file is opened
(or printed) on startup. A few applications can
accept more detailed instructions. Consult the
applications manual for information about how it
can be operated using the command line.
If you have Visual Basic or similar programming
language, you can extend the power of EXEC. You
can write an application using the advanced features
of Visual Basic, then call the application from
within ChemFinder using the EXEC command.
Using DDE is more complicated. You can operate
most Microsoft Office components and many
other programs to varying extents with DDE. For
example, practically every command on the Excel
Customizing ChemFinder 437
Communicating with Other Applications
 menu can be executed by DDE. The syntax is
rather difficult, but can usually be worked out by
experimenting and consulting ChemFinder help.
An example is given below.
Administrator
DDE is the most direct way of using Excel to view
data from ChemFinder.
To use MS Excel to view ChemFinder data:
1. Start MS Excel. You can start it manually using
a CAL script or by starting the application in
Windows.
2. In ChemFinder, obtain the hit list you want to
transmit to Excel. If you want to work with the
entire database, from the Search menu, choose
Retrieve All.
3. Execute a short CAL script (below) which
exports the hit list as comma-delimited text to
a temporary file, then instructs Excel with
DDE to load that file into a spreadsheet.
4. Activate Excel to work with the data in the
spreadsheet.
This procedure takes data one way, from
ChemFinder to Excel. Returning modified data
from Excel to ChemFinder can be done using other
techniques described in this chapter.
Here is a script to start up Excel:
*RUNEXCEL.CFS script to start Excel
* ChemFinder System directory, label a button
EXEC c:\msoffice\excel\excel.exe
If the Excel program is on your search path, you
can eliminate the complete pathname and just give
the executable name (exec excel.exe); if not, you
may need to modify this script to indicate where
EXCEL.EXE is located on your system.
Here is a script to transfer the current hit list from
ChemFinder to Excel:
*TOEXCEL.CFS script to send data
*to Excel
* small, it is adequate for a variety of data retrieval and
438 Customizing ChemFinder
WRITETEXT C:\DATA.TMP
DDE Excel System [OPEN(C:\DATA.TMP)]
DDE Excel
System [COLUMN.WIDTH(1,C1:C4,,3,1)]
The first line writes out the current ChemFinder hit
list as a temporary delimited ASCII file. By default,
all fields that appear in boxes on the current form
except structure, but including formula and
molecular weightare written. The second line
instructs Excel to open the file. Excel can
automatically recognize the file format as tab-
delimited. The third line instructs Excel to auto-size
column widths 14 to fit their contents.
NOTE: This example requires that the text export
delimiter be set to TAB in the General tab of the Preferences
dialog, otherwise Excel may not read the file correctly.
You can include either or both of these scripts on
the Scripts menu, and you can activate them with
buttons on the form. To include a script on the
Scripts menu, give it a filename with extension
.cfs, and place it in the ChemFinder System
directory, or in the directory containing the
ChemFinder application. To activate a script from a
button, label the button with a script filename or
string which can be converted into a filename. For
example, if TOEXCEL.CFS exists in the
ToExcel to start the script. For more
information, see Adding a Button on page 343.
Using Visual Basic
The second method of communicating between
ChemFinder and other applications such as Excel is
using OLE Automation. ChemFinder is an OLE
Automation server, meaning that it offers a
collection of data management capabilities to
outside programs capable of communicating with
OLE objects. While this collection is currently fairly
CambridgeSoft
Communicating with Other Applications
search tasks. This feature allows you to write a
custom Visual Basic procedure that directly
retrieves and manipulates data from ChemFinder.
The general procedure for accessing ChemFinder
data from within a Visual Basic script is as follows.
1. Create a ChemFinder Document object,
typically passing a filename so that you open a
form complete with its database connection.
2. Use methods of the Document object to move
through the database, search, and access data.
Document methods include some that access
Field objects, used to query the data in the data-
base, and Molecule objects, for accessing
details of molecular structures.
For more information, see the CambridgeSoft SDK
web site:
http://sdk.cambridgesoft.com/
Using Microsoft Access with
ChemFinder
The methods described above for communicating
between ChemFinder and Excel apply also to
Access. You can start Access using the EXEC
command. You can send it DDE commands
contained in a CAL script, although Access
provides fewer capabilities with DDE than does
Excel. Or you can write programs using Access
Basic that rely on the OLE Automation methods
found in ChemFinder. In addition, you can use
Access directly to operate on a ChemFinder
database.
A ChemFinder molecule database consists of three
components: the structure storage files (with file
extensions .mst and .msi), the data storage files,
which include a Microsoft Access database (file
Chem & BioOffice 2006 /ChemFinder
extensions .mdb and .ldb), and the forms (with file
extension .cfw) used to view the structures and the
data.
If you have Access on your system, double-clicking
an .mdb file in Explorer starts up Access and opens
the specified database.
When you open a ChemFinder database in Access,
you will see the same tables as displayed in the
ChemFinder Database dialog box, including the
main structure table (usually named MolTable),
but you will not see columns for structure, formula,
or molecular weight. These fields cannot be
manipulated directly using Access.
The following are some of the operations you can
perform on a ChemFinder database using Access.
Most of these capabilities are not available through
the current version of ChemFinder:
Compress or repair the database.
Change column (field) or names or formats.
Change table names.
Add or delete columns or tables.
Import or export tables.
Load non-structural data from various file
types, including delimited ASCII, Excel, or
Word.
Move quantities of data from one column or
row to another.
Carry out complex queries on non-structural
data.
Permanently change the sort order of a table.
For more information about these actions, please
consult the Microsoft Access Users Guide.
Do not add or delete records to the MolTable
within Access, because the data component of the
database will become out of synchrony with the
structure component.
Customizing ChemFinder 439
Communicating with Other Applications
Administrator

440 Customizing ChemFinder CambridgeSoft

Communicating with Other Applications
Chapter 22: Pro
Overview
Users familiar with ChemFinder will find that, for
the most part, ChemFinder/Oracle operates the
same way. You should be able to open a database,
browse, search, register, load and so forth, without
worrying about what sort of database is on the back
end. In practice, however, there are several visible
differences and a lot of invisible ones.
When you open an Oracle database in
ChemFinder/Oracle, you enter a new body of code
which connects directly to Oracle, and carries out
all searches and transactions on the server. This
new mode of operation requires a different
underlying technology, based on Microsoft ActiveX
Data Objects, and a different philosophy in some
aspects of usage, such as the handling of lists, and
new features, such as index management. All of
these are described in this document.
In ChemFinder/Oracle:
Searches are carried out on the server,
including structure searches.
Search results are automatically deposited
directly into tables in the Oracle database.
Hitlists are not saved in files, but to other tables
in Oracle.
Saved lists can be annotated, and on restore can
be selected from a pick-list directory.
Chem & BioOffice 2006 /ChemFinder
ChemFinder/Oracle
When working with large databases, you can
choose a new mechanism which eliminates
certain slow operations associated with large
recordsets (e.g., Move Last). This is a user
choice because there are trade-offs involved.
You cannot create an Oracle database, but if
you have the privileges you can create a table
within one. This causes import operations to
work somewhat differently.
To improve performance, you can create
indexes on selected columns.
Other more subtle differences are noted in the
sections below.
Setup
Before you can make use of the
ChemFinder/Oracle, your machine must be
configured as an Oracle client. If you are already a
user of the CS Oracle Cartridge, you are probably
all set. If not, you will need to enlist the help of an
Oracle administrator to set up the server and set
you up as a client.
For ChemFinder 10 installation instructions, see the
readme.txt included on the distribution media.
Ideally, ChemFinder/Oracle should access any
existing Oracle database in any format. In practice,
there are some limitations. See Pre-Setup
Procedures on page 491 for notes and
recommendations about preparing an Oracle
database for use with ChemFinder/Oracle.
ChemFinder/Oracle 441
Setup
 Opening an Oracle Data-
base
Administrator
To open an Oracle database:
1. Click the Oracle Database button in the
Database tab of the Properties dialog.
This brings up the CS Oracle Connection
dialog.
Oracle
Database
button
NOTE: The Oracle Database button is available to
any user. There is no check to see whether the machine
is a valid Oracle client.
2. Enter values for host name, user name, and
password the same values you use to log in
from any Oracle client. OR:
Choose a name from the drop-down list of
recently-used items. When you choose an item
from this list, it automatically fills in the user
name, and the password if Save password was
checked when the item was created.
NOTE: The first time you bring up the Oracle
Connection dialog box there is no list of recent items, so
ChemFinder offers to create one for you. If you accept, it
generates a list of all available hosts, as found in the file
tnsnames.ora created during Oracle client
configuration.
442 ChemFinder/Oracle
The database is opened and the list of tables
displayed.
NOTE: The list of tables shown in the tree consists of
all tables and views owned by the current user, plus
those to which the user has been granted certain
privileges. To see the details, you can turn on SQL
tracing while a database is being opened.
3. Proceed as you would for any ChemFinder
database: click to select the table you want to
display, set other desired options, and check the
box on the Form tab if you want to generate a
form automatically.
Notice the new Oracle tab of the dialog,
described in Setting Oracle Preferences on
page 444 The features on this tab are mainly for
advanced users and do not require adjustment.
NOTE: The Oracle tab appears in the Properties
dialog only when an Oracle database is open.
4. Click OK.
The database opens, in a display form if you
requested one.
The Database Wizard can also be used to open an
Oracle database. A button on the Wizard labelled
CS Oracle Cartridge brings up the appropriate
Oracle parts of the process.
When you have opened an Oracle database, note
that some Properties dialog tabs show entries not
available in ChemFinder, including:
Database tab: CS Oracle Cartridge version if
any.
Table tab: Table owner name; name of primary
index if any.
Field tab: Oracle native data type name; name
of associated index if any.
When you open an Oracle database and select a
table, ChemFinder/Oracle gathers information
about the columns. If you open a table you know to
CambridgeSoft
Opening an Oracle Database
contain structures, and ChemFinder/Oracle does
not show a structure (or formula or molweight)
column, then it may be necessary to set up some
configuration information about the table. For
details, see Configuration Via CF_SETTINGS
Table on page 492.
Searching
From the user's point of view, searching in
ChemFinder/Oracle works basically the same way
as in ChemFinder: you enter a query, search, then
work with the hitlist. Internally, however, the
ChemFinder/Oracle machinery is quite different.
There are three types of table involved in handling
hit lists. All are created in your own tablespace. One
is global, applying to all lists saved from any table;
others are connected to the particular table or view
being searched.
CF_HITLISTS. The directory of all saved
lists. This table is created the first time any list
is saved.
SAVED_tablename: All lists which have been
explicitly saved from a given table or view. This
is created the first time a list is saved.
HITS_tablename: All lists automatically saved
after every search over a given table or view.
This table is created the first time a search or
list operation is carried out and is deleted at the
end of the session.
Here's what happens when you present a query to
ChemFinder/Oracle:
1. If the query contains a structure, it is converted
to a text representation and copied to a
temporary table.
NOTE: The table is called temp_queries. It is
created in the CSCartridge tablespace, and removed as
soon as the search is finished or interrupted.
ChemFinder does not yet handle the case of multiple
structure boxes where more than one contains a query.
Chem & BioOffice 2006 /ChemFinder
2. The query is converted to a SQL select state-
ment. Query components in form boxes are
ANDed together (just as in ChemFinder), where
the structural parts are calls into the CS Oracle
Cartridge structure search functions.
3. The hits table is created, if it does not already
exist.
4. A unique ID is assigned to the new list which
will result from the search.
5. The select statement is wrapped in a larger
SQL statement which will cause the results to
be deposited directly into the hits table.
6. The SQL is executed.
7. When the search is complete, the results are
new rows in the hits table. Each row contains
the new list ID alongside the ID of a record
from the searched table.
8. The final list is prepared by a join, selecting
rows from the main table which have record
ID's matching those of the new list in the hits
table.
The resulting list is ready to browse, save,
export, etc.
NOTE: Text searches in Oracle are case sensitive. You will
get different hits from the query benz* than from
Benz*.
Handling Lists
There are differences between ChemFinder and
ChemFinder/Oracle in working with hitlists:
Save List does not bring up a file dialog in
ChemFinder/Oracle; instead, it presents a
dialog in which you enter a name and a line of
comments for each list.
Restore List presents a dialog in which you
choose from the available saved lists (see
screen shot below); double-click to select one.
ChemFinder/Oracle 443
Searching
 Restore Previous List is no longer dimmed after
you have done a single search; it is available,
and will return you to the full list. (This is true
also in ChemFinder 10.)
Administrator
Over Current List, Omit From List, and Find List
work as before.
Setting Oracle Prefer-
ences
When you are working with an Oracle database, the
Properties dialog contains a tab for Oracle settings.
Items currently in this tab are as follows:
Oracle
tab
Auto-sort on. Displays the default sort field.
All lists will be sorted in ascending order over
this field if no other sort criterion has been
specified. At present, the auto-sort field is
always the primary key, and cannot be changed.
Primary key. Names the primary key of the
current table, if any.
Saved hits. Displays the name of the table in
which saved hitlists are stored for the current
form, if one has been created.
444 ChemFinder/Oracle
Records per retrieve. Sets the size of the
ADO recordset cache, that is, the number of
records brought to the client for each retrieve
operation. This value can be adjusted for better
performance, but in practice it does not have
much effect.
Cache ID's for faster moves. Checking this
box enables a new record-retrieval scheme
designed for more efficient browsing of large
lists; details are given in Fast-Move Caching
Scheme on page 491. The state of this
checkbox is saved with the formfile. Currently,
when you check or uncheck this box, you must
save and reopen the form before proceeding.
SQL Trace to file. Check this box to generate
a text file of the SQL being sent from Chem-
Finder to Oracle. To specify an output file,
enter a pathname or use the browse
button. The file is never overwritten: new data
are always appended. Tracing begins when this
box is checked, and ends when it is unchecked.
If you exit ChemFinder with tracing in effect, it
will be in effect the next time you start up, and
you will be given a quick warning about it on
the status bar.
CAUTION
The trace file can become very large if you turn on this
feature and forget about it.
Updating and Adding
Data
If you have privileges to add, update, and delete in
the table connected to your form, then you should
be able to do these operations on records in the
database just as in ChemFinder. However, there are
some cautions:
CambridgeSoft
Setting Oracle Preferences
 Do not modify data in an existing Web Server,
RegDB, or E-Notebook database. Chem-
Finder/Oracle does not automatically prevent
you from doing this, but you are sure to foul up
those systems unless you go through their
normal registration procedures, or know
exactly what you're doing.
Most database alterations are possible, as in
ChemFinder: you can add, modify, and delete tables
and fields, assuming you have the appropriate
privileges. Differences include:
When you create a structure field, you can give
it any name you like.
Structure columns in tables managed by the CS
Oracle Cartridge can be in any of several
formats, but ChemFinder/Oracle does not
allow you to choose one: it defaults to a char-
acter (CLOB) column storing text-encoded
CDX.
ChemFinder/Oracle does not allow you to
create an Oracle database in the same way
ChemFinder creates an Access mdb file. The
equivalent in ChemFinder/Oracle is to create a
table.
Loading
You can build ChemFinder/Oracle databases by
loading from SDFiles or using Import Structures.
(RDFiles should work also, but have not been
tested.) However, because you cannot actually
create a new database, the procedure is somewhat
different from ChemFinder. You must already have
a database open, then you can import to an existing
table or have a new one created.
Chem & BioOffice 2006 /ChemFinder
To import data and structures into a new table:
1. On an empty form, right-click and choose Data
Source.
2. Click Oracle Database and proceed as
described under Opening an Oracle Data-
base on page 442. It doesn't matter what table
you select, since you will be creating a new one.
3. Click OK to return to the blank form.
You are now ready to import.
NOTE: When you click OK to dismiss the properties
dialog, you will get a warning if the selected table does
not have a primary key defined. You can ignore this if
you are about to create or load a new table. Otherwise,
you should consider using an Oracle tool to define a
primary key for the table.
4. Choose Import SDFile or Import Structures and
select the source file(s).
The Data Import dialog appears:
Import tab
Output database
text box
5. In the Output database box, you see the name
of the database followed by the table name in
brackets. To specify the table to load, edit the
table name by typing between the brackets. If
you want to create a new table, enter the name
you wish to give it. If you want to append to an
existing table, enter its name.
ChemFinder/Oracle 445
Loading
 6. Set other options as desired, and click Import to
begin the process.
TIP: for text fields being imported, make them wider
Administrator
ChemFinder provides information about these
indexes, and allows you to create or recreate them if
necessary.
To create a structure index:

than the value determined by the input scan. (To do this,

double-click the name under Input Field and enter a
larger Width value.) Otherwise you might have
problems if you append more records later.
7. After importing, you should create a primary
key and index; see Indexing on page 446.
To append to an existing table follow the procedure
above except:
Step 1: You can start with an existing form
instead of a blank one
1. Right-click on the structure box of an Oracle-
connected form, and choose Properties.
2. Go to the Field tab of the dialog.
If the selected field is indexed, the index name
is shown in the properties box. In the example
below, the index is named IX50.
Field
tab

Step 2: You should select the target table. When Index

you do, there will be no need to edit the table Name
name in Step 5.

Indexing
As every Oracle administrator knows, a key to good
performance is to index certain columns so that
searches over them become fast lookups. If you
intend to create, load, or manage tables, then you
NOTE: If there is no index, or the field is not
are an administrator, and need to know something
about indexing. ChemFinder/Oracle provides a indexable, the Index line does not appear in the list.
few tools to assist you.
3. If there is no index, click Create Index.
There are two types of index of interest to
ChemFinder/Oracle: NOTE: If this button does not appear, it means the
selected field is not a candidate for indexing.
Structure indexes. Any column containing
structures should have an index created by the 4. In the Create Index dialog, provide a name for
CS Oracle Cartridge. If there is no index, the new index and click OK.
searching is still possible, but very slow.
The index is created.
Primary keys. A table containing a column of
structures should also have a column of unique You will get an error message from Oracle if:
record identifiers for use in various list-
You provide an index name which is already in
handling operations. Preferably this column is
use, OR...
of type INTEGER and is designated as the
primary key of the table. The column already has an index.

446 ChemFinder/Oracle CambridgeSoft

Indexing
ChemFinder/Oracle does not provide a direct way
to delete or overwrite an index, but the CAL SQL
command can be used for this purpose.
integer).
To create a primary key index:
The process is the same as for a structure
index, except that you carry it out on a field of
type Long. This creates an index on the field
and also designates it as the primary key. It will
fail unless the column already contains unique,
non-null values.
$CURR_TABLE
NOTE: A new button, Set As Structure, may
appear if you have selected a certain type of column. This
is an advanced feature described in Configuration Via
CF_SETTINGS Table on page 492.
TIP: If you want to create a primary key, but don't
have a column of unique integer values, you can create
one using a CAL script. For example (assuming you've
already created a column and form box called ID):
loop
putdata ID $index
record commit
record next
endloop
CAL
Some new features have been introduced into
ChemFinder Automation Language (CAL) to progress...
support Oracle. Some are not specific to Oracle,
but of general utility:
SQL command. When you are connected to an
Oracle database, you can pass any SQL
command which does not return records. The
format is simply SQL <command> where the
command is not quoted.
Chem & BioOffice 2006 /ChemFinder
Example:
SQL create table mytable (id
CURR_TABLE variable. This variable
contains the name of the table connected to the
current form. This works whether or not you
are in Oracle.
Example:
MSG Current table is
OPENDB allows change of table. Normally
this command takes the name of a database,
followed optionally by the name of a table in
angle brackets. In ChemFinder 10, it can now
take just the table name, and causes the form to
become attached to a different table in the
current database as if you had brought up
Properties and clicked a different table name.
Example:
OPENDB <CHEM_STRUCTS>
causes the current form to be connected to the
table CHEM_STRUCTS.
STATMSG command displays a message on
the status bar. Format: STATMSG <message>.
Example:
STATMSG Search is now in
SEARCH SAVE LIST, RESTORE LIST
work with Oracle. Normally you can follow
either of these commands with the name of a
file; in ChemFinder/Oracle you can instead
provide a list name.
ChemFinder/Oracle 447
CAL
Administrator

448 ChemFinder/Oracle CambridgeSoft

CAL
Chapter 23: ChemFinder/Office
Overview Substructure
Full structure
ChemFinder/Office allows you to search data Similarity
sources (documents and databases) to find chemical
Identity
structures so that you do not need to search
manually. You can save frequently-used collections of data
sources (documents and databases) in Data Source
Using ChemFinder/Office, you can browse the Definition (.dsd) files. Instead of checking many
following types of files for chemical information: data sources that you want ChemFinder/Office to
MS Word documents search, ChemFinder/Office can search one .dsd
file.
MS Excel spreadsheets
ChemFinder databases You can also generate and store combinatorial
libraries from experiments performed with generic
ChemDraw files
reactions. For more information, Using
SD files ChemFinder/Office with CombiChem on page
Isis/Draw files 461.
In addition to browsing, ChemFinder/Office can ChemFinder/Office helps you to build databases
search files by: by extracting information from various sources and
exporting to another source.
Chemical structure
Chemical formula The ChemFinder/Office
Molecular weight
Graphical User Interface
Draw structures you want to find with the
ChemDraw plug-in. ChemFinder/Office can (GUI)
search for the whole structure, a substructure, ChemFinder/Office is installed when you install
or a structure similar to the one you draw. ChemOffice Ultra. The GUI window, titled Find
When searching by structure, you can specify a Chemical Structures, is shown in the following
search by: illustration:

Chem & BioOffice 2006 /ChemFinder ChemFinder/Office 449

The ChemFinder/Office Graphical User Interface (GUI)
 ChemFinder/Office
title bar Menu bar
Administrator

Standard Toolbar
Search Record toolbar

Structure tab Find Now button

Look In tab Stop button

Search Options tab New Search button

Structure window

Molecular Weight text box

Formula text box Search type radio buttons

Status bar Edit Structure button

Show/Hide Hit List

Selecting Files to Search 3. Click Open.

Use the File menu or the Look In tab to tell
ChemFinder/Office where to look for structures.
Selecting Files From the File
Menu
When you select a single file, the first structure in
the file appears in the Structure window as soon as
you open the file. You can browse through the file
using the forward and back arrows in the Search
Record toolbar.

Use the File menu to look for a structure in a

specific file or data source:
1. From the File menu, choose Open.
The Open dialog box appears.
2. Select a file or data source you want to search
by doing one of the following:
In the File Name text box, type the name of
the file to search.
Use the directory tree in the Open window
to browse to a file to search.
Selecting Files With the Look
In Tab
Use the Look In tab window to search for a
structure in multiple files. The Look In tab window
shows all the documents and databases (data
sources) on your mapped network, CD-ROM,
floppy, and hard drives. You can select entire folders
to search, or multiple individual files, by using the
checkboxes next to the file names.

450 ChemFinder/Office CambridgeSoft

Selecting Files to Search
To look for a structure in specific files or data For example, you want to find a specific benzene
sources: file you saved. However, you are not sure what part
of ChemDraw you saved it in. Click the ChemDraw
1. Click the Look In tab. box and all of the ChemDraw files are searched.
The files and data sources appear in a tree When you have selected your data sources, return to
directory. the Structure window by clicking the Structure tab.

Searching by Chemical
Structure
You can find chemicals based on their structure
with ChemFinder/Office.

NOTE: Any search method that you use in ChemFinder

you can also use in ChemFinder/Office

To search by chemical structure only:

1. Open ChemFinder/Office.
The Find Chemical Structures - Data Source
window, appears.

NOTE: You can set Preferences to keep the file names

hidden in the directory tree. For more information, see
Changing the ChemFinder/Office Preferences on
page 460.

2. In the Select files of type box, use the drop-

down menu to choose types of files in which to
search.
You can select all data sources or files with the
following extensions:
.cdx and .mol
.doc and .xls
2. Do one of the following:
.cfw
From the Look In tab, select files to search.
.sdf
From the File menu select Open, or choose
3. Click the box next to the file(s) or data a file name from the most recently used list
source(s) that you want to search. of files.

Chem & BioOffice 2006 /ChemFinder ChemFinder/Office 451

Searching by Chemical Structure
 For more information about opening files to
search through, see Searching .dsd Files on
page 455.
3. Click New Search.
Administrator
4. Click Edit Structure.
The ChemDraw plug-in tools palette appears.
5. Selecting appropriate ChemDraw tools, click in
the Structure window and draw the structure
you want to search for.
For more information about using the
ChemDraw plug-in, see the ChemDraw Users
Guide.
6. Alternately, you can select a structure from
ChemDraw or from a ChemFinder database
and paste it in the Structure window using the
context menu.
7. Click Find Now.
NOTE: If the Find Now button is grayed out, you have not
selected a file or directory to search. Click the Look In tab and
make a selection.
452 ChemFinder/Office
ChemFinder/Office shows all of the files with
the structure that you specify in the Hit List
window shown below. Each entry in the Hit
List is a record or a hit.
N NH2
8. Use the forward and back arrows on the
Record Search toolbar to navigate through the
hits.
If ChemFinder/Office finds no hits, a warning
message appears. To refine your search so that
ChemFinder has a greater possibility of finding
hits, use the Search Options tab.
Searching by Multiple
Properties
You can search for a chemical structure, chemical
formula, molecular weight, or any combination of
these properties simultaneously.
To search for other properties or more than one
property at a time:
1. Click New Search.
CambridgeSoft
Searching by Multiple Properties
 2. Take the appropriate action: Browsing Search Results
If you want to then in the You can view the search results in the Hit List. The
search for... Structure Hit List displays all of the files in which your search
window, ... found matching structures.

a specific molecular type a molecular

weight, weight (g) in the Mol.
Wt. text box.

a molecular weight type a range of molec- To view the search results:

within a range, ular weights (g) with
< or > in the Mol. To view the entire Hit List, use the scroll bars.
Wt. text box. To display each hit in a given file in the Struc-
ture window, select the file in the Hit List and
a chemical formula, type a chemical use the arrows in the Search Record toolbar.
formula in the
Formula text box.
To display the actual file double-click on a file
more than one crite- enter the appropriate name in the Hit List, or right-click and select
Activate, with any of the following extensions:
rion (structure, criteria.
formula, or molecular .docMS Word
weight), .xlsMS Excel
.cdxChemDraw
NOTE: When you search by chemical structure, .cfwChemFinder
formula, and molecular weight, ChemFinder/Office
The application in which the structure was
uses all the criteria together. The information about each
saved opens. In MS Word, the application
property adds to the search criteria of the other
opens directly to the first hit in the document.
properties.
When you view the structure in the original
3. Click Find Now. application, the Hit List record is not copied to
ChemFinder/Office shows all of the files with the other application.
the properties that you specify in the Hit List You can use the Hit List menu to add or remove
window below the Structures window. Hit List records.
If ChemFinder/Office finds no hits, a warning
To add or remove Hit List records with the Hit List
message appears.
menu:
To refine your search so that ChemFinder has
1. In a Hit List with records, right-click a record.
a greater possibility of finding hits, use the
Search Options tab. To expand your search, The record is selected and the Hit List menu
use the Look In tab. For more information, see appears.
Refining Your Search on page 457. 2. Select Add.

Chem & BioOffice 2006 /ChemFinder ChemFinder/Office 453

Browsing Search Results
 The Open Chemical Structures window
appears.
3. Double click the file you want to add to the Hit
List, or type the name of the file in the File
Administrator
Name text box.
4. Click Open.
The file appears as a record at the end of the
Hit List.
To take a record off the hit list, right-click and select
Remove.
Saving Files or Data
Sources
A data source, or file, can be any of the following:
A document, like an MS Word document or an
MS Excel spreadsheet.
A database, like a ChemFinder database.
Any combination of documents or databases.
You can save search results as a file to search
through again.
Saving Search Results as
.sdf Files
The .sdf file format saves the Hit List records as
complete structures in MDL SDFile format. You
can import .sdf files from ChemFinder/Office into
applications like ChemFinder.
To save search results in the .sdf format after a
search:
1. From the File menu, choose Export SDFile.
The Save As dialog box appears.
2. In the File Name text box, type a name for
the file.
3. Click Save.
The file is saved with an .sdf extension.
454 ChemFinder/Office
For more information about exporting files to
other applications, see Sending a File to Another
Application on page 455.
Saving Data Sources as .dsd
Files
After you complete a search, you can save all the
records from the Hit List as a Data Source
Definition (.dsd) file so that you can search through
them again.
You can use .dsd files to search for structures,
substructures, or structures similar to your previous
search through the .dsd file.
To save the results of a search as a .dsd file:
1. After completing a search, choose Save Source
As from the File menu, .
The Save As dialog box appears.
2. In the File Name text box, type a name for
the group of files.
3. Click Save.
The files are saved with a .dsd extension.
Saving Lists of Directory
Paths as .dsd Files
NOTE: Only advanced users familiar with text editors
should use this procedure.
You can save lists of directory paths that you search
as .dsd files. You can create these lists with a text
editor such as Notepad. Saving a list of directory
paths as a .dsd file saves the directories in which you
search frequently.
To save a list of directory paths:
1. Open Notepad or some other ASCII text
editor.
2. Type the directory or database paths you want
to search.
CambridgeSoft
Saving Files or Data Sources
 3. From the File menu in Notepad, choose Save
As.
The Save As dialog box appears.
4. In the File Name text box, type a name for
the file and include a .dsd extension.
For example, type a File Name like
search1.dsd.
5. Click Save.
6. Close Notepad.
Searching .dsd Files
To search for a structure in a .dsd file:
1. From the ChemFinder/Office File menu, choose
Open.
The Open dialog box appears.
2. In the Files of type: text box, select Data
source definitions (*.dsd) from the drop-down
menu.
3. In the File Name text box, type the .dsd file
name, or select the file from those listed.
4. Click Open.
The first structure associated with the last
saved version of the .dsd file appears in the
Structure window.
5. Click New Search.
ChemFinder/Office clears the Structure
window.
6. Click Edit Structure, and draw a structure to
search for.
7. Click Find Now.
ChemFinder/Office searches through the files
specified in the .dsd file. Any hits appear in the
Hit List.
Chem & BioOffice 2006 /ChemFinder
Sending a File to Another
Application
You can send a structure or a file of structures (like
.sdf files) to another application. You can cut a
single structure from an application and paste it
into another, or you can send more than one
structure directly into another application.
Use the items in the Send To menu to send files to
these applications:
MS Word
MS Excel
CS ChemFinder
CS ChemDraw
ChemACX.Com Search
To send a file to another application:
1. In the Data Source - Find Chemical Structures
window, click the Send To menu.
The Send To menu appears.
2. From the Send To menu, choose an applica-
tion to send a file to.
The Send To dialog box appears.
NOTE: When you send files to Chem.ACX.Com,
the Send To dialog box does not appear. The structure
associated with the file is sent directly to
ChemACX.Com.
ChemFinder/Office 455
Searching .dsd Files
 3. From the Molecules section, select one of the If you select Send all molecules in current hitlist,
following: ChemFinder/Office will create a table in your
document, and the molecules in the current
If you want to Then click hitlist, along with their molecular formulas,
Administrator

weights, and source file paths, will be entered

into the table.
send the structure Send current molecule.
If you select Send current molecule, Chem-
displayed in the
Structure window, Finder/Office will export only the structure.

NOTE: If you need to interrupt a long Send To Word

send all the structures Send all molecules in operation, bring ChemFinder/Office to the front and click
listed in the Hit List, current hit list. the Stop button

4. From the Document section, select one of the
following, if available:
If you want to... then click...
send structures to a Send molecule(s) to a
new (untitled) docu- new document.
ment in an applica-
tion,
send structures to a Send molecule(s) to a
document you already currently open docu-
have open in an appli- ment.
cation,
5. In the Document section select the name of
the file from the drop-down list, if necessary.
If the text box in the Document section is not
available, skip this step.
6. Click OK.
If you choose Send To MS Word or MS Excel, the
document type opens a new file or the file whose
name you entered. The structures you send to the
application appear in that application as follows:
To send a file to ChemFinder or ChemDraw, you
must save the file you want to send:
1. Click the Send To menu.
2. Select CS ChemFinder... or CS ChemDraw Files.
3. Select the appropriate radio button in the
Molecules section, and click OK.
A Save As dialog box appears.
NOTE: If you have a ChemFinder .cfw file open, you
have the option of selecting it in the Document section of
the Send To dialog box.
4. Type in a name in the File Name: text box.
NOTE: If you are sending multiple structures to
ChemDraw, choose a base name for the filesfor
example, if there are three molecules in the current
hitlist and you specify the base name molecule, the
files will be saved as molecule1.cdx, molecule2.cdx, and
molecule3.cdx.
5. Click Save.
If you send a file to ChemFinder, ChemFinder
opens and the file you save appears as a form.
If you send a file to ChemDraw, a warning
appears to tell you the path of the file you
saved.

456 ChemFinder/Office CambridgeSoft

Sending a File to Another Application
Refining Your Search If you want to... then click:
You can refine your search so that you have a
greater chance of finding the structure you want. see all the records in Retrieve All .
Use the Search tools and the Search Options tab to the search, including
change your query to refine your search. records without a
match to your search,
To refine your search:
1. From the Search menu, choose Restore search for the struc- Find Current Structure
Previous Query or click . ture currently .
2. Change your query with the Search Options. displayed in the struc-
ture window, but
3. Select the files and data sources you want to
ignore any other
search.
search properties like
4. Click Find Now. molecular weight,
ChemFinder/Office shows all of the files with
the structure that you specify. These files restore the previous Restore Previous
appear in the Hit List window below the Data search, so you can Query .
Source - Find Chemical Structures window. modify the search
If ChemFinder/Office finds no hits, your criteria,
search may be too narrow and you should
broaden your search options. For more information about the Search tools, see
the Searching chapter in the ChemFinder Users
Using the Search Tools Guide.

Some ChemFinder tools used to refine your search Refining Your Query With
can also be used in ChemFinder/Office. the Search Options
To use the search tools: You can refine your ChemFinder/Office search
From the Search menu or Search toolbar, take with the Search Options.
the appropriate action:

If you want to... then click:

begin a new search, Enter Query .

search for the current Find Current

properties (chemical Query .
structure, chemical
formula, molecular
weight),

Chem & BioOffice 2006 /ChemFinder ChemFinder/Office 457

Refining Your Search
 To use the Search Options:
If you want to... then click:
1. Click the Search Options tab.
The Search Options window appears. require that any reaction Hit must overlap reac-
Administrator

center present in the query tion center.

overlap with reaction
centers in the target. This
preference applies only to
reaction searching,

allow hits to contain Extra fragments may

molecular fragments in be present in hit.
addition to that which was
hit by the query,

allow uncharged carbon Match any charge on

atoms in the query to carbon.
match charged carbon
atoms in the target,
2. Take the appropriate action:
NOTE: Charged atoms in
the query must always
If you want to... then click: match charged atoms in
the target, regardless of
require that the tetrahedral Match tetrahedral this setting.
stereochemistry of the stereo.
target structure match that allow uncharged atoms in Match any charge on
of the query structure, the query to match heteroatom.
charged atoms in the
require that the double Match double bond target,
bond stereochemistry of stereo.
the target structure match NOTE: Charged atoms in
that of the query structure, the query must always
match charged atoms in
allow fragments in the Fragments may
the target, regardless of
query to overlap (share overlap.
this setting.
one or more atoms) in the
target, allow a query drawn as Absolute center hits
absolute (hash/wedge relative
bonds) to hit a target
stored as relative.

458 ChemFinder/Office CambridgeSoft

Refining Your Search
If you want to... then click: If you want to... then, from the
View menu, ...
match a relative relation- Relative tetrahedral
ship between tetrahedral stereo show the Status bar, make sure the box
stereocenters. next to the Status bar
is checked.
Changing Chem-
Finder/Office Settings hide the Status bar, click Status bar.

The status bar disap-

You can change ChemFinder/Office settings so
pears.
that ChemFinder/Office appears the way you want.
You can customize the way the
ChemFinder/Office window appears with the show the Hit List, click Show List.
items on the View menu. You can change some of which shows all of the
places that Chem- NOTE: This option
the ChemFinder/Office display features with the
Finder/Office has only appears when
Preferences window. the list is hidden.
found the structure
you want to find,
Customizing the Chem-
Finder/Office Window hide the Hit List, click Hide List.

Use the View menu to change the appearance of NOTE: This option
the ChemFinder/Office window. only appears when
the list is showing.
To use the View menu:
customize features, click Customize.
1. In the Data Source - Find Chemical Structures
including:
window, click the View menu. The Customize
Commands, Tool-
bars, Menu, and window appears.
The View menu appears.
Keyboard options,
NOTE: This is a
2. Take the appropriate action:
standard Windows
feature. For more
If you want to... then, from the information, see the
View menu, ... MS Word online
Help.
show the Standard make sure the box
toolbar, next to the Toolbar
option is checked.

Chem & BioOffice 2006 /ChemFinder ChemFinder/Office 459

Changing ChemFinder/Office Settings
 Changing the Chem-
If you want to... then...
Finder/Office Preferences
To change the ChemFinder/Office preferences: open the last file you click Reopen last
Administrator

used when you start source on startup.

1. From the File menu, choose Preferences. ChemFinder/Office,
The Preferences window appears.
show all files in the click Show files in
directory tree, directory tree.

use the ChemDraw click the ChemDraw

ActiveX control to style radio button.
draw and edit struc-
tures,

open ChemDraw to click ChemFinder style

2. Take the appropriate action: draw and edit struc- radio button.
tures,
If you want to... then... 3. Click OK.
The Preferences window closes.
choose a specific type the path in the
directory for the Startup directory text
Look In tab to open, box or click
to browse to a file in
NOTE: This setting
the Startup directory.
does not affect any
query properties.

specify the number of type the number or

most recently open click the Up and Down
files to show in the Arrows in the
File menu, Number of recently
used files to show on
File menu: box to
set a whole number
from zero to 10.

460 ChemFinder/Office CambridgeSoft

Changing ChemFinder/Office Settings
Chapter 24: Using ChemFinder/Office
with CombiChem
The CombiChem engine can be used with Reaction Template Basics
ChemFinder/Office to generate libraries of
combinatorial experiments. These libraries can be The example of a reaction template that follows is
drawn from any type of file that supported by CombiChem:
ChemFinder/Office can read, and stored as .mst R2

format databases.
R2
R1
R1
NH2
N H2O
H
O
N

CombiChem Overview
N
H

CombiChem, the CambridgeSoft engine for R2

generating combinatorial libraries, was previously R1

available only as an add-in extension for Microsoft NH3

NH

Excel for Windows. Starting with ChemOffice 8,

A reaction template must meet the following
the engine was incorporated into E-Notebook and
specifications:
other products by means of a new Automation
interface in MolServer. This new approach means All sites of variability require unique R-group
that the engine can be used by developers designations.
everywhere. For more information, see Solvents, catalysts, and other real-world
http://sdk.cambridgesoft.com/chemfinder. elements should not be included in the reaction
template drawing.
Working with Reaction Multi-step reaction templates are supported.

Templates Entering a Template

There are two ways of entering a CombiChem
CombiChem is a reaction-based combinatorial
template in ChemFinder/Office:
product. You first enter a reaction template with
R-groups at the variable sites in your starting by creating a generic reaction in ChemDraw or
materials, then search for reactants based on these with the ChemDraw ActiveX control.
structures. CombiChem puts your final product by creating a ChemFinder database of generic
structures together and creates a virtual library. reactions.

Chem & BioOffice 2006 /ChemFinder Using ChemFinder/Office with CombiChem 461
Working with Reaction Templates
 Using ChemDraw or the edit the reaction in ChemDraw by double
clicking in the window, or continue with the
ChemDraw ActiveX control: reaction as entered.
1. Open ChemFinder/Office
Administrator

2. Click the Edit Structure button. Depending on

your Preferences setting, this will open Chem-
Draw or activate the ChemDraw ActiveX
control.
3. Draw a generic reaction. For more information
on generic structures, see the ChemDraw
Users Manual.

Using a ChemFinder data-

base:
You can create a database of generic reactions in
ChemFinder. ChemFinder/Office can open .cfw
2. Click the Analysis tab.
files directly and browse through them.
An analysis of the reaction steps appears below
Once you have a generic reaction in the Structure the reaction display.
window, do the following:
1. From the Search menu, select Enumerate.
The Combi Enumerator window appears,
showing the reaction as you entered it in the
Structure window. You may add another step
to the reaction by clicking the Add Step button,

462 Using ChemFinder/Office with CombiChem CambridgeSoft

Entering a Template
 3. Click the tab for the first reactant. Use the
Browse button to select a ChemFinder or
SDFile database, or other source of chemical
structures such as a collection of ChemDraw
files. Click Search.
To view the results:
You may edit the hit list before continuing.
a. Click Edit Hitlist.
An instructional dialog box appears.
Chem & BioOffice 2006 /ChemFinder
b. Click OK to open ChemFinder. Edit the
hitlist by selecting Omit from List from the
Record menu.
4. Click the Enumeration tab. Use the Browse
button to select a database in which to store the
results. Click Go.
NOTE: You can create a new database file by typing
in a file name.
The results are stored in the database.
5. When you are finished, click OK to exit the
Combi Enumerator and return to Chem-
Finder/Office.
1. Open ChemFinder
2. From the File menu select Import, then click
Structures.
3. Select the database from the Open Chemical
Structures dialog box.
Using ChemFinder/Office with CombiChem 463
Entering a Template
Administrator

464 Using ChemFinder/Office with CombiChem CambridgeSoft

Entering a Template
Appendix J: Structural Query Features
Overview
To perform a substructure search in ChemFinder,
you must first draw the query structure itself. Query
structures can be drawn in many different
programs, but we recommend using ChemDraw,
and this Appendix is focused on using ChemDraw
to draw query structures. For more information
about the structure drawing and query capabilities
of ChemDraw, please consult the ChemDraw
Users Guide.
ChemFinder does its best to follow your
instructions even if those instructions are
contradictory. For example, you can create a query
such as the following:
Atoms
Atom types specified in the query must match
atoms at corresponding positions in the target.
Hydrogen is an exceptionsee Substituents on
page 466.
Bonds
All bonds explicitly drawn in the query must match
in the target. For certain caveats, see
Stereochemistry on page 467 and
Normalization on page 469. ChemFinder
recognizes the following standard bond types:
Bond Type Description

This bond must not Single target must have single bond
be in a ring. here
Chn

That bond is already in a ring, so ChemFinder Dashed same as Single

returns no hits for this query.
Hashed same as Single
General Properties
Thick same as Single
ChemFinder allows the following general
properties to be assigned to a query:
Wedged Hashed specifies stereochemistry down
Atom from the point end to the wide
end
Bond
Substituents Wedged specifies stereochemistry up
from the point end to the wide
Charges and radicals
end
Isotopes
Stereochemistry Wavy specifies stereochemistry
either at both ends
Normalization

Chem & BioOffice 2006 /ChemFinder Structural Query Features 465

General Properties
 Hydrogen atoms in the query must match
Bond Type Description hydrogens in the target when the query hydrogen is
at the end of an explicit bond. The matched
Hollow Wedged same as Wedged hydrogen in the target may be implicit in an
Administrator

unlabeled carbon atom.

Dative same as Single

H O
Double target must have double bond;
stereo dictated by geometry
H N
Double Either target must have double bond;
any stereochemistry ok finds any of: does NOT find any of:
OH

Double Bold same as Double Cl

O NH2
HN O

Triple target must have triple bond

here Br

O
H OH OH
NH2

Substituents H OH

H N

In ChemFinder, a substituent is defined as a non- Br

H NH2

hydrogen atom connected by a bond of any order.

For example, a carbonyl oxygen is a substituent of
the carbonyl carbon.
All unfilled valences in the query may be filled by
hydrogen atoms or by non-hydrogen substituents.
The normal valence of an atom is determined from
data in the Periodic Table window. For example,
carbon has a valence of 4, while sulfur has valences
of 2, 4, and 6. Any explicit charges, radicals, or
query properties modify the normal valence. For
example, a carbocation has a valence of 3.
Hydrogen atoms in the query may match non-
hydrogen substituents in the target if the hydrogen
in the query is implicit on an unlabeled carbon atom
or heteroatom.
Charges and Radicals
Charges or radicals specified on atoms in the query
must match those in the target. Uncharged atoms in
the query may or may not match charged atoms in
the target, depending on the state of the appropriate
check box in the Search tab of the Preferences
dialog.
The valence of a charged atom is taken to be the
valence of the isoelectronic neutral atom.
With a substructure search, the query:

N+

466 Structural Query Features CambridgeSoft

General Properties
 finds any of: does NOT find any of: Stereochemistry
OH
Stereochemistry specified on the query must match
Cl
the target if the relevant Match Stereo item is
NH2
selected in the Search tab of the Preferences.
Stereochemistry is specified at a tetrahedral site by
N O using stereo bonds (up, down, either).
Stereochemistry about a double bond is specified
Br
OH by the geometry of the drawing. ChemFinder
H OH cannot currently interpret other stereochemistry
OH
types (allenic, square planar, octahedral, etc.) and
NH2
H NH2 ignores them during a search.
N When evaluating a possible match, the following
rules are applied:
Isotopes Unspecified stereochemistry (a plain bond)
Isotopic labels specified in the query must match may match any stereochemistry (either a
the target. Unlabeled atoms in the query match wedged, hashed, bold, or a plain bond).
unlabeled or isotopically labeled atoms in the target. Specific bond types need not match as long as
Additionally, D is treated interchangeably with 2H, the overall stereochemistry at a given atom
and T is treated the same as 3H. does match.
Implicit hydrogens are taken into consideration
in both the query and the target if doing so
With a Substructure Search, the query: helps to determine the chirality of a stereo-
center.
D
13
O C
With a full structure search and the Match
finds any of: does NOT find any of: Tetrahedral stereo option selected, the query:
HO
O

13
13
HO CH3
C O OH
D finds any of: does NOT find any of:
T
13
2
O CH3
H
13
O CH3

HO
D
D

D
13
O C

Chem & BioOffice 2006 /ChemFinder Structural Query Features 467

General Properties
 HO
O
HO
O
MDL File Formats

All bond styles available in ChemDraw are retained

N OH N OH
H H
in CDX files. The same is not true of major MDL
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structure files: MolFiles, SDFiles, and RDFiles. In

H
H
N OH N OH
HO
O HO
O thick bonds are not recognized. This presents a
HO
O
HO
O
N OH
N
H H OH H ChemFinder addresses this problem by using a
Relative Tetrahedral Stereochemistry
Relative Tetrahedral Stereochemistry, or RTS,
specifies a given relationship between the centers.
That is, a known orientation of the substituents
with respect to each other, rather than a known
absolute configuration. To specify this, centers are
drawn, not with the standard hashed and wedged
bonds, but with thick (bold) stereo bonds.
Relative and absolute configurations may be
registered separately in ChemFinder, and can be
distinguished by various search options. The basic
ChemFinder search philosophy can be summarized
as follows: a more specific query is a more precise
request, and should get fewer hits than a more
general query. If the query represents a particular
absolute configuration, it should hit only that; if it
represents a mixture, it should hit any of the
components.
If you choose Same in the stereo search choices, you
are requesting that whatever stereochemistry is
specified in the query must match that of the target.
If the query has relative bonds and RTS is activated,
a hit must have the same relationship between
centers.
these formats, only three stereo bond types are
available: hash, wedge, or either (squiggly bond);
problem for the ChemFinder user wishing to
import or export structures having relative
stereocenters.
proprietary tag in the file, recognized only by
ChemFinder. The tag is BOND_RELS, and is
applied to every stereo bond of thick type. For
example, here is an excerpt from the bond table of
a molfile with relative bonds.
...
4510000
2611000 <- bond 5, marked as UP
4711000 <- bond 6, marked as UP
M CFW 5 BOND_RELS <- overrides type of
bond 5 to be UP/THICK
M CFW 6 BOND_RELS <- same for bond 6
The consequences of having a ChemFinder-only
tag are:
When any of the MDL file formats is saved
from within ChemFinder, the tag is written.
Reading these files back into ChemFinder will
retain the thick bond types.
If a structure is drawn in ChemDraw and saved
as MDL Molfile, thick bonds are lost, and are
converted to normal hash/wedge bonds. (This
is not true if the file is saved as CDX).
If a structure is saved as molfile from Chem-
Finder, reading it into ChemDraw loses the
thick bonds.

468 Structural Query Features CambridgeSoft

General Properties
 Mol- or SDFiles obtained from ISIS or other
programs do not know about this tag, and thus
cannot convey thick bonds. However, such
files may be edited by hand to include the
ChemFinder tag.
An MDL file written by ChemFinder,
containing tags, should in principle be readable
by any program which can import such a file.
The unrecognized tags should simply be
ignored.
Normalization
Closed rings of alternating single and double bonds
match their alternative resonance forms if aromatic
by the Hckel 4n+2 rule.
With a full structure search and the Match
Double Bond stereo option selected, the query:
OH
finds any of: does NOT find any of:
OH
OH
O
H
H Atom Lists
Chem & BioOffice 2006 /ChemFinder
Atom Properties
ChemFinder allows special atom properties to be
assigned to an atom in a query. These properties are
usually only meaningful during a search. They
generally serve to broaden or narrow the scope of
the search.
Special Atom Types
ChemFinder recognizes six special atom types that
can match any one of a predefined set of elements:
A matches any non-hydrogen atom.
Q matches any heteroatom (non-hydrogen,
non-carbon).
R matches any atom, including hydrogen.
X matches any halogen (F, Cl, Br, I, At).
LN matches a link node (placeholder for
unspecified atoms). See Searching Link
Nodes and Multivalent Rs (MVRs) on page
426 for details.
M matches any metal atom, shaded in the peri-
odic table below:
OH
OH
O
As with the predefined special atom types, an atom
list is a list of atoms, one of which must match the
target atom.
For example:
[Cl,Ag,N] atom must be Cl or Ag or N
Structural Query Features 469
Atom Properties
 Atom lists may contain only elements. Special atom Cl
types, nicknames (Ph), and structural fragments
(NH2, OCH2CH3) may not be included in an atom
list. ChemFinder recognizes a maximum of five
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atoms in an atom list.

O
Atom Not-Lists
HO
The opposite of an atom list is a list of atoms, none O

of which must match the target atom. For example: O

[NOT O,S,Se] atom must not be O or S or Se (but

may be any of the 100 other elements)
Atom not-lists have the same restrictions as atom
lists.
Substituents: Up To
Substituents: Exactly
This property specifies a precise value for the This property specifies a maximum value for the
number of substituents on an atom, including those number of substituents on an atom, including those
explicitly drawn. This property is only meaningful explicitly drawn. This property is only meaningful
in a substructure search. in a substructure search.

With a substructure search, the query: With a substructure search, the query:

X3 U2

This atom is marked This atom is marked

with the atom property with the atom property
Substituents Exactly:3 Substituents Up to:2

finds any of: does NOT find any of: finds any of: does NOT find any of:

HO

CH3

470 Structural Query Features CambridgeSoft

Atom Properties
Substituents: Free Sites
The Substituents: Free Sites property specifies the
maximum number of additional substituents that
may be present on an atom. This property is only
meaningful in a substructure search.
NOTE: Specifying Free Sites: 0 is a quick way to indicate
that you want no further substitution at a site. Target
structures will match the query structure as drawn, with no
additional ligands.
With a substructure search, the query:
2 Absent (all bonds to the atom are single). It also
This atom is marked
with the atom property
Substituents Free Sites:2
finds any of: does NOT find any of:
Cl
HO O with the atom property
O O
Implicit Hydrogens
This atom property may have either of two values:
Allowed (default) or Not Allowed. If implicit
hydrogens are Not Allowed, the atom must be fully
substituted in the target.
Chem & BioOffice 2006 /ChemFinder
This property is only meaningful in a substructure
search.
NOTE: This atom property does not affect the display of
implicit hydrogens, only their presence in a search. For more
information about displaying implicit hydrogens, see
Setting Preferences on page 429.
Unsaturation
Sometimes it is useful to specify that an atom must
or must not be attached to unsaturated (aromatic,
double, or triple) bonds. ChemFinder allows
searches for atoms whose unsaturation Must Be
allows searches for atoms with at least one multiple
(double, triple, or aromatic) bond. The default
value, Undefined, finds targets without regard to
the hybridization of the atom.
This property is only meaningful in a substructure
search.
With a substructure search, the query:
This atom is marked O
Unsaturation: must be present
OH
S
finds any of: does NOT find any of:
Structural Query Features 471
Atom Properties
 O O
Bond Type Description
OH OH
S/A target must have a single bond or
Administrator

O
an aromatic bond here
HO

HO

O Topology
If Ring or Chain is chosen, the target bond must or
OH
must not be in a ring, respectively.
OH
OH
O
Reaction Center
O
The reaction center refers to those bonds that are
Bond Properties directly affected by a reaction. This property allows
you to specify just how a given bond is affected.
ChemFinder allows special properties to be
assigned to bonds in a query. These properties Property Description
usually will only be meaningful during a search.
They generally serve to broaden or narrow the Unspecified target must have a bond here,
scope of the query. but the bond can participate
in the reaction in any fashion,
Special Bond Types or not at all
The table below describes the special bond types target must have a bond here
Center
that ChemFinder allows. that directly participates in
the reaction in some way
Bond Type Description
Make/Break target must have a bond here
that is either made (if in a
Aromatic target bond must be aromatic as product) or broken (if in a
defined by the Hckel 4n+2 rule reactant)

Any target can have any bond type here Change target must have a bond here
whose bond order changes
S/D target must have a single bond or over the course of the reac-
a double bond here tion, but is not made or
broken
Tautomeric same as S/D

D/A target must have a double bond or

an aromatic bond here

472 Structural Query Features CambridgeSoft

Bond Properties
Property Description
Make&Change target must have a bond here
that is either made (if in a
product) or broken (if in a
reactant) or whose bond
order changes over the
course of the reaction
Not Center target must have a bond here,
and that bond must not
participate in the reaction
Chem & BioOffice 2006 /ChemFinder
Property Description
Not Modified target must have a bond here,
and regardless of whether it
is part of the reaction center
or not, its order must not
change over the course of the
reaction
This property is only meaningful when searching a
reaction database.
Structural Query Features 473
Bond Properties
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474 Structural Query Features CambridgeSoft

Bond Properties
Appendix K: Formula Input Rules
Overview If symbols are not properly capitalized (such as all
lower-case), then, with the exception noted below,
When you type a formula in ChemFinder, you are the shortest symbol which matches is preferred.
not required to enter symbols in any particular case. Thus co is taken as carbon-oxygen instead of
This can give rise to ambiguities. This appendix cobalt.
describes how ChemFinder interprets formulas and
The exception is: if two characters represent a valid
resolves these ambiguities.
two-letter symbol and also a valid one-letter symbol
Consider an example. In entering a formula query, followed by an invalid one, then the two-letter
you type: symbol is favored. Thus cl is not taken as carbon
followed by the (invalid symbol) L, but instead is
cooh taken as chlorine.
Most chemists recognize this as a carboxyl group:
carbon, two oxygens, hydrogen. However, it might Examples
be interpreted as cobalt (Co), oxygen, hydrogen.
Similarly, CLI might be carbon-lithium or it There is an easy way to experiment with formula
might be chlorine-iodine. PHE might be interpretation: use the Periodic Table. Type a
phosphorus-helium or, since ChemFinder allows 3- formula into the text box at the bottom, then click
character amino-acid symbols as special atom types, anywhere outside that box. ChemFinder interprets
it might be phenylalanine (Phe). the formula and redisplays it with correct
capitalization.
One way to avoid ambiguity is to separate letters
with spaces. For example, the string c o cannot ChemFinder interprets some ambiguous formulas
possibly be interpreted as cobalt. Another way to as follows:
avoid ambiguity is to enter formulas using the
Periodic Table instead of typing them. ChemFinder Formula Chemfinder
allows free-format input, and attempts to make the Interpretation
most reasonable interpretations of them by using
the rules described below.
cooh COOH
Rules
Cooh CoOH
If a symbol is properly capitalized (first letter upper
case, followed by zero, one, or two lower-case cnosi CNOSI
letters), then the longest valid symbol which matches
is preferred. Thus Phe matches phenylalanine
cNoSi CNoSi
rather than phosphorus; Co matches cobalt.
Because of this rule, if you properly capitalize all bru BrU
symbols, no ambiguities will arise.

Chem & BioOffice 2006 /ChemFinder Formula Input Rules 475

Rules
 Formula Chemfinder
Interpretation
Administrator

b ru BRu

476 Formula Input Rules CambridgeSoft

Examples
Appendix L: Similarity Rules
Overview Consider the query and target compounds shown
graphically below. Both have similar numbers of
Often you might not be looking for a specific descriptors present - the query has 23, while the
compound, but any compound that is close target has 24. But are they close enough?
enough will do. ChemFinder uses the Tanimoto
equation to determine if compounds are similar.
Bitscreen Desc. # Name
You can specify how similar in the Searching tab
of the Preferences dialog.
Query 23 Q
Exact searching relies on the notion of an atom-
and-bond table: a specific set of atoms joined to
each other in a certain order by a given set of bonds. Target 24 T
If some atoms or bonds are missing, added, or
different, the query structure and the target Q and T 17 Q T
structure do not match.
Most similarity searching, on the other hand, relies Q or T 30 Q T
instead on the notion of molecular descriptors.
Each compound can be represented by a collection
of qualitative terms that describe general aspects of Complete Structure Simi-
the structure.
For example, benzoic acid might be described as:
larity
organic acid One of the hallmarks of a good similarity algorithm
contains 6-membered ring is whether it is commutative. That is, two compounds
contains delocalized ring should have the same similarity value no matter
contains C-double-bond-O which you compare to which. The full structure
Tanimoto similarity test is commutative. It
As you can see, the descriptors can be very broad,
and they can overlap. The set of descriptors used by compares the number of descriptors they have in
ChemFinder is very large. common (in the intersection of the query and the
target) to the number of descriptors they have in
When you draw a compound, ChemFinder
total (in the union of the query or the target). The
compares it against all of the descriptors it knows
ratio of these two values is known as a Tanimoto
about. Some descriptors will be present in your
compound and some will not. Since each descriptor coefficient, and is always a value between 0% and
for a given compound is either Present or Not 100%.
Present, they are often stored as bits, and another
name for a compounds set of descriptors is its Q
T
bitscreen. Tanimoto Coefficient
Q
T

Chem & BioOffice 2006 /ChemFinder Similarity Rules 477

Complete Structure Similarity
 For the two compounds above, the Tanimoto
coefficient is 17/30, or about 57%. This is not very
similar. Although ChemFinder will allow you to
specify any Tanimoto value down to 0%, for most
Administrator
cases you will likely be looking for compounds that
have Tanimoto coefficients of 90% or higher.
Substructure Similarity
Unlike full structure similarity, substructure
similarity is not commutative: you are comparing a
portion of one structure against the entire other
structure, and so it does matter which you compare
478 Similarity Rules
to which. In considering substructure similarity,
ChemFinder finds what percentage of descriptors
in the query are also present in the target.
This value will always be at least as large as the
complete-structure Tanimoto coefficient for the
same two compounds, and usually it will be larger.
The two compounds above are 17/23, or about
74% similar by substructure similarity. For a given
coefficient value, a substructure similarity search
will always return all of the hits in a full structure
similarity search, and will often return additional
ones as well.
CambridgeSoft
Substructure Similarity
Appendix M: CAL Commands
Overview CAL Help
ChemFinder Automation Language (CAL) is a set Information about the CAL command and
of commands that control many ChemFinder variables is available in the CAL Scripting Help
operations. window.
You invoke CAL commands in either of two ways: To access CAL Help:
Interactively Type commands and execute
1. From the Scripts menu select Command Line.
them one at a time on a command line.
ScriptsUse ASCII files containing a series of The Enter Cal Command dialog box appears.
CAL commands to be executed automatically 2. In the Enter Cal Command dialog box, click
in sequence. the Help button.
Arguments to commands consist of numbers and The CAL Scripting Help window appears:
text strings. You can enter a text string without
punctuation unless the argument is not the last one
on the command line and contains multiple words
or spaces. In this case, you must enclose the
argument in quotation marks.

New in ChemFinder
Two new features in CAL improve program
control:
IF / ELSE / ENDIF
bidirectional GOTO
Previously, a GOTO statement could only jump to a
Menu Commands
label which had already been encountered while the
Menu commands consist of a two-word command
script was being read, that is, could only jump
from the main menu and in some cases an optional
backwards. This limitation is now removed. GOTO
argument.
can jump to any label.
New Commands: Following are examples of commands:

TO/FROM_SMILES, _CANONICAL file new

SQL, SQLSELECT (Oracle) edit paste
SUBSTRextracts part of a string from a vari- search find
able. record next

Chem & BioOffice 2006 /ChemFinder CAL Commands 479

CAL Help
 You do not need to spell out menu commands. You
can enter just enough letters to uniquely identify the Box Type String
menu option. For example, to execute the Record
Next command, type: Text static text
Administrator

rec n
Picture pathname of a Windows meta-
Some menu commands open a dialog box and wait
file
for user feedback. To avoid this, a limited number
of menu commands can take explicit arguments:
Button pathname of a script file, or
FILE OPEN [filename] name as it appears on Scripts
FILE SAVE [filename] menu
RECORD GO TO RECORD [recno]
Subform <nothing>
Box Creation Commands
DBOX coords [fieldname] Arrowbox <nothing>
FRAME coords [text]
TEXT coords [text] Framedbox name of database field to be
PICT coords [filename] displayed in the box, and static
label for upper left
BUTTON coords [scriptname]
SUBFM coords If the text string is omitted, you can supply it later
ARROWBOX coords using SETFIELD or SETTEXT. For a button, you
FRAMEDBOX coords [fieldname] [text] must use SETTEXT if you want its visible label to be
different from the name of its script.
To create a new box on the form:
1. Specify the box type with the appropriate Box coordinates are specified in this order: left, top,
keyword. right, bottom. Units are in pixels; the origin is at the
2. Type four integers giving the rectangular coor- upper left, with coordinates increasing from left to
dinates of the box after the keyword. right and top to bottom, so that coordinates will
range from left = 0 to right = 640 or 1024 or
3. If desired, type a text string giving further
information appropriate to the box type, as whatever fits your screen, and from top = 0 to
shown below: bottom = 480 or 768 or similar.

When a new box is created, it adopts the current

Box Type String
font. To specify a particular font for a box, use the
FONT command prior to creating the box.
Data box name of database field to be
displayed in the box When specifying a script name, give one of the
following:
Frame static label for upper left
The complete pathname of the script file.

480 CAL Commands CambridgeSoft

Box Creation Commands
 A simple name without extension, if the script
is stored in the standard scripts subdirectory
with the standard file extension. If the script
name appears on the Scripts menu, you can
use the name from the menu.
The table below shows examples of Box Creation
Commands:
To work with a box or subform on the form, you
specify a keyword followed by a box identifier. A
box is identified in one of two ways:
By pointGive the coordinates of a point
anywhere within the box. When coordinates
fall in more than one box, the most recently
created box is used.

Command Action By textThe text you enter to identify a box

may be:
FRAME 10 10 300 create frame with label
60 Molecular The field name, if the box contains data
at upper left
Formula from a database.
DBOX 20 20 290 create data box for The text label, if the box contains static text,
50 formula formula in above frame such as frames or text labels.
TEXT 100 100 300 create a static text The box name assigned in Box Properties.
150 A Label string For subform boxes, the table name.
PICT 500 300 600 put specified picture at In all cases, you need not spell out the entire
400 C:\LOGO.WMF lower right name, just enough to be unique.
BUTTON 500 10 create button at upper Often, more than one box matches the text you
550 40 DEMO right to run script enter, for example a box displaying field
DEMO.CFS molweight within a frame labelled
MolWeight. In this case, preference is given
to the box connected to the database.
FORMEDIT controls the behavior of the SELECT
command. With FORMEDIT ON, SELECT affects
boxes. With FORMEDIT OFF, SELECT affects the
Box Manipulation contents of those boxes.
Commands SELECT and UNSELECT choose boxes to be
modified by editing operations. DELBOX is a
FORMEDIT ON|OFF shortcut for FORMEDIT ON, followed by SELECT,
SELECT box followed by Edit Clear. SETFIELD connects a
UNSELECT box database field to an existing box; for a button, it
DELBOX box attaches a script name (see above regarding script
names). SETTEXT attaches a text string to a box or
SETFIELD box fieldname
replaces the one currently attached; see box
SETTEXT box text creation commands (above) for a list of what the
ACTIVATE subform text strings mean for various box types.
DEACTIVATE
ACTIVATE and DEACTIVATE are the same as
SCALE SELECT and UNSELECT, but work on subforms.
SCALE_TO_FIT Following an ACTIVATE command, all subsequent

Chem & BioOffice 2006 /ChemFinder CAL Commands 481

Box Manipulation Commands
 commands apply to the active subform and any
boxes it contains. The DEACTIVATE command is
required to once again refer to the main form and
its contents.
Administrator
Program execution commands call up external
processes and pass data to them. All require an
argument, which may need multiple components.
CALL executes a specified CAL script. If the call is

SCALE scales all items in the current form by the made from within another script, when the called
percentage factor you specify. Use this to fit your script finishes executing it returns control to the
forms to different size screens. See SCALE_TO_FIT caller. CALL must be followed by a scriptname, as
below. described above.

SCALE_TO_FIT scales all elements in the form such DOS executes a DOS command line. Follow the
that the string you specify will fit in the form at the DOS keyword with any string you might type at a
currently selected font size. See FONT below. DOS command prompt. If you do not type any
arguments after the DOS command, you get an
The table below shows examples of Box interactive command prompt window. You can use
Manipulation Commands: this feature to manipulate files, execute programs or
batch files, get directory listings, format disks, etc.
During execution of the command, a command
Command Action
prompt window appears on the screen; when
SELECT 11 11 select formula frame created finished, the window goes away and control returns
to the calling script.
above
EXEC starts a Windows program and optionally
SELECT formu select formula data box passes it command-line arguments. Follow the
created above EXEC keyword with any string you might use in the
Program Managers File Run command. This
SETFIELD 21 change field for formula data command starts a program, but does not return
21 molweight box to molweight from it. To return to ChemFinder, you need to use
Task Manager or click in the ChemFinder frame
window.
DDE sends a Dynamic Data Exchange message to a
specified application. Follow the DDE keyword with
three arguments:
The service nameusually the name of the
Program Execution recipient application.
Commands The topic namea string recognized by the
recipient, identifying the nature of the message.
CALL scriptname
It is typically SYSTEM.
DOS doscommand
The commandan instruction to the service
EXEC wincommand indicating what you want it to do.
DDE ddecommand Details of these components depend on the service
LAUNCH filename youre addressing.

482 CAL Commands CambridgeSoft

Program Execution Commands
The table below shows examples of Program FONT changes the current font. Any boxes created
Execution Commands: subsequently adopt this font. Follow the keyword
with a name from your Windows font list, followed
Command Action optionally by:
1. Font size in points (default is 8).
CALL execute script file located in 2. Style from the list below (default is 0, or plain
myscript scripts directory text).
3. Color; three values for red, green, and blue,
DOS erase execute DOS command to each ranging from 0 to 255 (default is 0,0,0, or
junkfile.dat delete a file
black).

EXEC notepad
Font styles are sums of bold (1), italic (2), and
execute Windows program underline (4). Thus a style value of 1 means bold, 3
myfile.txt
means bold+italic, 6 means italic+underline, and so
DDE CHEM3D send DDE message to quali- on.
CFWIN "open fied service SEEPTAB briefly displays the periodic table window,
benz.mol" then closes it. The window will be displayed for the
amount of time specified (1 decisecond = 0.1
General Commands second). If the duration is omitted, it will be
displayed for four seconds.
MSG message
STATMSG message QUITECLOSE closes the active form. This
TIMEDMSG [n] <msg>W command is similar to FILE CLOSE, but
FONT fontname [size [style r g b]] automatically discards any changes instead of
SEEPTAB [decisecs] prompting the user what to do.
QUIETCLOSE HIDETABLE closes the Table View window for the
HIDETABLE current form. If a subform is active, it returns the
SET subform to form view.
CLEAN [cleanup, tidy, redraw, denovo]
SET allows you to modify basic ChemFinder
HELP
settings, including most of those found in the
GET [v] section number, itemnumber
Preferences dialog and several that cannot be
SOUND filename.wav accessed in any other way. See the online help for a
SYSMETRIC [v] index complete listing of parameters that can be SET.
MSG displays a message box with the specified text,
CLEAN will attempt to standardize the bond lengths
and waits for the user to click OK. and angles of the current molecule. It is the same as
STATMSG displays information on the status line. opening the molecule in ChemDraw, and selecting
the Clean Up Structure command. The arguments
TIMEDMSG displays a message box similar to the
are optional.
MSG command, but the message disappears
automatically after a specified number of seconds. HELP displays a list of all valid CAL commands.
For example: TIMEDMSG 10 This message will The valid parameter types are listed for each
disappear automatically after 10 seconds. command, as is a brief description.

Chem & BioOffice 2006 /ChemFinder CAL Commands 483

General Commands
 GET retrieves a value from the ChemFinder.ini file.
Follow the keyword with a variable name and the
section and item number of the value you want to
retrieve.
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created, otherwise it is overwritten. For both
READMOL and WRITEMOL, the format of the file
is determined by its extension; for example,
benzene.cdx is a ChemDraw file.

SOUND plays a .wav file you specify.
SYSMETRIC retrieves the specified system metric
into a variable.
The table below shows examples of General
Commands:
WRITETEXT exports the current list as delimited
text with whatever delimiter is specified in the
Preferences dialog.
The table below shows examples of File
Commands:

Command Action
Command Action
READMOL read specified file to become
MSG Click OK display message, wait for benz.mol current molecule
to continue click
WRITEMOL write current molecule to spec-
FONT Times 12 1 change font to red 12- saved.mol ified file
255 0 0 point Times bold
WRITETEXT export current list to a text file
GET V1,4,5 place the value of item hits.txt
number 5 in section 4 into
the variable V1
Database Commands
SOUND beep.wav play the sound in the files OPENDB [R / R / RE] dbname
beep.wav CRETABLE tablename
DELTABLE tablename
SELTABLE tablename
File Commands CREFIELD fieldname
READMOL filename DELFIELD fieldname
WRITEMOL filename SORT [D] fieldname
WRITETEXT filename Oracle database commands:
READMOL and WRITEMOL operate on the current
SQL <SQLStatement>
molecule. These commands will work only if there
SQLSELECT [v ] <SQLSelectStatement>
is at least one structure-related box (structure,
formula, or molweight) on the form, and you are OPENDB opens a standard molecule database.
positioned to a valid entry in the database. Specify a pathname to the .mdb file, or a name from
READMOL reads a specified structure file and the ODBC Data sources list. When connected to an
replaces the current molecule in the form. Oracle database, OPENDB takes a table name
WRITEMOL saves the current molecule to a instead of a database name. You can specify the
specified structure file; if the file doesnt exist, it is mode of database opening:

484 CAL Commands CambridgeSoft

File Commands
 Rread-only CRETABLE MyTable creates a new table
Eexclusive
REread-only and exclusive DELTABLE MyTable deletes a new table
CRETABLE creates tables in the current database.

DELTABLE deletes tables in the current database.

SELTABLE selects a table form the current database Variable Commands

and makes it the current working table for
subsequent field actions. SETVAL [v] text
READVAL [v] filename
CREFIELD creates fields in the current table in the
WRITEVAL [v] filename
current database. You can specify the field type and
width in the CREFIELD command. The default text INPUT [v] [prompt]
field is 50 characters wide. PASSWORD [v] [default]
DELFIELD deletes fields in the current table in the GETDATA [v] box
current database. PUTDATA box text
APPEND ON|OFF
SORT sorts the database contents on the specified
field. The default sorts the database in ascending APPENDVAL [v] [text]
order. You can specify descending order with D. INCREMENT [v]
DECREMENT [v]
SQL allows SQL to be passed directly from CAL.
SQLStatement is a SQL statement that returns no LET v v op v
results. It is therefore useful for data manipulation SUBSTR [v] <str> <from> [<to>]
operations. Available only when connected to an
CAL has nine variables called V1, V2, ..., V9. These
Oracle database.
are temporary storage locations you can use to
SQLSELECT returns a one-row recordset. It is move information between form boxes and other
useful for calculations or lookups. v is the name or data sources.
number of a variable to receive the results of a
Variable names can be substituted in any CAL
Select statement; SelectStatement is a SQL Select
command. Any item shown in italics in a command
statement designed to retrieve a single result. If v is
description may be replaced by the name of a
omitted, results go in V1. Available only when
variable, prefixed with a dollar sign.
connected to an Oracle database.
If you omit the password from the connection For example:
string, and you will be prompted for it when MSG messagemay be either:
running the command.
MSG "An explicit message"
The table below shows examples of Database
Commands: a message explicitly coded into the scriptor
MSG $V2
Command Action
a message taken from variable 2 at run time

Chem & BioOffice 2006 /ChemFinder CAL Commands 485

Variable Commands
 You may concatenate variables, and variables and
literals together in CAL commands. You must add
both a leading and trailing dollar sign to the variable
name.
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For example:
MSG$V2$$V1$
Displays a message box with the value of V2
immediately followed by the value of V1.
Most commands for manipulating variables take an
optional variable number as the first argument. If
the number is omitted, it is assumed to be 1.
SETVAL puts the specified text into a variable.
READVAL reads the contents of a text file into a
variable. WRITEVAL copies the contents of a
variable to a file.
INPUT displays a text input dialog, accepts data
from the user and stores it in a variable. An optional
prompt string is displayed in the box when it
appears.
PASSWORD is the same as INPUT, but displays all
characters as asterisks.
GETDATA retrieves the contents of a form box (as
long as it is not a structure) into a variable; see
above for how to identify a box. PUTDATA copies
specified text into a form box. Form names are
case-sensitive. Be sure to use the same case as the
form box name into which you want to store data.
APPEND determines whether data in a storage
location is kept if other data is being moved there.
This setting is now also consulted when you do a
File Export to SD or delimited text file.
APPEND ON causes any subsequent data
movements to append new data to old; APPEND
OFF causes old data to be overwritten. This applies
to all variable commands except PUTDATA. The
default at program startup is APPEND OFF.
486 CAL Commands
APPENDVAL is a shortcut designed to make it easier
to build string values. It is the same as setting
APPEND ON, doing a SETVAL, then restoring
APPEND to its original state.
TIP: The difference between APPEND ON and
APPENDVAL is that APPENDVAL does not add a
carriage return to the string being appended, whereas
APPEND ON does. If you want to insert a carriage return
at the end of the string, use APPEND ON.
INCREMENT adds 1 to the value of a variable. Use
INCREMENT in loops.
DECREMENT subtracts 1 from the value of a
variable. Use DECREMENT in loops.
LET allows you to perform mathematical
operations on variables that contain integer or real-
number values. Only one operator per line is
supported. It recognizes the following operators:
+ for addition
- for subtraction
* for multiplication
/ for division
SUBSTR extracts a substring from a variable. The
extracted substring extends from a specified
character to the end of the string, or from one
specified character to another.
The table below shows examples of Variable
Commands:
Command Action
SETVAL "some store text in V1
text"
SETVAL 2 "other store text in V2
text"
READVAL 9 read text from file into V9
tmpdata.txt
CambridgeSoft
Variable Commands
 $SYSTEM_DIR
APPEND ON turn on append mode
NOTE: To view a complete list of variables, click Help on
WRITEVAL append contents of V1 to the Enter Cal Command dialog box.
output.txt file
ChemFinder provides several variables to allow you
SETVAL 2 to retrieve information about the current
append text to contents of
"append me" ChemFinder environment. They cannot be set
V2
directly, but are modified as a consequence of other
APPEND OFF commands.
turn off append mode
For example, the menu command:
INPUT 2 "enter prompt and get user input Record Next
new data" to V2 increments the current RECNO by 1.
GETDATA 3 The table below shows examples of Environment
copy data from molname
molname Variables:
box to V3

PUTDATA molname store given string in Command Action

benzene molname box
SETVAL 1 V1 now equals the number
LET 3 $V1 + $V4 sets V3 equal to the value $RECNO of the current record
stored in V1 plus the value
stored in V4 SETVAL V1 V1 now equals total
$NUM_RECS number of records in the
SUBSTR 2 abcdef stores cde in V2
current list
3 5
SETVAL V1
Environment Variables $DTBA_NAME_
V1 now equals, for
example c:\chem-
LONG finder\mydb.mdb
$INDEX
$RECNO SETVAL V1 V1 now equals, for
$NUM_RECS $FORM_NAME_ example mydb
SHORT
$DTBA_NAME_LONG
SETVAL V1 V1 now equals, for
$DTBA_NAME_SHORT
$SYSTEM_DIR example, c:\chem-
$FORM_NAME_LONG fndr\system
$FORM_NAME_SHORT
$CFW_DIR Script-Only Commands
$FORM_DIR *text

Chem & BioOffice 2006 /ChemFinder CAL Commands 487

Environment Variables
 :label LOOP begins a section of code that will execute
repeatedly, until ENDLOOP is reached. By default,
label:
the number of times the code executes is equal to
GOTO label the number of records in the current list, but you
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can provide a specific count in the LOOP statement.

IF v1 op v2 stmt
IF v1 op v2 TIP: ENDLOOP can be used anywhere within a loop
clause to mean continue to the next iteration. Example:
<stmt(s)>
LOOP
[ELSE RECORD NEXT
IF $HAS_MOL = 0
<stmt(s)>] ENDLOOP
ENDIF
ENDIF
CLEAN
LOOP [count] ENDLOOP
In this example, if a record has no structure, the program goes
ENDLOOP to the next record and skips the CLEAN.
PAUSE [dseconds]
PAUSE temporarily stops the script from executing
EXIT for a specified number of tenths of a second. If no
INTERACTIVE ON / OFF number is given, the duration of the pause is 2
seconds.
STEP ON / OFF
EXIT ends the script immediately.
Script-only commands are useful only in script files, INTERACTIVE turns interactive mode on or off.
not interactive CAL.
STEP toggles single-step (debugging) mode on and
An asterisk (*) is used to mark a line as a comment off.
and not a command that should be executed.

Labels and GOTO give a mechanism for jumping

backwards or forwards in a script. A label may be
any text string starting or ending with a colon. It
may appear anywhere in the script. (Prior to Chem
& BioOffice 2006, it had to appear prior to any
GOTO that referenced it.)

IF is a standard conditional statement. It compares

two values according to an operator, then executes
its final statement if the result is true. In the IF/ELSE
format, it executes the ELSE statement when the IF
statement is false. Valid operators are:
= <> < >

488 CAL Commands CambridgeSoft

Script-Only Commands
The table below shows examples of Script-Only
Commands:

Command Action

start: a label

IF $V1 = "" provide an error message if the

MSG Empty variable V1 is empty
value!

PAUSE 100 pause 10 seconds

GOTO start go to specified label

LOOP 10 begin loop to repeat ten times

PAUSE pause the default time: 2

seconds

ENDLOOP return to LOOP statement

until done

NOTE: Script commands are subject to change. See the

Readme for up-to-date information.

Chem & BioOffice 2006 /ChemFinder CAL Commands 489

Script-Only Commands
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490 CAL Commands CambridgeSoft

Script-Only Commands
Appendix N:
Cartridge
Pre-Setup Procedures
Before you can use ChemFinder/Oracle to connect
to an Oracle database, some preparations are
required:
1. Download and install the Oracle Client
software (version 9i). This is available free from
Oracle.
The minimum install alone (called Runtime)
is not adequate to provide support for
ChemFinder/Oracle. In addition, you must
subsequently choose the Custom install, and
select Oracle Windows Interfaces. If you do
not have the requisite components installed, an
attempt to open an Oracle database will
generate the error: Provider cannot be found. It
may not be properly installed.
2. Have the Oracle administrator install CS
Oracle Cartridge (2.0.1 or later). You can use
ChemFinder/Oracle to access any Oracle data-
base, but one without the CS Oracle Cartridge
cannot be used to store or search chemical
structures.
3. Have the administrator set up a user account
for you. ChemFinder/Oracle requires that you
log in to a tablespace in which you have write
privileges. For access to corporate files, the
administrator needs to grant you read-only
privileges to tables and views of interest
outside your tablespace.
4. On your machine, use Oracle Net Configura-
tion Assistant to establish a connection to each
Oracle database you intend to use.
Chem & BioOffice 2006 /ChemFinder
CS Oracle
In principle, ChemFinder/Oracle can access any
Oracle database and make sense of it. In practice,
some preparations are recommended:
You can access data in Oracle databases which
do not have the CS Oracle Cartridge installed
for example, biological databases but you
cannot search or sort by structure or structure-
related properties. ChemFinder/Oracle has
been developed with CS Oracle Cartridge
version 2.0.1, and is not likely to work with
earlier versions. (To display the Cartridge
version, look in the Database tab of the Prop-
erties dialog. The version is listed, or None
if unavailable.)
Any table containing structures should have a
unique primary key. If you connect to a table
without a unique primary key, you get a
warning message. You can set up a primary key
in ChemFinder (see Indexing on page 446.)
ChemFinder/Oracle users must have sufficient
privileges to create tables in their own
tablespaces.
Fast-Move Caching
Scheme
Normally, when you open a database or do a search,
ChemFinder issues a select statement. The server
then processes the statement, prepares a set of
records, and provides a cursor for navigating
through them to retrieve the data. Unfortunately,
when the cursor is asked to move to a position N
records from the current one, it requires all N to be
downloaded to the client. In the worst case, you
CS Oracle Cartridge 491
Fast-Move Caching Scheme
 open a large table and use Move Last to see the last
record, and the entire table is sent down from the
server.
To get around this problem, an alternative
Administrator
mechanism is available in ChemFinder/Oracle. In
this scheme, instead of requesting complete forms-
full of data over a list or query, ChemFinder/Oracle
retrieves only the ID or primary key field, and
stores (caches) the results in an array in memory.
It then need not rely on the normal recordset
cursor. When a request is made to move to record
N, the key for that record is looked up in the array,
and a new select statement is issued to retrieve only
the corresponding record. Thus, Move Last takes no
more time than Move Next.
There are tradeoffs between the two schemes:
The new scheme takes time to retrieve the set
of ID's during a database open, or after a
search or sort. Normally, this is quite fast even
for a large table, and steps are taken to avoid
repeating the operation unless necessary. A
message on the status bar indicates when this
caching process is taking place.
In the new scheme, moving from one record to
the next is somewhat slower, since each move
involves a (fast, one-hit) search. This is not very
noticeable during list browsing, but slows
down multi-retrieve operations such as filling
table view.
Because of these drawbacks, the new caching
scheme is OFF, by default. To turn it ON for an
Oracle-connected form:
1. Choose File Database or otherwise bring up the
Properties dialog.
2. Go to the Oracle tab of the dialog.
3. Check the Cache ID's for faster moves box.
4. Click OK.
You will get an alert instructing you to:
492 CS Oracle Cartridge
5. Save the form, close it, and reopen it. This is
currently necessary in order to reinitialize the
database connection with the caching scheme.
Configuration Via
CF_SETTINGS Table
When you select a table in an Oracle database,
ChemFinder determines and displays the types of
columns in the table. Heres how it decides whether
a particular column contains structures:
The column must be of type CLOB or BLOB.
If the column has been indexed by the CS
Oracle Cartridge, then it is a structure column.
If there is no index, then ChemFinder/Oracle
looks for a table of configuration info called
CF_SETTINGS. If the column is listed in that
table as being of type STRUCTURE, then it is a
structure column.
The CF_SETTINGS table is also used to determine
whether a particular column of type BLOB contains
ChemFinder pictures (Windows metafiles).
To designate an unindexed column as a structure
column:
1. In the Field tab of the Properties dialog, select
a column of type BLOB or CLOB.
2. Click Set As Structure.
If the CF_SETTINGS table has not yet been
created, an alert indicates that it is about to be
created.
3. Click OK to proceed and create the table, or
Cancel to abort without creating.
If the table already exists and there is already an
entry for the selected column, you are given an
alert and a chance to cancel.
4. Click OK to proceed.
A new entry is created in the table, marking the
selected column as a structure column.
CambridgeSoft
Configuration Via CF_SETTINGS Table
To designate a BLOB column as a picture column:
1. If the CF_SETTINGS table does not exist,
create it using steps 1-3 of the above
procedure.
2. Edit the table one of two ways:
Chem & BioOffice 2006 /ChemFinder
a. with an Oracle client tool such as SQL*Plus,
OR...
b. by opening it in ChemFinder and creating a
form.
3. Add a row containing the table name, column
name, and a column of type PICTURE.
CS Oracle Cartridge 493
Configuration Via CF_SETTINGS Table
Administrator

494 CS Oracle Cartridge CambridgeSoft

Configuration Via CF_SETTINGS Table
Section III: CombiChem
Overview Reaction Template Basics
The example of a reaction template that follows is
CombiChem, the CambridgeSoft engine for supported by CombiChem:
generating combinatorial libraries, was previously
R2

available only as an add-in extension for Microsoft R1

R2

R1
NH2

Excel for Windows. Starting with ChemOffice 8,

N H2O
H
O
N
N

the engine was incorporated into E-Notebook and

H

other products by means of a new Automation

interface in MolServer. This new approach means R2

that the engine can be used by developers NH3

R1

everywhere. For more information, see NH

http://sdk.cambridgesoft.com/chemfinder.
Working with Reaction
Templates
CombiChem is a reaction-based combinatorial
product. You first enter a reaction template with
R-groups at the variable sites in your starting
materials, then search for reactants based on these
structures. CombiChem puts your final product
structures together and creates a virtual library.
A reaction template must meet the following
specifications:
All sites of variability require unique R-group
designations.
Solvents, catalysts, and other real-world
elements should not be included in the reaction
template drawing.
Multi-step reaction templates are supported.
The following sections describe the use of
templates in both CombiChem/Excel and in
ChemFinder/Office.

Chapter 25: CombiChem/Excel

Working with Excel Users Guide.

CombiChem/Excel Initializing
The CombiChem/Excel add-in requires Microsoft
CombiChem/Excel
Excel 2000 or later. The following procedures When you install ChemFinder or ChemOffice, the
assume you are familiar with Excel for Windows. CombiChem/Excel add-in is automatically
For more information about using Excel, see the installed.

Chem & BioOffice 2006 /CombiChem CombiChem/Excel 495

Working with Reaction Templates
 To activate CombiChem/Excel:
1. Open Microsoft Excel.
2. From the Tools menu, choose Add-ins.
Administrator
The Add-Ins dialog box appears.
3. Select the CombiChem for Excel and ChemDraw
for Excel add-ins and click OK.
NOTE: CombiChem must have the ChemDraw for Excel
addin in order to work.
The CombiChem/Excel add-in is available until
you cancel it by unchecking the box. Excel will save
the setting, so you dont have to activate each time
you use Excel.
Using Help
CombiChem/Excel provides abridged Help right
in the worksheets. If you would like to see a fuller
explanation of any of the steps, do the following:
On the ChemOffice menu, point to
CombiChem, then select Help from the
submenu.
496 CombiChem/Excel
The CombiChem Help dialog box appears.
Help drop-down list
Navigation buttons
To use Help, do one of the following:
Choose a topic from the drop-down list.
Browse through the topics using the navigation
buttons, Previous and Next.
To close Help:
Click Exit.
Using CombiChem/Excel
with secured databases like
ChemACX:
ChemACX and ChemACX-SC have security which
prevents programs like CombiChem/Excel from
using them. To get around this, the ChemFinder
samples directory has included two special forms,
ACX2005INDEXA.CFW and
ACXSC2005INDEXA.CFW, as alternate forms
which do allow access. To use these forms:
If ChemACX is installed on a hard drive:
CambridgeSoft
Working with CombiChem/Excel
 Copy <CFW
dir>\samples\ACX2005INDEXA.CFW and
<CFW dir>\samples\ACXSC2005INDEXA.CFW
into the directory with the other ChemACX
and ChemACX-SC files, respectively.
5. If there are any existing paths, DO NOT
remove them. Make sure all paths are separated
by semi-colons.
6. Click OK.

If you are using ChemACX from the DVD-ROM,

the forms should be left in the samples directory. Creating a New CombiChem
You must, however, configure ChemFinder to Workbook
point the ACX2005INDEXA.CFW form to find
the data on the DVD-ROM. To use CombiChem/Excel, you first create a
To do this, you will need to edit your registry. Reaction worksheet in which to store your reaction
templates.
CAUTION
To create a Reaction worksheet:
CAUTION: Editing your registry can cause serious
problems with your system if you are not careful. On the CombiChem submenu click New Reac-
tion.
1. Launch Regedit. (Go to the Start menu,
choose Run, and type regedit in the text entry
box).
2. Open the following location:
HKEY_CURRENT_USER\Software\Cambridg
eSoft\ChemFinder\10\Pro\Options
3. Right click on the DB_SEARCH_PATH key in
this folder and choose Modify.
4. Add the exact path to the directory that
contains the database.
i.e. E:\ChemACX\ (where E is the letter for
your DVD-rom drive).

NOTE: The last backslash is important. Do not omit

A new worksheet, named Reactions, appears
it.
in your workbook.

Chem & BioOffice 2006 /CombiChem CombiChem/Excel 497

Working with CombiChem/Excel
 Adding a Reaction Template
to the Reaction Worksheet
To add a reaction template to your worksheet:
Administrator
if you... then...
have a reaction 1. Click the Load Molecule
saved as a Chem- icon on the ChemOffice
Draw file toolbar or select Load from
the Molecule submenu of
the ChemOffice menu.
2. Browse to the location of
the file and click Open.
The reaction appears in the
A1 cell of the Reactions
worksheet.
do not have a 1. Double-click the cell on the
saved reaction Reactions worksheet
file labeled: Reaction - double-
click to edit.
2. Click Yes in the dialog box
that asks if you want to add
a molecule to the worksheet.
ChemDraw opens.
3. Draw a reaction.
4. When you are finished,
choose Close and Return to
New Molecule from the
ChemDraw File menu.
The reaction appears in the
A1 cell of the Reactions
worksheet.
498 CombiChem/Excel
TIP: The cell will display Structure 1. You can display
or hide the reaction at any time with the Show Picture
and Hide Picture icons.
You can edit the reaction in ChemDraw at any time
by double-clicking the cell that contains the reaction
template. You must double-click the cell, not the
picture. (That will open Excels Format Picture
dialog box.) Hide the picture, or click near the edge
of the cell, to avoid clicking the picture.
CAUTION
Do not add more than one reaction to a reaction template.
If you want to start a new combinatorial experiment, save
your workbook and open a new one.
Processing the Reaction
Template
CombiChem analyzes your reaction and creates a
worksheet for each generic reactant (reactant
containing R-groups) in the template.
To create Reactant worksheets:
On the CombiChem submenu of the ChemOf-
fice menu click Make Reactant Worksheets.
New worksheets are added to your reaction
workbook.
The Reactant worksheets are named Reactant1,
Reactant2, and so on, up to the number of initial
generic reactants in your reaction. If your reaction
is a multi-step reaction, intermediates (products of
a prior step in the reaction) are not included.
When you create worksheets, note the following:
If you edit the reaction template by
double-clicking on the structure in Excel, it is
not automatically reprocessed. You must repeat the
Make reactant worksheets step after editing
your template.
CambridgeSoft
Working with CombiChem/Excel
 If you process a reaction template and there are Searching Databases
already Reactant sheets in the workbook, a
message appears asking if you want to delete To search a database:
the existing sheets.
1. On the CombiChem submenu click Search for
Reactants.
If you want to then
A dialog box appears asking if you want to
search in ChemFinder or search directly.
replace the previous Click Yes
worksheet(s) 2. Select the appropriate choice.

preserve the previous 1. Click No
worksheet(s)
2. From the File menu,
select Save As and
save the workbook
under another name.
NOTE: If you are searching an SD format datafile,
select Search Directly.
3. Use the Browse button, or type in the full-path
name of the database file you wish to search.
Click Go.

3. Process the reaction
template
Working with Reactant Lists
After you process a reaction template, the reactant
worksheets have the generic reactants at the top,
one per worksheet. These worksheets hold your
reactant lists.
Reactant lists contain the building blocks from
which you create a product library. The source of
these lists can be a ChemFinder database or any
data source in your institution capable of exporting
MDL SDFiles. When CombiChem processes the
reaction template, it creates query structures. These
structures are set up with all the proper parameters
to perform a general search on any structure-
searchable database.
If you selected Search Directly, the hit list is
imported into the worksheet.
If you selected Search in ChemFinder,
ChemFinder displays the hit list in the selected
database. You can work in ChemFinder to
refine the list by modifying the search
conditions and repeating the search and using
Omit Record if you like. When the list contains
the reactants you want to import, return to
Excel and use Import Current ChemFinder Hitlist
on the CombiChem menu to import the list.
You can also copy and paste the query structure
into ChemFinder to perform a search.
1. Select the cell containing the structure.
2. Click the Copy Molecule icon on the
ChemOffice toolbar.
3. Open a ChemFinder database, click the Search
Query icon, and select Paste from the Edit
or context menu.
4. After performing the search, use Import Current
ChemFinder Hitlist on the CombiChem menu,
or the import hitlist icon on the ChemOffice
toolbar , to import the list.

Chem & BioOffice 2006 /CombiChem CombiChem/Excel 499

Working with CombiChem/Excel
 Reactant List Format performing some property calculations on these
products, you might decide that 10% of these
A Reactant sheet with imported data contains the products are worth synthesizing in the lab. You
following columns: could then create a new experiment with just those
Administrator

Structure products that the calculations show to be

promising.
Use (Y/N)
To create a new experiment:
NOTE: Other columns may be included, depending on the
method used to import the data. 1. On each reactant sheet, select the reactants to
use by typing a Y in their Use(Y/N) column.
Structure Column Type a N for those reactants you do not wish to
use.
The Structure column is headed by the generic
structure that represents all of the reactants on this NOTE: Cells without n or N default to Y.
sheet. Use the Show Picture/Hide Picture
commands to toggle the display. 2. On the CombiChem submenu, point to Experi-
ments then click New.
Use (Y/N)
CombiChem/Excel adds a Use (Y/N) column to
your imported data. When you create experiments,
you enter Y or N in this field to select whether you
want to use that reactant in that experiment. For
more information, see Creating Experiments
below.

Other Data
Other columns contain data from the SDFile or
ChemFinder database you imported, such as A dialog box appears asking if you want to
formula, molecular weight, or Mol_ID. This data is create the experiment with the selected number
not used by CombiChem. You can delete it if you of reactants.
wish.

Creating Experiments
A experiment is a library of product molecules,
created from the reaction template and the reactant
lists you imported or entered manually. You can use NOTE: Enumeration of a product library may take a long
CombiChem/Excel to create, or enumerate, time, especially if there are many reactants or you are using a
multiple experiments per workbook. slower processor.
For example, you can take all the reactants you
imported and enumerate an experiment containing 3. Click Yes when you are satisfied with the
all possible combinations of reactants. After number of reactants to process.

500 CombiChem/Excel CambridgeSoft

Working with CombiChem/Excel
 A file browser appears. CombiChem/Excel
saves your enumeration to a database, so that
there is no longer any limit on the number of
products that can be generated. When the
enumeration is done, CombiChem/Excel
imports your data to a worksheet. If your
experiment exceeds the maximum data
memory for an instance of Excel, (typically,
more than 8000 products) you are warned and
advised to save your workbook in case the
import fails.
After the experiment is created, several new sheets
are added to your workbook:
Experiment Reactant sheetscontain lists
of the reactants actually used in the experiment.
There will be one Experiment Reactant sheet
for each Reactant sheet.
Experiment Product sheetcontains the
enumerated products in the experiment.
Using the Products Only Option
The Experiment Product sheet normally shows the
products by displaying the entire reaction. You can
elect to generate only products by selecting the
Make Products Only option on the Experiments
submenu.
Select the option by clicking it. When you next run
a new experiment, the menu option will be checked
and the new Experiment Product sheet will have
only products, not full reactions.
Chem & BioOffice 2006 /CombiChem
Working With Experiments
After enumerating a experiment, you can do several
things with it. For example, you can calculate
properties of the products in your experiment using
ChemDraw/Excels property calculation methods.
For more information, see Using ChemProp Pro
Functions in the ChemDraw Users Manual.
Configuring Plates
You can assign your products to product wells and
your experiment reactants to reactant block plates
with CombiChem/Excel. This is especially useful if
you are going to use a robotic synthesizer. You can
configure plates of up to 50 rows and 50 columns.
To set up assignments:
1. Navigate to an Experiment Reactant or
Experiment Product worksheet.
2. On the CombiChem submenu, point to Plates,
then click Configure Plates.
The Plate Configuration dialog box appears.
The numbered buttons represent wells in the
product or reactant plates.
3. Use the drop-down Configuration of: menu
to select Product Plate or Reactant Block Plate.
4. Enter the number of rows and columns.
CombiChem/Excel 501
Working with CombiChem/Excel
 The Plate Configuration dialog box display
resets according to the values you enter.
You can configure plates with three types of
wells:
Administrator
reactant or product (green)
empty (white)
controls (orange).
By default, all wells have reactants or
products assigned to them. Clicking on
a well cycles through the well types.
5. When you are finished, click Save.
The template is used when assigning
experiment reactants or products to plates.
Assigning Plates
You have to make assignments to plates on each
reactant and product worksheet separately.
To assign the reactants or products to plates:
1. Select a reactant or product worksheet.
2. On the CombiChem submenu, point to Plates,
then click Assign To Wells.
Three columns are added to the reactant or
product worksheet: Well plate, Well row, and
Well column.
To change plate assignments:
Edit the values on the worksheet.
502 CombiChem/Excel
To remove all plate assignments:
1. Select the worksheet where you want to
remove assignments.
2. On the CombiChem submenu, point to Plates,
then click Remove Assignments.
Browsing Plates
After assigning reactants or products to wells, you
can view them.
1. On the CombiChem submenu click Browse
Plates.
The Plate Browser dialog box appears. The
numbered buttons represent the wells in your
plate.
2. Click the appropriate button to move to the
corresponding reactant or product worksheet
row.
3. To move between plates, click the navigation
buttons at the top of the dialog box.
Viewing Related Structures
After enumerating an experiment, you may want to
see which reactants went into a product or which
products arose from a given reactant.
CambridgeSoft
Working with CombiChem/Excel
To highlight products or reactants: 3. Draw a generic reaction. For more information
on generic structures, see the ChemDraw
1. Select a row on a Experiment Reactant or Users Manual.
Experiment Product sheet.
Using a ChemFinder database:
2. On the CombiChem submenu, point to High-
light, then click Highlight Related Records. You can create a database of generic reactions in
ChemFinder. ChemFinder/Office can open .cfw
The related records on the Experiment files directly and browse through them.
Reactant Reactant and Experiment Product
sheet are displayed in color. Once you have a generic reaction in the Structure
window, do the following:
To remove the highlighting from all rows:
1. From the Search menu, select Enumerate.
On the CombiChem submenu, point to High-
light, then click Unhighlight All.
The Combi Enumerator window appears,
showing the reaction as you entered it in the
Structure window. You may add another step
Using CombiChem with to the reaction by clicking the Add Step button,
ChemFinder/Office edit the reaction in ChemDraw by double
clicking in the window, or continue with the
The CombiChem engine can be used with reaction as entered.
ChemFinder/Office (formerly known as
ChemFinder for Word) to generate libraries of
combinatorial experiments. These libraries can be
drawn from any type of file that
ChemFinder/Office can read, and stored as .mst
format databases. For general information on using
ChemFinder/Office, see ChemFinder/Office on
page 449.
There are two ways of entering a CombiChem
template in ChemFinder/Office:
by creating a generic reaction in ChemDraw or
with the ChemDraw ActiveX control.
by creating a ChemFinder database of generic
reactions. 2. Click the Analysis tab.

Using ChemDraw or the ChemDraw ActiveX

control:

1. Open ChemFinder/Office
2. Click the Edit Structure button. Depending on
your Preferences setting, this will open Chem-
Draw or activate the ChemDraw ActiveX
control.

Chem & BioOffice 2006 /CombiChem CombiChem/Excel 503

Using CombiChem with ChemFinder/Office
 An analysis of the reaction steps appears below You may edit the hit list before continuing.
the reaction display.
a. Click Edit Hitlist.
An instructional dialog box appears.
Administrator

b. Click OK to open ChemFinder. Edit the

hitlist by selecting Omit from List from the
Record menu.
4. Click the Enumeration tab. Use the Browse
button to select a database in which to store the
results. Click Go.

3. Click the tab for the first reactant. Use the NOTE: You can create a new database file by typing
Browse button to select a ChemFinder or in a file name.
SDFile database, or other source of chemical
structures such as a collection of ChemDraw The results are stored in the database.
files. Click Search.
5. When you are finished, click OK to exit the
Combi Enumerator and return to Chem-
Finder/Office.

To view the results:

1. Open ChemFinder

2. From the File menu select Import, then click

Structures.

3. Select the database from the Open Chemical

Structures dialog box.

504 CombiChem/Excel CambridgeSoft

Using CombiChem with ChemFinder/Office
Section IV: E-Notebook
Chapter 26: Introducing
E-Notebook 10.0
E-Notebook 10 is an electronic notebook that
facilitates daily record-keeping for scientists.
E-Notebook makes it possible for you to manage
diverse types of data on electronic pages that are
much like the pages of a paper notebook. The
electronic pages make it easy to organize
information and streamline your workflow.
E-Notebook also provides a full audit trail and
change tracking features for compliance with 21
CFR Part 11.
E-Notebook has many advantages over traditional,
paper notebooks. With E-Notebook, you can set up
Notebooks and Pages to manage information
about organic syntheses and related information
such as stoichiometry calculations, reaction preps,
spectra, analytical methods, notes, and
spreadsheets. Since E-Notebook has electronic
rather than paper pages, you can conduct searches
by substructure, key word, date, and so on. You can
set up templates to avoid reentering information
that you often use. Also, E-Notebook fully
automates stoichiometric calculations.
With E-Notebook, you can create a customized
electronic notebook that matches your workflow.
You can develop new fields to manage specialized
types of data, and configure your own forms to
manage the information that is important to you.
You can also add your own data analysis tools and
customized searches to E-Notebook.
Chem & BioOffice 2006 /E-Notebook
You can use E-Notebook to organize a wide variety
of other information critical to your work processes
as well. For example, common reactants used in
reaction preps can be stored in the E-Notebook
database and shared among researchers. In large
enterprises, E-Notebook can be configured to both
supply and retrieve information from other
Enterprise systems, such as chemical registration or
chemical inventory management systems.
E-Notebook supports the Oracle database format.
New Features
NOTE: Note: the label Enterprise indicates that the
feature is only available in Enterprise versions of
E-Notebook, not in the Desktop version.
E-Notebook 10 offers many new features,
including:
Reaction Section Enhancements E-Note-
book now updates the stoichiometry grid auto-
matically when you edit a reaction drawing.
Additional features for working with salt codes
and solvents have been added as well.
Reaction Toolbar a new toolbar makes it
easy to manage reactants and products in
your reactions.
AutoText text in the preparation is
updated automatically, based on change you
make to the reaction drawing or
stoichiometry grid.
Introducing E-Notebook 10.0 505
New Features
 Reaction Explorer you can now view a
reaction tree that displays the predecessors
and successors of a batch or compound.
(Enterprise version only).
Administrator
Enterprise ISIS/Draw Integration with
the E-Notebook's ISIS Draw Tool, you can
draw and store chemical structures and
reactions in the Chemical Structure Field
just as you would do with ChemDraw Tool.
New Section Enhancements Some more
sections have been added to E-Notebook envi-
ronment to increase the range to express your
ideas.
Captured Image Sections allow you to
manage PDF files in E-Notebook.
MS PowerPoint Sections You can use MS
PowerPoint Sections to manage MS Power-
Point slideshows in E-Notebook.
Formulas You can now associate your own
custom formulas with tables or property lists in
E-Notebook. The formulas can refer to other
values in an E-Notebook form.
Enterprise PDF Rendering You can now
export Collections to PDF, then manage them
as you would PDF documents.
Searching enhancements You can now
perform a search that is a union or an intersec-
tion of two searches. Or, you can subtract one
set of search results from another.
Enterprise Inbox It is now possible to
send data to an E-Notebook experiment or
another E-Notebook user.
Acronyms database E-Notebook provides
a database of 2400 acronyms, which you may
add to your reactions.
506 Introducing E-Notebook 10.0
Enhanced table of contents You can now
create a customized table of contents: hiding
columns, showing additional columns, and
sorting items in an ascending or descending
order.
Enterprise Offline data management
You can create or modify experimental records
off-line, then upload them at a later time.
Send2ENotebook/Send2File It is now
possible to render the contents of a document
using a print driver, and insert the contents into
a collection.
Enterprise E-Signatures You can now get
your experiments electronically signed then
stored in PDF format once they are finished.
Terminology
Many of the terms used to describe the features of
E-Notebook are the same terms that one would use
in describing a paper notebook. In some cases,
however, the terminology is different, and familiar
wordssuch as collection or sectionmay have
different meanings. The following terminology is
used in the E-Notebook application and
throughout this guide:
Administrator The person who configures
E-Notebook and sets up security permissions.
Collection A set of related items in E-Note-
book. Collections are the items that appear in
the E-Notebook Collection Tree.
Collection Listener Collection Listeners
modify the behaviors of collections, such as
creating, hiding, renaming, duplicating and
moving behaviors. Administrators assign them
to collections.
Collection Type A unit of configuration
that contains business rules for organizing
collections and sections. Each collection type
has a name, an icon for displaying collections
CambridgeSoft
Terminology
 of that type in the collection hierarchy and a set
of business rules that describe what kinds of
operations can be performed on collections of
that type
Field A description of a unit of data within a
section type. Each field has a type, which
describes the type of data stored in the field,
and a name. Examples of different types of
fields include a property list, a table, a chemical
structure, a spectrum, a Microsoft Word docu-
ment. Depending on the type of data stored in
the field, the field may also contain additional
configuration information. For example, a
property list field contains a list of the proper-
ties that can be included in the property list.
Form the layout of a section is determined by
the Form, which contains Fields, Boxes, and
possibly Form Tools.
Form Tool a Form Tool is used to perform
particular function in an E-Notebook section,
such as data analysis or data import/export.
Full Control privilege The privilege
required to manage the security settings of a
collection. The Full Control privilege
subsumes all of the features associated with the
Read & Write privilege
History A list of the versions and transitions
that have been made to a collection.
Home The collection that appears when you
first log in to E-Notebook. It is the collection
associated with you as a user.
Logging In Entering E-Notebook by
providing a user name and password.
Meta-data Data that describes other data.
For example, you can use meta-data such as
creation date or owner's name as parameters
when searching for data and information in
E-Notebook.
Owner, of a Collection the E-Notebook
user who created the collection.
Chem & BioOffice 2006 /E-Notebook
Property List A list of data properties corre-
sponding to a particular section. For example,
the property list in a reaction section may
contain pressure, temperature, etc.
Read privilege The privilege required to
view a collection in the collection tree, along
with its contents
Read & Write privilege The privilege
required to modify the contents of a collection.
The Read & Write privilege subsumes all of the
features associated with the Read privilege.
Region A geographic area that is used to
specify characteristics of a user, such as the
name of the template used when converting
the contents of a set of sections to MS Word
document.
Table A section (or part of a section) in
which you can record data in a tabular format.
Template A collection containing data or
information that you wish to reuse multiple
times. You can use the template as the basis for
new collections.
Section A set of related pieces of data. Each
piece of data is described by a field. For
example, a reaction section might contain a
chemical structure drawing, a table of reactants,
a table of solvents, a table of products and a
description of the procedure used to create the
drawing.
Section Listener Section Listeners modify
the behaviors of sections, such as renaming and
moving behaviors. Administrators assign
Section Listeners to various types of sections.
Section menu icon The icon that
appears when sections are displayed. Right-
clicking the icon displays the Section menu.
Section tools icons The icons that appear
immediately below the Section menu icon if
there are tools (such as import or export tools)
associated with the section displayed.
Introducing E-Notebook 10.0 507
Terminology
 Section Type A unit of configuration that
contains a set of fields, form tools and a form.
In addition, you can associate section listeners
with a section type to implement business rules
Administrator
associated with sections of this type.
TransitionAn action performed by a user to
move a collection from one state to another.
Transition ListenerTransition Listeners
modify the effect of a transition, usually by
performing an operation that is associated with
the transition. System administrators configure
Transition Listeners.
UserA person who uses E-Notebook. User
is also the term that E-Notebook uses to iden-
tify a person.
VersionThe contents of a collection saved at
a particular time.
About the E-Notebook
Guide
The E-Notebook Guide provides you with step-by-
step instructions for using the features of
E-Notebook. The left frame of this guide displays
the Table of Contents; you can open book icons to
display topics and the sub-topics they contain. The
right frame displays the specific topic you have
selected. Each topic includes hyperlinks to related
topics in the guide. This helps you to find the
information you need quickly and easily.
The E-Notebook Guide is organized into three
main portions:
1. Introducing E-Notebook 10 provides an
overview of E-Notebook, including new
features and E-Notebook terminology.
2. E-Notebook User's Guide provides
detailed instructions for using E-Notebook.
508 Introducing E-Notebook 10.0
3. E-Notebook Administrator's Guide
provides detailed instructions for configuring
E-Notebook.
In addition, this guide contains instructions for
using the Reagent Selector and CombiChem in
E-Notebook. (Each of these add-in features is sold
as a separate component).
Introducing the Reagent Selector allows
you to search ChemACX for chemical struc-
tures, and to add their properties and structures
to E-Notebook. (Enterprise version only).
Enterprise Introducing CombiChem for
E-Notebook makes it possible for you to set
up and manage combinatorial chemistry
libraries in E-Notebook.
Getting Started in
E-Notebook
To start E-Notebook, you must log in to the
application. Then, you can begin to browse or
search through E-Notebook.
Logging In
Depending upon your particular E-Notebook
setup, you may be logging-in in one of two ways:
Start Menu Login
To log in from the Windows Start menu,
1. Select the Start menu, then All Programs.
The programs you may launch are displayed.
2. Point to Chem & BioOffice 2006, then select
E-Notebook Ultra 10.
You are logged into E-Notebook. The
Collection Tree appears, displaying your Home
Collection.
CambridgeSoft
About the E-Notebook Guide
Logging in with Internet Explorer
To log in to E-Notebook with Internet Explorer:
1. In the address field of your browser, type in the
address corresponding to E-Notebook.
Either you will be logged in automatically, or
the E-Notebook login page will appear,
prompting you to enter your username and
password.
2. If prompted, enter your username and pass-
word, then click the Enter button.
The Collection tree appears, displaying your
Home Collection.
Navigation Overview
E-Notebook is composed of two main areas,
Browse and Search, each of which is represented by
a button at the top of the screen.
The Browse area displays the collections, organized
in a tree structure. To expand a collection and view
its contents, either double-click it or click the plus
sign next to it. Clicking an individual collection
allows you to view and/or edit it in the right frame.
There are a number of options for specifying your
view of the Collection Tree. See Browsing the
Collection Tree on page 527 for more
information.
Browse button
Chem & BioOffice 2006 /E-Notebook
From within the Search area, you can construct a
query to search for information. For example, you
may want to search for all of the sections that
contain a certain structure, or all of the collections
created by a particular user. When you run a query,
you can save both the results list and the query
itself. Clicking any item in the results list allows you
to browse to that item.
Certain menus in E-Notebook are accessed when a
particular item or icon is right-clicked. For example,
right-clicking a collection in the Collection Tree will
display the Collection menu.
If at any point you would like to expand the size of
a field in a section, you can double-click the titlebar
of the field. The field will expand to take up the
entire section area, increasing your working space.
To shrink the field, simply double-click the titlebar
again.
Security Overview
Each user of E-Notebook has a unique username
and password. Thus, only valid users may log in to
E-Notebook.
Once a user has logged in, security in E-Notebook
is set up on a collection basis. Security properties
may be set up for any collection in the Collection
Tree whether it be a User, a Notebook, a Folder,
etc. The security properties of a collection
determine who has Read, Write, or Full Control
Introducing E-Notebook 10.0 509
Getting Started in E-Notebook
 access to that collection. These access privileges
may be assigned to individual E-Notebook users or
to user groups.
Administrator
Read permission to view the collection, but
not edit it.
Read and Write permission to view the
collection and edit it, if it is in a state that
permits edits.
Full Control Read and Write permission,
and also the ability to assign and remove secu-
rity permissions for the collection.
By default, each collection inherits the security
properties of its parent in the Collection Tree. The
inherited security option may be disabled, however,
so that the security properties of a collection can be
configured independently of its parent.
Examples of some common types of E-Notebook
Collections are:
510 Introducing E-Notebook 10.0
In addition to security at the collection level,
security may also be configured for collection
transitions, specifying which users may or may not
perform certain transitions on collections.
If you have Full Control permission to a collection,
you may determine who has access to the
collection. See Changing Collection Security
Properties on page 593.
The Administrator Guide provides additional
information for system administrators.
E-Notebook Overview
E-Notebook manages numerous types of data on
electronic pages that are much like the pages of a
traditional, paper notebook. This information is
organized into collections sets of related items
that appear in a tree structure in the left frame when
you are browsing E-Notebook.
Notebook and Page
Therapeutic Area
CambridgeSoft
E-Notebook Overview
 Project
Experiment
Reaction Scheme
Synthesis
For example, you could create a collection that
contains all of the reaction steps for a specific
synthesis. Typically, primary research data is stored
in Experiments or Pages, which are organized
within Notebooks, just like the paper pages in paper
notebooks. In this case, the synthesis could be a
Notebook, and each of the steps could be a Page.
Each of the Pages may come from a different
Notebook and may have been created by a different
Chemist, but the Notebook for this, particular
synthesis could collect all of these Pages in a single
place.
You can organize collections in other ways, too. For
example, you may want to create a collection of all
of the syntheses that lead to a certain product, or all
Chem & BioOffice 2006 /E-Notebook
of the E-Notebook users who are working on a
specific project. E-Notebook enables you to set up
these relationships easily.
Collections are extremely flexible, because they are
designed to allow you to organize your information
in the way that is best suited to your workflow.
E-Notebook allows you to browse through
collections and to search them for important
information. Also, you can create references to
them, duplicate them, and, to prevent further
changes, you can transition them to a closed, read-
only state.
Just as you would use pages in a paper notebook for
recording various types of data, you can use
sections in E-Notebook for recording reactions,
spectra, or any other kind of information. For
example, within an Experiment, there may be
sections for Reactions, Notes, Reactants, etc.
whatever you need to record and display your
information the way you would with a paper
notebook. You also have the option to use
Introducing E-Notebook 10.0 511
E-Notebook Overview
 templates, so that sections are set up automatically
and uniformly with each new Experiment you
create.
Administrator

Your system configuration determines the types of

collections and sections that you can create within
E-Notebook and the rules that define their
contents. The permission to view, edit, and create
collections can be set up on a per-collection basis.

512 Introducing E-Notebook 10.0 CambridgeSoft

E-Notebook Overview
Chapter 27: Working with E-Notebook
This portion of the guide describes how to use
notebooks, experiments, and other features that Enterprise Working Offline
E-Notebook offers for managing your data.
See the following topics for more information:
Notebooks, Pages,
Notebooks, Pages, Experiments and Other
Experiments, and Other
Collections Collections
Using Templates
This portion of the User's Guide describes how to
Working with MS Office Sections, Reactions, work with notebooks, experiments, and other types
and Other Sections of E-Notebook collections.
Send2ENotebook and Send2File

See the following topics for more information: Working with Reactants Collections

Working with the User Collection
Working with Pages and Experiments
Working with the Inbox
Working with Folders
Working with User Configurations and Auto-
text Definitions
For information about copying, renaming,
exporting collections, etc., see Organizing
Collections on page 588.

Chem & BioOffice 2006 /E-Notebook Working with E-Notebook 513

Notebooks, Pages, Experiments, and Other Collections
 Working with the User
Collection
Each user of E-Notebook has an associated user
Administrator
collection. Your user collection is your home
collection, and appears at the top of the Collection
Tree when you first log into E-Notebook.
When your user collection is selected in the
Collection Tree, your home page appears in the
right frame. The home page displays summary
information about your open pages or experiments.
You may add several different types of collections
directly to your user collection:
Notebooks
Folders
User Configurations and AutoText Definitions
Searches Collection Searches, Section
Searches, Text Searches, Unannotated Version
Searches, Chemical Structure Searches.
Page or Experiment Templates
References to Notebooks
References to Folders
References to Page or Experiment Templates
514 Working with E-Notebook
Adding a New Collection to
the User Collection
To add a new collection:
1. In the Collection Tree, right-click your user
collection.
A menu appears.
2. Select New, then select a type of collection.
3. The new collection appears and you are
prompted to rename it.
Adding a Reference within
the User Collection
1. In the Collection Tree, click the Notebook,
Folder, or Template to which you wish to
create the reference.
2. While holding the CTRL and SHIFT keys, drag the
collection until the user collection is high-
lighted.
3. Release the mouse.
The Reference appears in the Collection Tree.
Alternatively, you may right-click the collection you
wish to reference, and select Copy from the
Collection menu. Then, right-click the user
collection and select Paste Reference.
CambridgeSoft
Working with the User Collection
Browsing up to the User
Group
If you have the required security permissions, you
may browse up to the next highest level in the
Collection Tree and view the user group at that
level. To do this, right click your user collection,
select Go Up To, then the name of your user group.
Alternatively, you may select View from the menu
bar, then Go Up To.
Working with Note-
books
Notebooks contain Page or Experiment
collections. Each Notebook has a table of contents
associated with it, which displays summary
information for each collection in the Notebook.
Chem & BioOffice 2006 /E-Notebook
Creating a Notebook
To create a new Notebook collection:
1. In the Collection Tree, right-click your user
collection.
A menu appears.
2. Select New, then Notebook.
3. A new Notebook collection appears and you
are prompted to rename it. Its Table of
Contents section appears in the right frame.
TIP: If you would like to create a new Page/Experiment
within the Notebook, simply click the New Experiment icon
.
Each Notebook has a Table of Contents section
associated with it. The Table of Contents
summarizes all of the Pages/Experiments that the
notebook contains. Double-clicking the number
associated with any of the contained
Pages/Experiments listed will allow you to navigate
to that Page/Experiment. You may also print the
Table of Contents to create a hardcopy of it; see
Printing Sections on page 585 for more
information.
Working with E-Notebook 515
Working with Notebooks
 When you rename a Notebook, the names of the Spectra Section
Pages or Experiments within it will change to match
Table Section
the name of the Notebook.
MS Excel Spreadsheet Section
Working with Pages and
Administrator

Experiments
Pages/Experiments in E-Notebook may contain
several different types of sections for experimental
data.
Creating a Page or Experi-
ment
To create a new Page or Experiment collection:
1. In the Collection Tree, right-click the
Notebook collection to which you would like
to add the Page or Experiment.
A menu appears.
MS PowerPoint Section
Captured Image Section
Creating a Page or Experi-
ment from a Template
To create a new Page or Experiment collection
from a template:
1. In the Collection Tree, click the template to
select it.
2. Drag the template into the Notebook.
A new Page or Experiment is created, based on
the template.
Alternatively, you may right-click the template and
select Copy. Then, right-click the Notebook and
select Paste. (See Working with Templates on
page 520 for information about creating the initial
template).

Closing and Reopening

Pages and Experiments
Pages and Experiments have several states which
2. Select New, then Page (or Experiment). define their lifecycles. You may perform transitions
A new Page or Experiment collection appears on a Page or Experiment to move it from one state
within the Notebook. It is numbered to another.
automatically. Open writable, optional annotation of
You may associate several types of sections with the changes
Page/Experiment: Closed read-only
Reaction Section Reopened writable, required annotation of
MS Word Document Section changes, changes visible on the screen and in
the printed copy. (See Changes and Audit
Ancillary Data Section
Trail on page 601 for information about visu-
Spectrum Section alization of changes and providing annotation).

516 Working with E-Notebook CambridgeSoft

Working with Pages and Experiments
 Enterprise Working with the
Inbox
E-Notebook makes it possible for data to be sent
from external sources to an Inbox or temporary
holding area. For example, you could send spectral
data to a particular E-Notebook user or to a specific
experiment. This could be done with, for example,
the Send2 feature. The section will appear in an
Inbox, and from there you can move it into the
appropriate experiment.
For more information, see Using the Inbox on
page 549.
Working with Folders
You can use folders to organize and manage other
types of collections:
other Folders
Saved Searches Collection Searches, Section
Searches, Text Searches, Chemical Structure
Searches, Unannotated Version Searches
References to any type of collection
Chem & BioOffice 2006 /E-Notebook
Creating a Folder
To create a new Folder collection:
1. In the Collection Tree, right-click your user
collection.
A menu appears.
2. Select New, then Folder.
3. A new Folder collection appears and you are
prompted to rename it.
Or, you may right-click an existing Folder collection
and select New, then Folder, to create a Folder
within a Folder.
Adding a Reference to the
Folder
You may add references to a folder if, for example,
you would like to keep the information from several
Pages/Experiments together, but the Pages/Exper-
iments exist in separate notebooks.
1. In the Collection Tree, click the Collection to
which you wish to create the reference.
2. While holding the CTRL and SHIFT keys, drag the
collection until the folder collection is high-
lighted.
3. Release the mouse.
The Reference appears in the Collection Tree.
Working with E-Notebook 517
Working with the Inbox
 Alternatively, you may right-click the collection you
wish to reference, and select Copy from the
Collection menu. Then, right-click the folder
collection and select Paste Reference.
Administrator
Working with the User
Configuration Folder
Within your user collection, there is a User
Configuration Folder, which can contain Reactants,
AutoText, and Templates.
To expand your User Configuration folder and view
its contents, either double-click it in the Collection
Tree or click the plus sign next to it:
Reactants Folder contains reactants whose
structures and properties you can add to Reac-
tion Sections. See Working with Reactants
Collections on page 518 for information.
AutoText Definitions contains predefined
text fragments that you can reuse to simplify
text entry in, for example procedure text. See
Creating New Autotext Definitions on page
546 for information about configuring Auto-
Text
Templates folder contains templates of
various types that you can use to avoid unnec-
essary reentry of data. See Working with
Templates on page 520 for more information.
518 Working with E-Notebook
Working with Reactants
Collections
Reactants are named shortcuts for a commonly
used compounds. These could be either common
reagents, or named compounds that you use
frequently.
You may populate reaction sections with the
properties of reactants.
E-Notebook provides 2477 commonly used
reactants, as shown below:
Adding a New Reactant to
an Existing Reactant Collec-
tion
To add a new reactant section to an existing collec-
tion.
1. Browse to the Reactants collection to which
you wish to add the Reactant, clicking the
collection in the Collection Tree to select it.
The Reactants collection appears, with the
existing reactants displayed in the right frame.
2. In the right frame, click the New Reactant
button.
CambridgeSoft
Working with the User Configuration Folder
 A new reactant section appears.
3. To rename the section, click the Section menu
icon and select Rename Section from the
menu that appears. Then type in a name.
4. Draw or import the structure using the Chem-
Draw tools.
The formula and molecular weight properties
are updated automatically. The compound
name may be updated as well. The compound
name will be displayed in the table of contents
for the Reactants Folder that contains this
reactant. (Click the Reactants Folder in the
Collection Tree to view its table of contents).
Adding a New Reactant
Collection
You can add a new Reactant Collection to your User
Configuration folder in E-Notebook. To add a new
Reactant Collection:
1. Right-click the Reactants Folder and select
New, then Reactants.
A Reactants collection appears, and you are
prompted to rename it.
2. Enter a name for the Reactants collection.
3. Click the New Reactant tool in the right frame.
Chem & BioOffice 2006 /E-Notebook
A new Reactant section appears.
You may populate reaction sections with the
properties of reactants.
Working with Table of
Contents
E-Notebook collections often have Table of
Contents sections associated with them. The Table
of Contents lists all of the collections that fall
directly within the selected collection in the
Collection Tree. For example, if a
Notebook contains Experiments, all of the
Experiments in the Notebook will be listed. Or, if a
Folder contains templates, all of the templates in the
Folder will be listed.
Double-clicking the link by any of the contained
collections listed will allow you to navigate to that
collection. You may also print the Table of
Contents to create a hardcopy of it. See Printing
Sections on page 585 for more information.
You can customize a Table of Contents to display
only the columns that are of interest to you. It is
also possible to sort items in the TOC in either an
ascending or a descending order.
Hiding Columns
You can hide columns in the Table of Contents. To
do this:
1. Right-click the column you wish to hide.
A menu appears.
2. Select Hide followed by the name of the
column.
The screen refreshes, and the column is hidden.
Working with E-Notebook 519
Working with Table of Contents
 Showing Columns
To show additional columns that are hidden, or are
not currently displayed in the Table of Contents.
Administrator
1. Right-click one of the columns in the Table of
Contents.
A menu appears.
2. Select Show Columns.
The Show Columns dialog appears, listing the
columns you may select for display in the TOC. The
columns that are currently displayed are denoted
with checkmarks.
3. Select and deselect columns to customize the
TOC display.
The columns you selected appear with checkmarks
next to them.
4. Click OK to close the dialog.
The dialog closes, and the screen refreshes to
display the additional columns.
520 Working with E-Notebook
Sorting Items in the TOC
You may sort items in the TOC in either an
ascending or descending order. To sort items in an
ascending order:
1. Right-click the column by which you wish to
sort the Table of Contents.
A menu appears.
2. Select Sort Ascending.
The items are sorted in ascending order according
to the column you selected.
To sort items in an descending order:
1. Right-click the column by which you wish to
sort the Table of Contents.
A menu appears.
2. Select Sort Descending.
The items are sorted in descending order by the
column you selected.
Working with Templates
E-Notebook gives you the ability to use templates
so that you can avoid reentering information
unnecessarily. For example, you may create a
template for a particular type of Experiment or
Page. It may contain data and notes that you often
use, or typical values for various properties.
CambridgeSoft
Working with Templates
To create a new template:
1. Within your User Configuration Folder, there
should be a My Template folder. Right click
this folder and select New, then the type of
template you wish to create.
The template appears within the folder.
2. Add any data you wish to the template.
In order to use the template as the basis for a new
experiment:
1. Select a notebook in the tree, and click the New
Experiment button:
A list of the available templates is displayed.
2. Select the desired template.
A new experiment appears within the
notebook. It contains all of the data that was in
the template.
Alternatively, simply click a template in the tree to
select it, then drag it into the notebook to create a
new Experiment.
Working with MS Office
Sections, Reactions, and
other Sections
Pages/Experiments in E-Notebook may contain
several different types of sections for your
experimental data. Just as you would use pages in a
paper notebook for recording various types of data,
you can use sections in E-Notebook for recording
MS Excel data, reactions, images, and other types of
information.
You may associate several types of sections with the
Page/Experiment:
Chem & BioOffice 2006 /E-Notebook
Working with MS Office Sections, Reactions, and other Sections
Reaction Sections
Captured Image Sections
Ancillary Data Sections
Table Sections
Spectrum and Spectra Sections
MS Word Sections
MS PowerPoint Sections
MS Excel Spreadsheet Sections
Your system configuration determines the types of
sections that are available in E-Notebook.
Reaction Sections
Reaction Sections can be used to show one step in
a reaction. You can draw and store a reaction using
the ChemDraw reaction field. The ChemDraw
Toolbar allows you to create a chemical structures
in the reaction field. The section contains a
stoichiometry grid as well, that analyzes the reaction
drawing automatically. The AutoText feature
updates the preparation text when you change the
reaction drawing and/or information in the
stoichiometry grid.
For detailed information about all the features of
Reaction sections, see Reactions in E-Notebook
on page 530.
Captured Image Sections
Captured Image Sections allow you to view and
annotate PDF images and documents, using the
same tools as Adobe Acrobat software. With
Captured Image Sections, you have the capability
for importing, exporting, viewing, and annotating
PDF documents. The section supports all image file
types such as JPG, GIF, PNG, TIFF and BMP.
For detailed information about importing,
exporting, clearing etc., see Working with
Captured Image Sections on page 556.
Working with E-Notebook 521
 Ancillary Data Sections
Ancillary Data Fields make it possible for you to
associate a file type which is not supported by
Administrator
E-Notebook. Although the file cannot be viewed
from within E-Notebook, a user can export it to a
selected location, then open it and view or edit it
from there.
When you import the file, the checksum, source
path, source file name, source file size and source
file type are populated automatically into the
E-Notebook.
For detailed information about all the features of
Ancillary Data Sections, see Working with
Ancillary Data Sections on page 569.
Table Sections
Tables enable you to organize data in an easily
interpreted, tabular format. The Table sections in
E-Notebook can be used to organize the chemical
properties of compounds that interest you. You can
add properties to a Table, pivot a Table, resize
columns and rows, and organize columns and rows.
Tables may contain several basic types of data
text data, numerical data, dates, or structures. You
may set up tables in different sections in
E-Notebook to contain different types of
information.
Another feature of tables is the ability for you to
add references to them. You can insert links to
other E-Notebook sections or collections into a
table. When you add a reference or link to a table,
you may navigate to the collection or section you
have referenced, simply by clicking a link in the
table cell.
See Working with Table Sections on page 570 for
more information.
522 Working with E-Notebook
Working with MS Office Sections, Reactions, and other Sections
Spectrum and Spectra
Sections
Spectrum Sections allow you to view and analyze
spectrum images, using the same tools as Galactic
GRAMS32 software. Thus, you can manage your
spectra data easily and effectively using Spectrum
and Spectra sections. You can import spectrum
images of various types. The section allows you to
copy and export spectrum images as well.
While the Spectrum Section can contain a single
spectrum, the Spectra section can contain multiple
spectra, organized in subsections or subtabs.
For more information, see Working with
Spectrum and Spectra Sections on page 566.
MS Word Sections
MS Word Sections allow you to view and edit MS
Word documents within E-Notebook sections, thus
managing the information that you normally record
in MS Word. You can import MS Word documents
from external sources, or export MS Word
documents and edit them in MS Word. The
toolbars displayed with an MS Word field in
E-Notebook are the toolbars that appear when you
open MS Word.
For more information, see Working with MS
Word Sections on page 558.
MS Excel Spreadsheet
Sections
MS Excel Section allows you to manage Excel
spreadsheets in E-Notebook. Its main purpose is to
provide you with a facility to create, modify, and
save your Excel spreadsheets within E-Notebook
environment.
You can import the MS Excel spreadsheets into
E-Notebook. The section allows you to export and
clear the slideshows as well. The toolbars displayed
CambridgeSoft
with an MS Excel field in E-Notebook are the 2. Select Print and a Print dialog box appears.
toolbars that appear when you open MS Excel
spreadsheets.

For detailed information on this topic, see

Working with MS Excel Spreadsheets on page
555.

Send2ENotebook and
Send2File
You can send a file from another application to
E-Notebook with Send2ENotebook, and have it
appear within E-Notebook in PDF format. The
objective of the Send2 feature is to allow the 3. Select the printer Send2ENotebook from the
convenient capture or various types of data from dropdown and click OK button.
other applications into E-Notebook system. This is
A dialog appears prompting you to log into the
typically output from either instrument control
E-Notebook.
applications or from various scientific analysis
software. PDF is the format for Send2 feature.

With the Send2File feature, you can also send such

a file in PDF format to your network outside the
E-Notebook so that you can bring it later into the
E-Notebook whenever you require. This is useful
for sending files from workstations that do not have
the E-Notebook application installed. Click Connect button to send to E-Notebook and
click the Send2File button to send to file.
To start the'Send2ENotebook or Send2File process:

1. Open the document you wish to send and Working with

expand File (or whichever menu option Send2ENotebook
accesses to the Print option).
To Send a document to E-Notebook,

1. Open the document in the appropriate

application (outside of E-Notebook).

2. Select the Print option in the application.

3. After you have selected the printer

Send2ENotebook, a dialog appears prompting
you to log into E-Notebook. Click the Connect
button to send to E-Notebook

Chem & BioOffice 2006 /E-Notebook Working with E-Notebook 523

Send2ENotebook and Send2File
 The following dialog box appears and you can set a. Click to open the User Collection.
the destination where you wish to send the
document in E-Notebook. A dialogue appears:
Administrator

4. Click the Set Target Collection Type button and

it displays a dialog where you can fill in the type
of your collection and click OK.

b. Click Select and you can select the User.

5. Select the Notebook or Collection where you
wish to send the document with the help of 7. Type the name of the section by which the
dropdown list. document will appear in the E-Notebook
collection in the following box:

The checkmark below is

8. Fill the properties in the Property Values List:
for the option to send the document in the Inbox
of the Collection.
6. Alternatively, you can select User In Box if you
wish to send the document to the Inbox in the
User Collection.

524 Working with E-Notebook CambridgeSoft

Working with Send2ENotebook
Click Send button to finish the Send to E-Notebook 5. Select File option as:
process:

6. Alternatively, click the Send2File button to send

to a location outside E-Notebook.

The following dialog box appears:

The document in PDF format gets added to your

collection in E-Notebook as a different section.

Working with Send2File 7. Click to open the following destination

To start Send2File, window and you can set the destination where
you wish to send the document. PDF is the
1. Open the document in the appropriate only format:
application (outside of E-Notebook).
2. Select the Print option in the application.
3. After you have selected the printer
Send2ENotebook, the E-Notebook Login
dialog appears.
4. Click the Connect button and the following
dialog box appears.

8. Click Save and the dialog appears as:

Chem & BioOffice 2006 /E-Notebook Working with E-Notebook 525

Working with Send2File
 9. Click the Send button to send the file to the The document in PDF format gets saved to your
specified location and close the Send2File specified location and you can bring it into the
process: E-Notebook later.
Administrator

Enterprise Working Offline

E-Notebook makes it possible for you to work in
offline mode. In offline mode, you are
disconnected from the network. When you
reconnect, you can upload the changes you made
offline to the central, E-Notebook database. See
Working Offline on page 550.

526 Working with E-Notebook CambridgeSoft

Working Offline
Chapter 28: E-Notebook Features
The following chapters of the guide provide Changes and Audit Trail information
instructions for using the features that are available about how to save and view your changes in
in E-Notebook. E-Notebook.
See the following topics for more information:
Browsing the Collection
Browsing the Collection Tree informa-
tion about how to browse through the E-Note-
Tree
book application Collections, and their contents, are organized in a
E-Notebook Workflows description of tree structure, called the Collection Tree, on the left
reactions and other workflows in E-Notebook side of the browsing screen. E-Notebook offers a
Working with E-Notebook Data informa- number of options for browsing collections.
tion about working with the various E-Note- To begin browsing collections, click the Browse
book fields, such as MS Word, chemical button at the top of the screen.
structure, and property lists and tables
The Collection Tree appears.
Rendering in E-Notebook description of
how to create various types of output from
E-Notebook, e.g., PDF's and MS Word docu-
ments. This topic also contains a description of
how to use the E-Notebook E-Signatures
feature

Enterprise Using the Inbox instructions

for working with your Inbox in E-Notebook

Enterprise Working Offline description

of how to work in offline mode
Working with Sections information about
the various features of E-Notebook sections:
renaming, copying, deleting, etc.
Working with Form Tools descriptions of
the E-Notebook form tools, such as the tools
used import documents and create new
sections
Working with Collections information
about the various features of E-Notebook
sections: renaming, copying, moving up and
down in the tree, etc.
See the following topics for more information:
Limiting Collection Browsing
Browsing from Home
Browsing at a Higher Level
Browsing the Entire Collection Tree
Use the Back and Forward arrows to the left of the
Browse button to navigate the Collection Tree view.
These arrows perform a similar function for the
collection tree that Back and Forward web browser
buttons perform for the browser window.

Chem & BioOffice 2006 /E-Notebook E-Notebook Features 527

Browsing the Collection Tree
 It is only possible for one E-Notebook user to edit To view the Collection Tree again,
an individual collection at a time. If another user is
1. Move your cursor to the left boundary of
editing a particular Collection and you select the
the section, until the double-headed
Collection in the tree, you will be presented with a
arrow appears again.
Administrator

message informing you that the Collection is locked

for editing by the other user. 2. Double-click.(Or, you may click the
touch bar at the left boundary of the
Showing and Hiding Collec- E-Notebook window).
tions The Collection Tree reappears.

The Collection Tree provides you with a means of
expanding and contracting collections so that you
only see the information you need.
To show the contents of a collection:
Click the plus sign next to the collection whose
contents you wish to see.
The collection is expanded, and you can view
its contents.
To hide the contents of a collection:
Click the minus sign next to the collection.
The collection is minimized, so that you cannot
see its contents.
Hiding the Collection Tree
Limiting Collection Browsing
You can limit your browsing by selecting a root
collection for the Collection Tree. The root
collection becomes the highest browsing level in
the Collection Tree. Limiting the Collection Tree
view can make it easier to find specific information.
To set a root for the Collection Tree:
1. Click the Browse button at the top of the
screen.
The Collection Tree appears.
2. Right-click the collection you wish to be the
root collection for browsing.
A menu appears.

It is possible to hide the Collection Tree if you

would to increase the screen area you have for
entering data into a section.
To hide the Collection Tree:
1. Move your cursor to the right boundary of the
tree, so that the cursor becomes a double-
headed arrow.
2. Double-click.
The Collection Tree is hidden.
Alternatively, you may click the touch bar at 3. Select Browse Here.
the right-border of the Collection Tree.

528 E-Notebook Features CambridgeSoft

Browsing the Collection Tree
 The collection you selected appears at the top Alternatively, you may select View, then Go To, then
of the collection tree. Home from the E-Notebook menu bar:

Browsing from Home

Browsing at a Higher Level
You can browse from your Home Collection, which
contains all of the collections associated with you as You can browse at a higher level in the Collection
a user of E-Notebook. This is the collection that Tree, and see all of the collections at that level.
appears when you first log in.
To browse at a higher level:
To browse to your Home Collection and bring the
Home Collection to the top of the Collection Tree: 1. Click Browse.

1. Click Browse. 2. The Collection Tree appears.

The Collection Tree appears. 3. Right-click a collection in the tree.

2. Right-click any blank area of the Collection A menu appears.
Tree.
A menu appears.

3. Click Go Home.
The Home Collection appears at the top of
Collection Tree.
4. Select Go Up To.
The collections that either contain or reference
the item are listed.
5. Select the collection that you wish to bring to
the top of the Collection Tree.
The collection you selected appears at the top
of the tree. Its contained collections and
contained references are displayed.

Chem & BioOffice 2006 /E-Notebook E-Notebook Features 529

Browsing the Collection Tree
 Alternatively, you may select View, then Go Up To
from the E-Notebook menu bar.
Administrator
Browsing the Entire Collec-
tion Tree
Browsing the entire Collection Tree enables you to
see all of the E-Notebook collections at once.
To browse the entire tree:
1. Click Browse.
The Collection Tree appears.
2. Do one of the following
Right-click any blank area of the Collection
tree, and select Browse All from the menu
that appears.
Right-click any collection in the tree, and
select Browse All from the menu that
appears.
530 E-Notebook Features
In E-Notebook menu bar, select View, then
Go To, and Browse All.
NOTE: The Browse All command will only be available if
you have the Read privilege for the collection at the top of the
collection hierarchy. If you do not have Read privilege for the
collection at the top of the hierarchy, it may be necessary to
conduct a collection search in order to view some of the
collections to which you have access. See Searching on page
609 for more information.
E-Notebook Workflows
This portion of the guide describes the workflows
in E-Notebook. The E-Notebook features can be
combined to support a number of different
workflows.
Reactions in E-Notebook
The following topics describe the features that are
used in an E-Notebook reaction section:
Drawing and Analyzing Reactions
Enterprise Editing Structures Using
ISIS/Draw
Working with the Name to Structure Feature
Working with the Reaction Toolbar
The Stoichiometry Table
Enterprise Working with Batch Explorer
Working with AutoText
CambridgeSoft
E-Notebook Workflows
Drawing and Analyzing Reactions 2. Using the ChemDraw tools, draw a reaction,
with reactants to the left of the arrow and prod-
You can draw a reaction using the ChemDraw
ucts to the right.
reaction field. When you draw a reaction, the
stoichiometry grid is automatically populated with
the properties of the reactants and products. If you NOTE: You can access a drawing menu by right-clicking in
remove a reactant or product from the the structure window. This menu allows you to, among other
stoichiometry grid, the corresponding structure will things, copy and paste structures.
be removed from the reaction drawing.
The ChemDraw Toolbar allows you to create a
chemical structure by connecting frequently used
Expanding the Drawing Window
substructures together. For more information
To expand the drawing window:
about using the ChemDraw Toolbar, please see the
ChemDraw User's Guide.
1. Double-click the titlebar of the chemical
Drawing a Structure or Reaction structure field.

To draw a reaction: The chemical structure field expands.

1. Click within a reaction field. 2. Using the ChemDraw tools, draw the structure
The ChemDraw toolbar appears. or reaction.

When you are finished editing, double-click the

frame of the chemical structure field to return it to
its original size in the form.

Enterprise Working with ISIS/

Draw
N
O 2

M
e
N
O 2
E-Notebook allows you to draw a reaction using
M
e
H
C(O
Et)3
ISIS Draw. If your system is configured to use
T
sOH

N
H2 N O
Et ISIS, you will be able to draw chemical structures
using the ISIS/Draw tools. For more information
about using the ISIS Draw Tool, please see the ISIS
Draw User's Guide.

Drawing a Structure or Reaction

To draw a reaction:

Chem & BioOffice 2006 /E-Notebook E-Notebook Features 531

E-Notebook Workflows
 1. Double-click within the reaction field and ISIS Working with the
Draw page will launch as shown:
Name=Struct Feature
With this feature, the names of compounds you
Administrator

draw in a reaction are added to the stoichiometry

2. Using the ISIS Draw tools, draw a reaction,
with reactants to the left of the arrow and prod-
ucts to the right:
When you are finished editing, click on the close
icon, to return to E-Notebook:
grid automatically, using ChemDraw's
Name=Struct feature. Prior to using this feature,
you need to have ChemDraw Ultra installed on your
machine.
The Name=Struct feature is designed to be as
smart as a real chemist, interpreting chemical names
into their most reasonable structures as they are
actually used by chemists.
To convert a name to a structure,
1. Draw the structures in the reaction section.
2. Save your changes.
The structure names appear in the stoichiometry
grid.
If you make changes to the reaction drawing, the
names will be updated automatically.
If you manually change the name of any structure in
the grid, your change will not be overwritten if you
alter the corresponding structure drawing.
Working with the Reaction
Toolbar
The reaction toolbar provides a number of features
for managing the reactants and products in your
reaction section.
The reaction toolbar normally appears just below
the reaction field.

532 E-Notebook Features CambridgeSoft

E-Notebook Workflows
Adding Structures with the Reaction
Toolbar
With the reaction toolbar, you can add reactants
and products from your Acronyms collections in
E-Notebook. There are two methods for adding a
structure with the reaction toolbar:
Using the Add Dialog to Add a Structure
Using Quick Add to Add a Structure
Using the Add Dialog to Add a Structure
The Add button on the reaction toolbar brings up a
dialog that allows you to select a structure and add
it to your reaction section.
To add a structure:
1. Click the Add button in the reaction toolbar.
The Select and Add Structure dialog appears,
displaying the acronyms in your Reactants
Folder:
2. Click the name of a structure in the list that
appears in the right frame to select it.
The structure is selected, and its structure
drawing appears.
Chem & BioOffice 2006 /E-Notebook
3. Click the down arrow by the Add button to
display the options for adding the structure to
the reaction section.
The options are:
Left of Arrow as Reactant adds the
structure to the reaction drawing to the left
of the arrow, and adds it to the reactants
table in the grid.
Top of Arrow as Reagent adds the
structure to the reaction drawing above the
arrow, and adds it to the reactants table in
the grid.
Right of Arrow as Product adds the
structure to the reaction drawing to the right
of the arrow, and adds it to the products
table in the grid.
To Grid as Reagent adds the structure to
the grid only, in the reactants table.
4. Select the option you desire from the menu.
5. Click the Add button.
The structure is added to the reaction section
in the manner you selected.
There are several options for filtering the acronyms
displayed in the dialog. See Filtering Acronyms
with the Reaction Toolbar on page 534.
Using Quick Add to Add a Structure
With the Quick Add button, you can bypass the
Add Structure dialog and remove several steps
from the process of adding a structure to your
reaction.
E-Notebook Features 533
E-Notebook Workflows
 To add a structure with the Quick Add button: Filtering Acronyms with the Reaction
Toolbar
1. Select an acronym from the dropdown list that
The reaction toolbar offers several options for
appears in the reaction toolbar. This dropdown
filtering acronyms before selecting one to add to
Administrator

lists all of the acronyms in your Reactants

Folder.
2. Click the down arrow by the Quick Add button
in the reaction toolbar.
The options for adding the structure to the reaction
section are displayed. The options are:
Left of Arrow as Reactant adds the
structure to the reaction drawing to the left
of the arrow, and adds it to the reactants
table in the grid.
your reaction section.
To jump to a particular structure:
1. Click the Add button in the reaction toolbar.
The Select and Add Structure dialog appears,
displaying the acronyms in your Reactants
Folder.
2. Begin typing the name of the structure you
wish to select.
The selected structure changes to match the
text you have typed.

Top of Arrow as Reagent adds the

structure to the reaction drawing above the beginning
arrow, and adds it to the reactants table in of
structure
the grid. name

Bottom of Arrow as Solvent adds the

structure to the reaction drawing below the
arrow, and adds it to the reactants table in
the grid.

Right of Arrow as Product adds the

structure to the reaction drawing to the right
Applying a Filter
of the arrow, and adds it to the products
table in the grid. To filter the acronyms that are displayed in the dia-
log:
To Grid as Reagent adds the structure to
the grid only, in the reactants table. 1. Click the Filter button at the top of the dialog.
The Apply Filter window is displayed.
To Grid as Solvent adds the structure to
the grid only, in the solvents table.

3. Select the option you desired.

4. Click the Quick Add button in the reaction

toolbar.

The structure you selected is added to your 2. From the dropdown list, select either Names
reaction. Starting with or Names Containing.

534 E-Notebook Features CambridgeSoft

E-Notebook Workflows
 3. Enter the text for the filter. In this example,
chloro was entered.
4. Click OK to close the Apply Filter window.
The filtered list of acronyms is displayed.
Removing a Filter
To remove a filter:
1. Click the Remove Filter button.
The filter is removed, and the entire list of
acronyms is displayed.
Defining a New Acronym with the Reac-
tion Toolbar
You can use the reaction toolbar to add new
acronyms to reactants collections in E-Notebook.
To do this:
1. In the reaction drawing, use the ChemDraw
tools to select the structure you wish to define
as an acronym.
2. Click the down Define button in the reaction
toolbar.
A dialog appears, prompting you to select the
Acronyms collection where you wish to add the
new acronym.
graphic
3. Select the collection and click the Create Here
button.
Chem & BioOffice 2006 /E-Notebook
The structure you selected is added to the
collection.
4. Close the dialog.
Deleting a Structure with the Reaction
Toolbar
You can use the reaction toolbar to delete structures
from a reaction.
To do this:
1. In the reaction drawing, use the ChemDraw
tools to select the structure you wish to delete.
2. Click the down Delete button in the reaction
toolbar.
The structure is deleted.
Working with the Stoichiom-
etry Table
The stoichiometry table calculates and stores
stoichiometric data for a reaction. It is filled in
automatically as you modify a reaction drawing. You
may change values manually as well.
It is also possible to add reactants from the
Collection Tree to the stoichiometry table.
Depending upon your system configuration, certain
of these properties may not appear, or additional
properties may be present.
Reactant properties:
Name the text name of the reactant.
Molecular Formula (MF) the chemical
formula that shows the number and kinds of
atoms in a molecule of the reactant.
Limiting? a yes or no value, indicating
whether the reactant is the limiting reactant in
the reaction.
Sample Mass the total quantity of the reac-
tant sample.
E-Notebook Features 535
E-Notebook Workflows
 Reactant Mass the total quantity of the
reactant.
Molecular Weight (MW) sum of the atomic
masses (atomic weights) of the atoms in the
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molecular formula, as set forth in the periodic
table.
Formula Mass sum of the atomic masses
(atomic weights) of the atoms in the formula of
the compound. This tends to be a more general
term than molecular weight, and can be applied
to compounds such as ionic compounds.
% by Weight (%Wt) the percentage of reac-
tant in the sample.
Moles the number of molecules of the reac-
tant / 6.023 x 1023.
Equivalents the proportion of the reactant
relative to the other components in the reac-
tion.
Molarity the number of moles per volume of
the reactant.
Volume (Vol) the three-dimensional
measurement of the reactant, such as mL, L, etc.
Density (D) the mass per unit volume of the
reactant.
Loading the number of reactant moles per
amount of the reactant sample.
Product Properties:
Name the text name of the product.
Molecular Formula the chemical formula
that shows the number and kinds of atoms in a
molecule of the product
Theoretical Mass the calculated mass of
product the reaction yields.
Actual Mass the actual mass of product the
reaction yields.
% Yield the ratio of the actual amount to the
theoretical amount.
% Purity the percentage of the actual
amount that is the product.
536 E-Notebook Features
Molecular Weight the sum of the atomic
masses (atomic weights) of the atoms in the
molecular formula, as set forth in the periodic
table.
Formula Mass the sum of the atomic
masses (atomic weights) of the atoms in the
formula of the compound. This tends to be a
more general term than molecular weight, and
can be applied to compounds such as ionic
compounds.
Theoretical Moles the calculated number of
moles of the product that the reaction yields.
Actual Moles the actual number of moles of
the product that the reaction yields.
Equivalents the proportion of the product
relative to the other components in the reac-
tion.
Loading the number of product moles per
amount of the product.
Adding Information to the Stoichiometry
Table
You can manually type stoichiometric information
into the stoichiometry table of a reaction section, as
well as add reactants from the Collection Tree.
To manually add information to a Stoichiometry
Table:
1. In the reaction section, click a cell in the
stoichiometry table.
2. Type the information into the cell.
The information is saved, and the text is
displayed in blue. If you have entered a number
and there are default units associated with the
property, the units are displayed. (See
Working with Numerical Units in Tables on
page 575 for more information).
3. Repeat the process for other cells in the table,
if necessary.
CambridgeSoft
E-Notebook Workflows
To enter reactant information into the Stoichiome- Information about the reactant is displayed on
try Table: the right side of the dialog box.
4. Click Add .
1. Right-click the a cell in the the Reactants
section of the Stoichiometry Table. The dialog box closes, and the Stoichiometry
Table is populated with information about the
A menu appears. reactant.

Removing Reactants and Products from

the Stoichiometry Table
You can remove all of the information pertaining to
a particular product or reactant from the
Stoichiometry Table automatically. If the reactant
you remove is the limiting reactant in the reaction,
the first remaining reactant becomes the limiting
reactant.
To remove a reactant or product from the stoichi-
ometry table:
1. Right-click the reactant or product you wish to
remove.
2. Select Add Reactant After, to add a reactant after A menu appears.
the selected item or Add Reactant Before, to add
a reactant before the selected item.
A dialog box appears. You are prompted to
browse for the reactant you wish to select.

2. Select Remove Product if it is a product, or

3. Browse to the reactant section with the reac-
tant you wish to add. (See the Working with
Reactants portion of this guide for information
about creating and using reactants collections.
If you wish, you may add a new reactant to
E-Notebook from the Add Reactant dialog).
Remove Reactant if it is a reactant.
A message appears, asking you if you are sure
you want to delete the reactant or product.
3. Click Yes.
The reactant or product is removed from the
Stoichiometry Table. If it was present in the
reaction drawing, it is removed from the
drawing as well.

Chem & BioOffice 2006 /E-Notebook E-Notebook Features 537

E-Notebook Workflows
 Working with Salts and Solvates in a
Reaction Section
In an E-Notebook reaction section, it is now easier
to represent a compound that is present in a salt or
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hydrated form. You can enter a formula that
accounts for salts and hydrates.
To enter a formula,
1. In the stoichiometry grid, double-click the
molecular formula cell.
A dialog appears.
2. Select a salt code or solvate from the dropdown
list. This list displays all of the salt codes and
solvates in your User Configuration folder.
3. Click OK to close the dialog
The formula you entered appears in the
stoichiometry grid.
Adding New Solvates and Salts
To add a solvate or salt that does not appear in the
dropdown list:
538 E-Notebook Features
1. Click the New Solvate button. (Or, to add a
new salt code, click the New Salt Code button).
A dialog appears and you can browse to solvate or
salts in your User Configuration folder.
2. Click New Solvate (or New Salt Code) and
enter the structure and name.
Working With Batch
Enterprise
Explorer
With the batch explorer, you can view a reaction
tree showing successors and predecessors of a
selected batch or compound.
To view Batch Explorer in the reaction section:
Click the Batch Explorer tool icon in
the reaction section.
A menu appears:
The options are:
Create Chemistry Experiment As Next
Step In same Chemistry Notebook
creates a new page/experiment within the
same notebook. To do this, select the product
CambridgeSoft
E-Notebook Workflows
 of the reaction and click the Create Chemistry
Experiment As Next Step In Chemistry Notebook
link.
Create Chemistry Experiment As Next
Step In Another Notebook creates a new
page/experiment in the same/different chem-
istry notebook.
To do this:
1. Select the product of the reaction and click the
Create Chemistry Experiment As Next Step In
link.
A dialog appears, prompting you to select the
Notebook collection where you wish to create
the experiment.
2. Click Select.
Chem & BioOffice 2006 /E-Notebook
Another dialogue appears which tells you that
a link is set and asks you to navigate to the
Reaction section of the selected Notebook
collection.
Create step Link To Existing Chemistry
Experiment creates a link between two
existing E-Notebook reactions in
same/different notebooks such that the
product of one reaction is a reactant in the
other. Both the reaction sections should
contain valid reactions. Hence a link is created
between two pre-existing pages.
To do this,
1. Click the Create Chemistry Experiment As Next
Step In link.
A dialog appears, prompting you to select a
section that contains a Reaction.
2. Click Select.
Another dialogue appears which tells you that
a link is set and asks you to navigate to the
Chemistry Experiment of the selected Notebook
collection.
View Batch Explorer displays a reaction
tree showing successors and predecessors of a
selected batch or compound.
To do this, select View Batch Explorer.
E-Notebook Features 539
E-Notebook Workflows
 A dialogue appears, prompting you to select a 1. To view the panning window, right-click within
molecule to explore. Use the scroll buttons to a blank portion of the Batch Explorer window.
select a molecule and click OK. A menu appears:
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2. Select Panning.
A dialog appears which allows you to use the
panning feature to zoom in on a particular
portion of the reaction tree.

The Batch Explorer window appears, and you

can right-click the molecule to view the options
to display predecessors or successors or all
steps of the batch.

3. Select the portion of the reaction tree in the

panning dialog and zoom to see the selected
portion as:

Panning Experiments in Batch Explorer

You can use the panning feature to zoom in on a
particular portion of the reaction tree.
For panning an experiment:
Flipping Experiments in Batch Explorer
You can flip experiments vertically or horizontally
in the Batch Explorer window in E-Notebook.
To flip an experiment:

540 E-Notebook Features CambridgeSoft

E-Notebook Workflows
 1. To view the flipping window, right-click within
a blank portion of the Batch Explorer window.
A menu appears.
2. Select Flip then Vertical or Horizontal.
A dialog appears which tells you that flipping
will change the way the entities are laid out and
asks you to continue.
3. Click the Yes button to flip and the following
window with flipped reaction sequence
appears:
Saving Experiments as Bitmap in Batch
Explorer
E-Notebook provides you with this feature to save
your Experiment Links Diagram from Batch
Explorer window as Bitmap files.
Chem & BioOffice 2006 /E-Notebook
To save an experiment as Bitmap:
1. Right-click within the blank portion of the
Batch Explorer window and a menu appears:
2. Click Save As Bitmap... to open the following
destination window and you can set the desti-
nation where you wish to save the Experiment
Link Diagram. Bitmap is the only format:
3. Click the Save button in the destination
window to save the Experiment Link Diagram
and dismiss the dialog.
Copying Experiments in Batch Explorer
E-Notebook provides you with this feature to copy
your Experiment Links Diagram from the Batch
Explorer window.
To copy an experiment:
E-Notebook Features 541
E-Notebook Workflows
 1. Right-click within a blank portion of the Batch 2. Select Print...
Explorer window to copy the experiment. A A Print Diagram dialog is displayed which
menu appears: allows you to make your selections:
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2. Click Copy to copy the Experiment Link

Diagram. 3. Click the Margins button to set the page
3. Paste the Experiment Link Diagram at your
margins.
desired location. 4. Click Preview button to see the Print Preview as
shown below:
Printing Experiments in Batch Explorer
You can print your Experiment Links Diagram
from the Batch Explorer window to maintain your
hardcopy archives.

To print an experiment:

1. Right-click within a blank portion of the Batch

Explorer window. 5. Click the Select Printer button to select the
printer.
A menu appears:

542 E-Notebook Features CambridgeSoft

E-Notebook Workflows
 The Print Setup dialog box appears, and you
can select the printer:
6. Make all your selections and click the Print
button.
The whole Experiment Link Diagram or
portion of the reaction tree you selected is
printed.
Selecting Experiments in Batch Explorer
E-Notebook provides you with this feature to select
the whole Experiment Links Diagram at once in
Batch Explorer window and perform other
functions.
To select the whole experiment:
1. Right-click within a blank portion of the Batch
Explorer window to select the experiment. A
menu appears:
Chem & BioOffice 2006 /E-Notebook
2. Click Select All to select the whole Experiment
Link Diagram, which looks like:
3. Perform the desired action on the selected
Experiment Link Diagram.
Working with Autotext
With the Autotext feature, you can add predefined
fragments of text to a field. This allows you to
create the contents of a text field quickly. You may
also add text that is pulled from other fields, for
example, reaction properties or values in the
stoichiometry grid of a reaction section. As you
update the reaction drawing and the stoichiometry
grid, your changes are reflected in the AutoText.
The example below shows the Preparation field of
the reaction section.
Inserting Reactants and Products with
AutoText
When you modify reactants and products in the
reaction drawing or stoichiometry grid, the
AutoText will be updated automatically.
E-Notebook Features 543
E-Notebook Workflows
 Inserting Reactants and Products from the
Stoichiometry Grid
To insert a reactant or product from the stoichiom-
etry grid,
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1. Right-click within the text field.
A menu appears.
2. Select Insert, followed by the name of the reac-
tant or product.
The name and properties of the reactant or
product you selected are inserted. The text
appears in a different color, and will be updated
automatically if you change the name or
properties in the stoichiometry grid.
Inserting New Reactants and Products
To insert a new reactant or product that is not yet
present in the stoichiometry grid,
1. Right-click within the text field.
2. Select Insert New Reactant... or Insert New
Product... from the menu that appears.
A blank row is added to the reactants or
products table.
3. Add information about the reactant or product
to the blank row.
The reactant or product is inserted into the
stoichiometry grid, and into the text field.
544 E-Notebook Features
You may also use the reactants/products button to
populate the AutoText. To do this,
1. With your cursor in the text field at the point
where you wish to insert the reactant or
product, click the reactants/products button
,
A menu appears.
2. Select one of the options:
Insert Reactant... allows you to browse
to a new reactant, and add it to the text and
stoichiometry grid.
Insert Product... allows you to browse to
a new product, and add it to the text and
stoichiometry grid.
Insert [Reactants] AutoText inserts
the text [Reactants], which you may then
right-click to select a reactant from the
stoichiometry grid, or to browse to a new
reactant.
Insert [Products] AutoText inserts
the text [Products], which you may then
right-click to select a product from the
stoichiometry grid, or to browse to a new
product.
The text is updated automatically if you change
the properties of the reactant or product.
Adding Items from the AutoText Pane
You can populate the text field by selecting items
from the AutoText pane. If you wish to add your
own, custom AutoText to this pane, you can set up
your own AutoText definitions. See Creating New
Autotext Definitions on page 546.
CambridgeSoft
E-Notebook Workflows
To add AutoText items to the text field: Organic was selected, and filled in
automatically:
1. Click the triangle button next to the word
AutoText in the upper left corner of the text
field.

The AutoText pane appears, listing the

available AutoText items. 4. You may right-click the colored text again to
modify your selection.
Certain items in the AutoText list may refer to other
data in the section. In the example below, double-
clicking Conditions in the AutoText pane
automatically fills the Reaction Conditions into the
text field. (The Reaction Conditions are shown in
the right side, below).

2. Double-click any of the items in the list to

insert the corresponding AutoText. (In this
example, Back extract was double-clicked).

Inserting Links with Autotext

From a text field, you can insert links to other
sections and collections in E-Notebook
To do this,

3. If words appear in different colored text 1. Click the Link button in the toolbar of
between brackets, this indicates that there are the text field.
multiple, possible values for the text. Right- A dialog appears, prompting you to select a
click the text within brackets to view a drop- collection or section for the target.
down list of the choices, and select one of the
values. In the example shown below, several
possible choices are listed for the layers.

Chem & BioOffice 2006 /E-Notebook E-Notebook Features 545

E-Notebook Workflows
 2. Browse to the collection or section, and click
the OK button.
A dialog appears, prompting you to enter the
text that will appear with the link.
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3. Enter the text or accept the default text, and
click the OK button.
The link appears within the text field.
4. Double-click the link to browse to its target.
Alternatively, you may right-click within the text
field, and select Insert Link... from the menu that
appears. Then follow the steps given above.
Inserting Custom Autotext
From a text field, you can insert custom AutoText.
To do this,
1. Right-click within the text field
A menu appears.
2. Select Insert Custom AutoText...
546 E-Notebook Features
The Insert AutoText dialog appears.
3. Select one of the AutoText items in the left
frame. In this example, Products is selected.
4. Click OK .
The AutoText appears in the text field.
5. Right-click the AutoText to see the options
associated with it, as shown in the example
below.
Creating New Autotext Definitions
Depending upon your system configuration, it may
be possible for you to set up your own AutoText
definitions for use in E-Notebook text fields. You
can then use these predefined fragments to add text
to the styled text field automatically.
1. Right-click the User Configuration point to
New, then select AutoText Definitions. (Or, select
an existing AutoText collection to modify, by
clicking the collection in the tree).
2. Enter a name for the new collection.
3. Enter the following information:
In the example below, AutoText has been set up so
that a user may automatically enter a sentence
regarding a machine type, and select from a list of
several machine types. Double-clicking Machine
Type in the AutoText list for any styled text field
CambridgeSoft
E-Notebook Workflows
would cause the corresponding sentence to appear.
Then, the user would right-click [MACHINE TYPES]
to select from the list of machine types.
TIP: The title of the keywords tab must match the field
descriptor exactly. In this case, MACHINE TYPES is the
name of the keywords tab, and [MACHINE TYPES]
appears in the AutoText item.
Autotext Based on Other Fields in the Section
You may also set up autotext that will fill in the
values from property lists and tables in a section. To
do this, you use a field name as a keyword in an
AutoText Item. The keywords and the field names
must match exactly in order for the substitution to
take effect.
Property Lists
For the AutoText Item to populate the styled text
field with all of the properties in a property list,
simply use the name of the property list as the
keyword in the AutoText Item. For example, say
there is a Conditions field, which is a property list
that contains reaction conditions. The AutoText
Item
Conditions: [CONDITIONS] will fill in all of the
Chem & BioOffice 2006 /E-Notebook
properties in the Conditions property list, for
example, Conditions: (Pressure: 200 atm,
Temperature: 100 C).
The keyword CONDITIONS followed by a property
name, such as [CONDITIONS:Temperature], will
populate the styled text field with that specific
property for example, Temperature: 100 C.
Tables
As with Property Lists, the AutoText Item referring
to a Table should contain bracketed UPPERCASE
keywords. For example:
[REACTANTS1] is added dropwise to a 500 ml
round-bottom flask charged with [REACTANTS2]
in [SOLVENT].
[REACTANTS1], [REACTANTS2], and [SOLVENT]
are replaced by the complete description of a
compound from one of these tables. REACTANTS1
refers to a column in the table REACTANTS (or, if
the table is pivoted with properties appearing as
columns, it refers to a row). REACTANTS is the name
of the table field.
In this case, the number such as in
REACTANTS1 and REACTANTS2 is used to
indicate that different compounds are to be used in
the AutoText. In order to determine which reactant
is to be used where more than one is present in the
reactants table, the user right-clicks the keyword
that appears within brackets. This displays a popup
menu containing all of the possible values.
The description that populates the styled text field
consists of the name (or text of the form Reactant
1 if the name is absent) followed by a list of the
properties of that compound.
To select individual properties, an AutoText Item
can contain a keyword followed by a property
name, e.g., [REACTANTS:Amount] is replaced by the
value from the Amount property for a reactant.
E-Notebook Features 547
E-Notebook Workflows
 Section Names as Categories 1. Right-click a cell in the Solvents Table of the
If you add multiple sections to an AutoText reaction section.
Collection, the section names will appear as A menu appears.
categories in the autotext list. For example,
Administrator

Standard and My AutoText are two section names

that appear as categories below:

Working with Solvents in a

Reaction Section
In E-Notebook, you may populate the solvents in
the reaction section from the solvents folder in
User Configuration Folder. These solvents are
named shortcuts for the commonly used solvents.
2. Select Add Solvent After to add a solvent after
the selected item, or Add Solvent Before to add
a solvent before the selected item.
A dialog box appears. You are prompted to
browse for the solvent you wish to select.

To enter a solvent into the Solvents Table:

548 E-Notebook Features CambridgeSoft

E-Notebook Workflows
 3. Browse to the solvents folder with the solvent To view the Inbox of a particular collection:
you wish to add. Select a solvent from the list.
This list displays all of the solvents in your User 1. Double-click the collection (or click the plus
Configuration folder. sign next to it) to expand it and view its
contents.
4. Click Add to close the dialog.
The collection expands to show the Inbox.
The formula you entered appears in the
solvents table.
If a solvent which you wish to add in the solvents
table is not listed in Solvents Folder in your User
Configuration Folder, then you can manually add
that in the table cell. To do this:

1. In the reaction section, right-click a cell in the

solvents table.
2. Select Add Solvent After or Add Solvent Before,
to add the solvent.
2. Click the Inbox to select it.
The Add Solvent dialog appears once again.
3. Checkmark the box Add Blank Solvent at the
The sections in the Inbox appear in the right
bottom of the dialog box. frame.

4. Click Add to close the dialog. 3. Click the Section menu to select one of the
sections to cut, copy, etc. as shown:

A blank row is added to the solvents table in the

reaction section where you can fill the solvent of
You can export the PDF document in the
your choice manually.
Inbox to a location outside the E-Notebook
Repeat the process for other cells in the table, if just as you would do in the Captured Image
necessary. sections.
4. Click Export PDF:
Enterprise Using the Inbox
The Inbox in E-Notebook allows the addition of
various types of documents as well as graphical data
into the E-Notebook system, typically output from
either instrument control applications or from
various scientific analysis software.

Chem & BioOffice 2006 /E-Notebook E-Notebook Features 549

Using the Inbox
 Enterprise Working Offline 3. Alternatively, click Work Offline button in the
Login dialog box when you are logging into
E-Notebook makes it possible for you to work in E-Notebook to go directly to the Offline
offline mode. In offline mode, you are folder:
disconnected from the network. When you
Administrator

reconnect, you can upload the changes you made

offline to the central, E-Notebook database.
In some cases, the system will be configured to
prevent you from working offline if you are
connected to the network.

Working With the Offline Folder You can work in Offline just as you would
To work in offline mode: normally work when you are connected.
4. You can go online again by clicking Connect
1. Select the Collection or Page you wish to work
button in the upper right corner of the screen.
in and drag it to Offline folder.
A dialog appears prompting you to log into the
When a collection is available offline, all of the
E-Notebook.
data associated with that collection, as well as
the references associated that collection, are
copied to the offline database.
2. Click the Work Offline button in the upper right
corner of the screen. This takes you to the
offline mode in which the Users home collec-
tion contains only two collections, the User
5. Click Connect button
Configuration folder and the Offline Collec-
tion. The contents of only these two collec- The Synchronization Changes Dialog
tions are available offline. appears listing each collection that has changed
and each new collection added.

550 E-Notebook Features CambridgeSoft

Using the Inbox
 6. Click the Synchronize button to update all the Creating an Offline Folder
changes that are stored offline in the online
If you do not yet have an offline folder, you can
content.
create one.To create a new, Offline collection:
7. Click the Show Details button.
1. In the Collection Tree, right-click your user
A dialog appears showing list of changes,
collection.
original contents and updated contents.
A menu appears.

a. Click OK to go back online and synchronize,

2. Point to New, then select Offline.
or...
A new Offline collection appears and you are
b. Click Discard Changes to remove the new
prompted to rename it.
collection or changes made in that
collection. A button, Work Offline appears in the upper right
corner of the screen. Clicking this button will
8. Click the Cancel button to cancel the login.
enable you to work in offline mode.
NOTE: Depending on your configuration, the Discard
Changes button may not always be available to you when NOTE: You should have to create the offline folder only
synchronizing the contents of a collection that has changed once. You can then continue to use the same folder.
offline.

Chem & BioOffice 2006 /E-Notebook E-Notebook Features 551

Using the Inbox
Administrator

552 E-Notebook Features CambridgeSoft

Using the Inbox
Chapter 29: Working with Data in
E-Notebook
E-Notebook enables you to work with many,
diverse types of data, then keep related data
together in collections such as Experiments and
Pages.
See the following topics for information about
working with various types of data:
Working with Chemical Structure Data
Working with Images in Chemical Structure
Fields
Working with Database Tables
Working with Captured Image Sections
Working with Image Viewer Sections
Working with MS Excel Spreadsheets
Working with MS Word Sections
Working with MS PowerPoint Slideshow
Sections
Working with Property Lists
Working with Spectrum and Spectra
Sections
Working with Styled Text
Working with Ancillary Data Sections
Working with Subsections
Working with Table Sections
Chem & BioOffice 2006 /E-Notebook
Working with URL Displays
NOTE: Your system configuration determines what types of
data you can add to the sections in E-Notebook. To model
your workflow and ensure that E-Notebook accommodates
the data types you frequently use, your system configuration
may include modified versions of these data types. Also,
certain data types may not appear in your configuration, and
additional, custom data types may have been added.
Working with Chemical
Structure Data
Chemical structures can be drawn with the use of
the ChemDraw Toolbar. The ChemDraw Toolbar
allows users to create a chemical structure by
connecting frequently used substructures together.
For more information about using the ChemDraw
Toolbar, please see the ChemDraw User's Guide.
It is also possible to paste standard image files into
chemical structure fields, then user the ChemDraw
toolbar for annotation, such as text and arrows.
Text in the chemical structure fields is searchable.
Drawing a Structure
To draw a chemical structure:
Working with Data in E-Notebook 553
 1. Click within a chemical structure field. You can paste standard image files into chemical
The ChemDraw toolbar appears. structure fields, then use the ChemDraw toolbar for
annotation, such as text and arrows. Text in the
chemical structure fields is searchable.
Administrator

Inserting an Image a Structure

To insert an image into a chemical structure field:

1. Copy the image onto the clipboard. You may

do this by, for example, selecting the Select All
and Copy commands when the image file is
open in Microsoft Photo Editor.
2. Right-click within the structure field in
E-Notebook.
A menu appears.
3. Point to Edit, and click Paste.
2. Using the ChemDraw tools, draw a structure or The image appears in the chemical structure
reaction. field.

TIP: You can access a drawing menu by right-clicking in the 4. Use F7 to zoom in, and F8 to zoom out.
structure window. This menu allows you to, among other
things, copy and paste structures. Annotating the Image
To annotate the image:
Expanding the Drawing Window
1. Click the text tool in the ChemDraw
To expand the drawing window:
toolbar.
1. Double-click the frame of the chemical
2. Click in the chemical structure field, and type
structure field. any text you would like to enter.
The chemical structure field expands.
The text appears in the field.
2. Using the ChemDraw tools, draw the structure
or reaction. 3. Click the arrow tool in the tool bar to select it
if you would like to draw arrows to annotate
3. When you are finished editing, double-click the
the image.
frame of the chemical structure field to return
it to its original size in the form.
Working with Database
Working with Images in Tables
Chemical Structure Fields Database Tables are used to pull in data from an
Chemical Structure Fields can also be used to external database and display it in E-Notebook.
display and annotate standard image files. The data is for display only and cannot be edited.

554 Working with Data in E-Notebook CambridgeSoft

The table of contents is an example of a database
table.
In some configurations, database tables may be
filled in based on a value that you enter elsewhere in
a form. For example, the value you enter into a
particular property list field may be used to look up
and display related data, which will appear within
the database tables.
Working with MS Excel
Spreadsheets
You can use MS Excel spreadsheets to manage
Excel data in E-Notebook.
To create a new MS Excel Section:
1. In the Collection Tree, click the Page or
Experiment to which you would like to add the
section.
2. Click the New Section button.
A list of the section types that can be added
appears.
3. Select MS Excel Spreadsheet.
A new MS Excel Spreadsheet appears in the
right frame.
4. Edit the spreadsheet just as you would
normally edit a spreadsheet in MS Excel.
Chem & BioOffice 2006 /E-Notebook
Importing an MS Excel document
To import an MS Excel document,
1. Click the import tool icon for the MS Excel
field.
A menu appears when you click the icon.
2. Select Import MS Excel Spreadsheet.
A dialog box appears, and you are prompted to
select the file.
3. Select the file and click the Open button.
The spreadsheet appears in E-Notebook. The
section of the spreadsheet that was most
recently active is displayed.
To export the file:
1. Click the import tool icon:
A menu appears.
2. Select Export MS Excel Spreadsheet
A dialog appears prompting you to select a
location for the exported file.
3. Enter a destination for the file and a file name,
and click the Save button.
The file is exported to the location you
selected.
To clear an MS Excel file from a section in
E-Notebook:
1. Click the import tool icon:
A menu appears.
2. Select Clear MS Excel Spreadsheet
Working with Data in E-Notebook 555
 You are prompted to confirm whether you 1. Click the import tool icon for the PDF field.
wish to clear the document file. A menu appears when you click the icon.
3. Click OK. 2. Select Import PDF.
The file is cleared.
Administrator

Working with Captured

Image Sections
You can use Captured Image Sections to manage
both PDF files and standard image files in
E-Notebook in PDF format. A dialog box appears, and you are prompted to
select the file.
To create a new Captured Image Section:
3. Select the file and click the Open button.
1. In the Collection Tree, click the Page or The PDF document appears in E-Notebook.
Experiment to which you would like to add the
section. Enterprise To export the PDF file:
2. Click the New Section button.
1. Click the import tool icon.
A list of the section types that can be added
appears.
3. Select Captured Image.
The new section appears within the Page. The
image below is an example of a PDF Viewer A menu appears.
section.
2. Select Export PDF.
With this field you may import a PDF document or
A dialog appears prompting you to select a
a standard image file in PDF format.
location for the exported file.
3. Enter a name and destination for the file, and
click the Save button.
The file is exported to the location you
selected.
To clear a PDF file from a section in E-Notebook:
1. Click the import tool icon:
A menu appears.
2. Select Clear PDF.
You are prompted to confirm whether you
wish to clear the document file.
Importing and Exporting a PDF File 3. Click OK.
To import a PDF document: The PDF file is cleared.

556 Working with Data in E-Notebook CambridgeSoft

Importing an Image File 2. Select any of the editing tools present in the
menu to edit or add some text in the image.
You can import any GIF, JPG, JPEG, TIF, TIFF,
PNG or BMP image. Once imported, the image file For example, you can click the Note Tool button
gets converted to a PDF document and you may to add your comments. A dialog is displayed
edit or add text, as the Adobe Acrobat menu and within the image field where you can type your
editing tools are also present. comments as shown:
To import an image,
1. Click the import tool icon for the image field.
A dialog box appears, and you are prompted to
select the file.
2. Select the file and click the Open button.
The image in the form of a PDF document
appears in E-Notebook.

Annotating an Image File

In the Captured Image section the image is
converted to PDF upon import and you may edit or Similarly, you can use the other annotation
add text, as Adobe Acrobat menu with editing tools tools in the image field.
are also present.
To annotate, Working with Image Viewer
1. Go to the PDF converted imported image file. Sections
You can use MS PowerPoint Sections to manage
images in E-Notebook.

1. To create a new, Image Viewer Section:

2. In the Collection Tree, click the Page or Exper-

iment to which you would like to add the
section.

3. Click the New Section button:

The Adobe menu with Acrobat annotation

tools is present above the image in the
Captured Image section, as shown below:
A list of the section types that can be added
appears.

4. Select Image.

Chem & BioOffice 2006 /E-Notebook Working with Data in E-Notebook 557
 A new Image section appears in the right
frame. With this field, you can import images
such as GIF, JPG, JPEG, TIF, TIFF, PNG,
BMP, etc. and add text for explanation.
Administrator
Importing and Exporting an Image File
To import an Image File:
1. Click the import tool icon for the Image field.
A menu appears.
2. Select Import Image.
A dialog box appears, and you are prompted to
select the file.
3. Select the file and click the Open button.
The image appears in E-Notebook.
558 Working with Data in E-Notebook
To export the Image file:
1. Click the import tool icon:
A menu appears.
2. Select Export Image.
A dialog appears prompting you to select a
location for the exported file.
3. Enter a file name and destination for the file,
and click the Save button.
The file is exported to the location you
selected.
To clear an Image file from a section in
E-Notebook:
1. Click the import tool icon:
A menu appears.
2. Select Clear Image.
You are prompted to confirm whether you
wish to clear the document file.
3. Click OK.
The image is cleared.
Similarly, you can copy the images from the Image
sections and paste them in the other sections in
E-Notebook or in other applications.
Working with MS Word
Sections
You can use MS Word Sections to manage
information that you would normally record in MS
Word. This feature makes it possible for you to
keep MS Word information with related,
E-Notebook information. You can edit this data
just as you would edit an MS Word document,
either editing it within E-Notebook, or exporting it
to MS Word to take advantage of the full MS Word
feature set.
To create a new MS Word Section:
CambridgeSoft
 1. Click the collection in the collection tree to
which you would like to add the MS Word
Section.
NOTE: In the preconfigured E-Notebook, you can
only add an MS Word Section to a Page).
2. Click the Sections icon on the right side of the
screen.
A menu appears.
3. Select New.
A list of the Section types that can be added
appears.
4. Select MS Word Document.
A new MS Word Document appears in the
right frame.
NOTE: An MS Word Section is one of the preconfigured
Sections of E-Notebook. Depending upon how your system
administrator has chosen to configure E-Notebook, this
Section may not be available to you, or it may be available in
a modified form. For example, an MS Word document may
exist as one of multiple fields within a section.
Working with MS Power-
Point Slideshow Sections
You can use MS PowerPoint Sections to manage
MS PowerPoint slideshows in E-Notebook.
Chem & BioOffice 2006 /E-Notebook
To create a new MS PowerPoint slideshows Section:
1. In the Collection Tree, click the Page or
Experiment to which you would like to add the
section.
2. Click the New Section button:
A list of the section types that can be added
appears.
3. Select MS PowerPoint Slideshow.
A new MS PowerPoint slideshow appears in
the right frame.
4. Edit the slideshow just as you would normally
edit a slideshow in MS PowerPoint.
Importing and Exporting an MS Power-
Point slideshow
To import an MS PowerPoint document,
1. Click the import tool icon for the MS
PowerPoint field.
A menu appears.
2. Select Import Slideshow
A dialog box appears, and you are prompted to
select the file.
3. Select the file and click Open.
The slideshow appears in E-Notebook.
The notes associated with a slide will be rendered
along with the slide.
To export the MS PowerPoint file:
1. Click the import tool icon.
A menu appears.
2. Select Export Slideshow
Working with Data in E-Notebook 559
 A dialog appears prompting you to select a You are prompted to confirm whether you
location for the exported file. wish to clear the document file.
3. Enter a file name and a destination for the file, 3. Click OK.
and click Save. The slideshow is cleared.
Administrator

The file is exported to the location you

selected. Working with Property Lists
Property Lists are used in forms to record various
To clear an MS PowerPoint file from a section in
types of data properties. An example is shown
E-Notebook:
below:
1. Click the import tool icon:

A menu appears.
2. Select Clear.... Property lists may contain the following data types:

Data type Action to take

Date Click the date box, and select a date and time.

Text Enter text.

Number Enter a number. Certain properties may have default

units associated with them, which will appear when
you enter the number.

Enumerated Value Choose a value from the drop-down list.

560 Working with Data in E-Notebook CambridgeSoft

Adding Properties to Property Lists
To add a property to a property list:
1. Right-click the within the property list in a
section.
A menu appears.
2. Select Add Property....
The Add Property dialog box appears, listing
the properties you may add.
3. Click the property you wish to add. You may
use CTRL+click to select multiple properties,
or SHIFT+click to select a range.
4. Click Add.
The property or properties appear in the list.
You system configuration determines which
properties may be added to the list, and which
properties appear by default.
Chem & BioOffice 2006 /E-Notebook
Removing Properties from a Property
List
To remove a property from a property list:
1. Right-click the property you wish to remove
from the Property List.
A menu appears.
2. Select Remove Property.
A message appears, asking you if you are sure
you want to remove the property.
3. Click Yes.
The property is removed from the Property
List.
Setting and Editing Values in a Property
List
You can set and edit values for the properties in a
property list, such as the list shown below.
To set or edit the value of a property:
1. Click a cell in the property list.
The values you can enter will depend upon the
data type of the specific property.
2. Enter an appropriate value.
Data Action to take
type
Date Click the date box, and select a
date and time.
Text Enter text.
Working with Data in E-Notebook 561

Data Action to take
type
Administrator
Number Enter a number. Certain prop-
erties may have default units
associated with them, which
will appear when you enter the
number.See Working with
Numerical Units in Property
Lists on page 563 for more
information.
Enumer- Choose a value from the drop-
ated Value down list.
3. Click elsewhere in the section.
The value is displayed in the cell.
Depending upon your system configuration, certain
properties may have one or several of the following
attributes:
Read Only certain properties may be for
display only, and it may not be possible to edit
them.
Required it may not be possible to delete a
particular property from a property list. If a
property is required, you will be presented with
an error message when you attempt to delete it.
Not Blank it may be necessary to enter a
value for a particular property before you can
perform a transition on the collection. For
example, an experiment collection may be set
up such that it is necessary to enter an equip-
ment ID before you can close the experiment.
If this is the case, you will be prompted to enter
the values when you attempt to perform the
transition.
562 Working with Data in E-Notebook
Validated Values you enter into property list
may be checked against an external database, to
ensure that they are valid values. In this case, if
you enter an invalid value, you will receive an
error message, and E-Notebook will not accept
the value.
Enumerated from a database values
displayed in a dropdown list for any particular
property may be pulled from an external data-
base.
When searching with the Property Query Field,
numeric values for properties are interpreted by
evaluating the longest possible set of characters that
are converted into a number, starting with the first
character. For example, a search for 37.5 will find
37.5g. A search for 2 will find 2 ATM/50. Also,
conversion is performed to find equivalent values.
For example, when searching over a volume
property for which mL are the default units, a
search for 50 mL will return both 0.05 L and 50 mL.
Working with Enumerated Lists in Prop-
erty Lists
Property lists may contain enumerated lists, which
may have default values associated with them. Your
system configuration determines the enumerated
values for any given property.
A property in E-Notebook may be configured so
that it will contain a list of enumerated values. You
may then select one of the values from a dropdown
list that appears in the property cell. This list of
values displayed in a dropdown list for any
particular property may be some values either
manually entered or pulled from an external
database by the administrator.
CambridgeSoft
For example, there may be a property of stored as grams. You may also enter any of the
Collection's Name under Metadata Properties permitted mass units shown below, such as mg or
in search mode. Once you select the checkbox, you kg.
may enter the values only from the dropdown list as
shown: Type of Permitted Units
Measurement

density g/ml
g/ml
mg/ml
g/l
mg/l
Similarly, you can select the values for other g/l
properties in the list from the dropdown lists after kg/l
clicking the checkboxes opposite them. kg/m3

Working with Numerical Units in Prop- length m

erty Lists
Property lists may contain numerical properties, nm
which may have default units associated with them. m
Your system configuration determines the default mm
units for any given property. The following types of cm
measurements may be specified or displayed in the
permitted units shown below. mass g
g
For example, there may be a property of mass mg
and its default units may be grams (g). If you enter kg
a numerical value into the property without
specifying units, the units will be displayed and
molality (quantity per mass mol/kg
of solvent or substrate) mol/g
mmol/kg
mmol/g
mol/kg
mol/g

molar mass g/mol

kg/mol
dalton
D
kD

Chem & BioOffice 2006 /E-Notebook Working with Data in E-Notebook 563
 Type of Permitted Units Type of Permitted Units
Measurement Measurement
Administrator

molarity (quantity per mol/l volume ml

volume of solution) molar l
mmolar l
molar m3

moles (quantity of mmol When you are in Search mode, the property query
substance) mol field allows you to find all equivalent values entered
mol in various units that share the same unit type. For
example, a search for a volume of 500 mL will
return both 500 mL and 0.5L. The search will
normality (ion equivalents N assume the default units for the property if you do
per volume of solution) mN not enter units. Using the same example, if mL were
N the default unit for a volume property, and a search
were conducted for a property value of 0.5, no hits
pressure atm would be returned. A search for 0.5 L would return
Pa both 500 mL and 0.5 L.
kPa
torr Creating a Reference within a Property
bar
List
mbar
Within a property list, you can add a link to another
temperature C collection/section in E-Notebook or a link to an
K external URL. This makes it easy to browse back
F and forth between related data.

time s Adding a Link from a Property List to an

ms E-Notebook Collection
s
min To add a link from a property list cell to a collection
hr in E-Notebook,

1. In the Collection Tree, click the collection

velocity m/s containing the property list, then select the
km/hr section containing the property list.
mi/hr
The section containing the property list
appears.
2. Click the cell of the property list to which you
wish to add the reference.

564 Working with Data in E-Notebook CambridgeSoft

 3. In the Collection Tree, click the collection you 4. Right-click within a property list cell and select
would like to reference and, holding the mouse Paste Reference from the menu that appears.
button down, drag the collection into the
The reference is added to the property list cell,
upper-left corner of the property list cell, until
and a small arrow appears in the upper-left
the cursor displays a small arrow, as shown
corner of the cell. Clicking the arrow will
.
display the section you have referenced.
4. Release the mouse.
The reference is created, and a small arrow
appears in the upper-left corner of the property
list cell. Adding a Link from a Property List to an External
URL

5. You can click the arrow in the property list cell
to navigate to the collection you have refer-
enced, and click the Back arrow to
return to the property list.
Alternatively, you may right-click the collection you
wish to reference and select Copy. Then, right-click
within the property list to which you are adding the
reference, and select Paste Reference.
Adding a Link from a Property List to an
E-Notebook Section
To add a link from a Property List cell to an external
URL or an intranet URL,
1. Right-click within the property list cell to
which you wish to add the reference.
A menu appears.
2. Select Edit Reference.
The Edit Reference dialog appears.
3. Enter the URL and click OK.

To add a link from a property list cell to a section in

E-Notebook:
1. In the Collection Tree, click the collection
containing section that you would like to
reference, then select the section.
The section to which you would like to make a
reference appears.
2. Right-click the Section menu icon, and select
Copy Section.
3. In the Collection Tree, click the collection The reference is added to the property list cell,
containing the property list to which you are and a small arrow appears in the upper-left
adding the reference, then click the section that corner of the cell. Clicking the arrow will
contains the property list. display the URL you have referenced.

Chem & BioOffice 2006 /E-Notebook Working with Data in E-Notebook 565
 Working with Spectrum and The new section appears within the Page. The
image below is an example of a spectrum
Spectra Sections section.
You can manage your spectra data easily and
Administrator

effectively using Spectrum and Spectra sections.

This topic refers to sections that contain Galactics
GRAMS32 software tools.

NOTE: Spectra may be handled differently in your specific

configuration of E-Notebook.

To create a new Spectra section for multiple spectra:

1. In the Collection Tree, click the Page or
Experiment to which you wish to add the
Spectra section.
2. Click the New Section button.
A list of the section types that can be added
There are two types of sections for spectra. Each appears.
type of section can also contain a set of properties
3. Select Spectra.
for each spectrum, and notes about each spectrum.
The new section appears within the Page. You
Spectrum Section this section can contain a
may add as many spectrum subsections as you
single spectrum.
wish (by clicking the New Spectrum button).
Spectra Section this section can contain The image below shows a spectra section with
multiple spectra, organized in subsections or two spectrum subsections.
sub-tabs.
To create a new Spectrum section for a single spec-
trum:
1. In the Collection tree, click the Page or
Experiment to which you wish to add the
Spectrum section.
2. Click the New Section button.
A menu appears, listing the types of sections
that you may add.
3. Select Spectrum.

566 Working with Data in E-Notebook CambridgeSoft

Adding a Spectrum
To add a spectrum:
1. From within a section with a spectrum field,
click the import/export button:
A menu appears.
2. Select Import Spectrum.
The Import Spectrum dialog box appears and
you are prompted to select a spectrum image
file.
3. Select a spectrum and click Open.
The Import Spectrum dialog box closes and
spectrum image appears in the section.
Replacing a Spectrum
If you would like another spectrum image to take
the place of an image within a spectra or spectrum
section, you can replace the image. To do this, you
may either import a new image, as described above.
The new image will replace the old. Or, you may
copy an image from another section.
Chem & BioOffice 2006 /E-Notebook
To replace a spectrum image by copying and past-
ing another image:
1. From within the section containing the image
you wish to copy, click the spectrum
button:
A menu is displayed.
2. Select Copy Spectrum.
3. Browse to the section containing the spectrum
image you wish to replace.
4. Click the spectrum button.
5. Select Paste Section.
The new spectrum image is replaces the image
in the section.
Zooming in on a Spectrum Peak
To zoom in on a spectrum peak:
1. Click the spectrum image and drag your mouse
to draw a box around the area you wish to
zoom.
2. Click within the box.
The zoomed view appears.
3. To zoom out again, simply right-click in the
spectrum image.
Other Fields in a Spectrum Section
Spectrum Properties List use this list to
store Analyst, Type, and Date.
Notes Record any notes that pertain to a
Spectrum in the text field.
Working with Data in E-Notebook 567
 Working with Styled Text
Styled text boxes can be used to record notes,
preparation information, etc. A styled text box is
Administrator
often included in a form with other types of data,
making it possible to combine text notes with
related data. Certain styled text fields in your
configuration may have Autotext associated with
them. You can use the Autotext feature to populate
the styled text field automatically. See Working
with Autotext on page 543 for more information.
To format the text:
1. From within a section, click within the styled
text box.
A cursor appears in the box, and you can begin
typing.
Immediately above the box, there may be a
toolbar for formatting the text.
You may change the following formatting options:
Font type
Font size
Bolded Text
Italicized Text
Superscript
Subscript
Left-alignment
Center-alignment
Right-alignment
568 Working with Data in E-Notebook
You can also type the text, highlight it, then select
the text options you wish to apply to it. Standard
editing keys such as Control+C (for copy) and
Control+V (for paste) may be used as well.
Note that in your system configuration, the styled
text box may not include the formatting toolbar. In
addition, a styled text box may be read-only,
meaning that you can view but not edit its contents.
A styled text box may also be required: it may be
necessary for you to enter text into the box before
you can perform a transition on a particular
collection. For example, it may be necessary for you
to enter text into a text field before you can close a
Page or Experiment.
Working with Subsections
In E-Notebook, certain sections may be set up to
contain other sections, known as subsections. The
subsections appear as subtabs within a section.
To add a subsection to a section, for example to a
Spectra section:
1. Click the New Spectrum button.
A new spectrum in the form of a subsection
appears within the Spectra section.
NOTE: The options for a subsection button under the
section will differ according to your configuration.
You can manage a subsection just as you would a
section. See Working with Sections on page 583
for more information.
CambridgeSoft
Working with Subsections in Button To create a new Ancillary Data section:
View 1. In the Collection Tree, click the Page or
Experiment to which you would like to add the
You can manage subsections as you would sections.
Ancillary Data Section.
Your system administrator may configure
2. Click the New Section button in the right
E-Notebook such that the subsections are forced
frame:
into button view and VCR style buttons are
A list of the section types that can be added
displayed to navigate the sections in a subsection, as
appears.
shown below.
3. Select Ancillary Data.
A new Ancillary Data section appears in the
right frame.
You may then scroll through the subsections using 4. Click the import tool to import a file:
the arrow buttons, or right-click a subsection name 5. A menu appears.
and select Go To in order to browse to a specific 6. Select Import....
subsection. A dialog box appears, and you are prompted to
select the file.
Working with Ancillary Data 7. Select the file and click Open.
Sections The type of file and its size are displayed in
E-Notebook.
You can use an Ancillary Data section to associate To edit a stored document file, you must first export
a file which is not supported by E-Notebook with it to another location.
an E-Notebook page or experiment. When you
1. Click the import tool.
import the file, the checksum, source path, source
file name, and your user name are populated A menu appears.
automatically.

Although the file cannot be viewed from within

E-Notebook, it can be exported to a selected
2. Select Export....
location, then opened, viewed, or edited from there.
A dialog appears prompting you to select a
location for the exported file.
3. Enter a destination for the file and a file name,
and click Save.
4. Open the appropriate application, and open
the file you created.
5. Edit the file just as you normally would.
6. Save the file.

Chem & BioOffice 2006 /E-Notebook Working with Data in E-Notebook 569
 7. From the section in E-Notebook, click the To add a column:
import tool again.
1. Browse to the section that contains the table.
A menu appears.
2. Right-click the table at the location where you
Administrator

8. Select Import....
would like to add the column.
A dialog appears and you are prompted to
select the file to import. A menu appears.

9. Select the file and click Open.

The edited document with your changes is

stored in E-Notebook.

To clear a stored document file from a section in

E-Notebook:

1. Click the section tools icon.

A menu appears.

2. Select Clear Stored Doc.
3. You are prompted to confirm whether you
wish to clear the document file.
3. Select Add Property Before, to add a property
before the current property, or Add Property
After, to add a property after the current prop-
erty.

A dialog box appears with a list of the

properties you may add.

Click OK. The file is cleared.

Working with Table Sections

You can use Table sections to organize the chemical
properties of compounds that interest you. You can
add properties to a Table, pivot a Table, resize
columns and rows, and organize columns and rows. 4. Highlight the property you wish to add to the
You can also insert links to other E-Notebook table.
sections or collections into a table.
5. Click Add.
Adding Columns and Rows to a Table
The property appears as a column in the table,
You can add columns and rows to a table in immediately in front of the location you
E-Notebook. selected.

570 Working with Data in E-Notebook CambridgeSoft

To add a row: To remove a column:
1. Right-click the table at the location where you 1. Right-click the column or property you wish to
would like to add the row. remove from the table.
A menu appears.
A menu appears.

2. Select Add Row Before, to add a row before the

current row, or Add Row After, to add a row
after the current row.
2. Select Remove Property.
NOTE: If the Table has been pivoted, you would select A dialog box appears, asking you if you are sure
Add Property to add a row, and Add Column to add you want to delete the property from the table.
a column. (Pivoting transposes the rows and columns in
the table). 3. Click Yes.

The column is removed from the table.

Removing Columns and Rows from a
Table NOTE: If the table has been pivoted, right-click a row to
You can remove columns and rows from a table. remove a property.

To remove a row:

1. Right-click the row you wish to remove from

the table.
A menu appears.
2. Select Remove Row.

A dialog box appears, asking you if you are sure

you want to delete the row from the Table.
3. Click Yes.

The row is removed from the Table.

Chem & BioOffice 2006 /E-Notebook Working with Data in E-Notebook 571
 Organizing Columns and Rows in a Move a Row
Table To move a row up or down:
You can easily rearrange rows and columns in a
table, organizing them so that the information is 1. In the table, right-click the row you wish to
Administrator

displayed more effectively. You can move columns move.

left or right, move rows up or down, and sort data A menu appears.
in the table in ascending or descending order.
Move a column
To move a column left or right:
1. In the table, right-click the column you wish to
move.
A menu appears.

2. Select Move Row Up or Move Row Down.

The row is moved either up one place or down
one place in the table, depending upon your
selection.
Sort Data by a Property

To sort the table by a particular property:

2. Select Move Property Left or Move Property
1. Right-click the row or column corresponding
Right.
to the property by which you wish to sort the
The column is moved either one place to the table.
left or one place to the right, depending upon A menu appears.
your selection.

572 Working with Data in E-Notebook CambridgeSoft

 2. Select either Sort Ascending or Sort
Descending.
The data in the table is sorted according
to the values of the property you
selected.
Resizing Columns and Rows in a Table
You can easily resize rows and columns in a table,
so that the information is displayed more
effectively.
To resize a row or column:
1. Move the cursor to the border of the row or
column in a table.
A double-headed arrow appears.
2. Drag the border in the direction you desire
until the column or row is the correct size.
The resized column or row appears in the table.
To autofit a column or row to the size of its
contents, move your cursor to the name of the row
or column and double-click. The column or row
resizes.
Pivoting a Table
You can transpose the columns and rows of a table
to alter the way the information is displayed.
To pivot a table:
1. Right-click the table.
A menu appears.
2. Select Pivot Table.
The rows and columns of the table are
transposed.
Figure 29-1Before
Chem & BioOffice 2006 /E-Notebook
Figure 29-2After
Adding Information to a Table Cell
There are a number of ways to add information to
a table cell. Data may be text, numbers, dates, or
structures. Your system configuration determines
what type of data it is possible to add to any
particular cell.
There are three ways to add information to a cell:
Choose a value from the dropdown menu that
appears in the cell. You will use this option
when the cell has a list of possible values asso-
ciated with it.
Enter a value using the keyboard.
Draw a Chemical Structure -- See Working
with Structures and Images in Tables on page
573 for more information.
In some cases, your system administrator may have
configured E-Notebook such that a particular
property in the table has one or more qualities, such
as Read Only. See Setting and Editing Values in a
Property List on page 561 for details on qualities.
Certain numerical properties in a table may have
units associated with them.
Working with Structures and Images in
Tables
Tables may contain chemical structure fields, which
you can use to manage data about the structures of
compounds that interest you. You can also add
standard image files to the chemical structure fields.
Working with Data in E-Notebook 573
 To add a structure or image to a table:
1. Double-click a table cell corresponding to a
structure or image.
The Edit Structure dialog box appears, and
Administrator
you can use the ChemDraw tools to draw the
structure. Or, you may copy a standard image
file into the field.
2. Draw the structure or paste in the image and
click OK. Copy in an image by right-clicking
within the field and selecting Edit, then Paste.
The structure or image appears in the table.
574 Working with Data in E-Notebook
Editing a Structure or Image
To edit a structure or image in a table:
1. Double-click the table cell containing the
structure or image.
The Edit Structure dialog box appears, and
you can use the ChemDraw tools to edit the
structure, or you may copy an image file into
the field.
2. Edit the structure or change the image and
click OK.
The modified structure or image appears in the
table.
Delete a Structure
To delete a structure or image from a table:
1. Double-click the cell of the structure or image
you wish to delete.
The Edit Structure dialog box appears.
2. Using the ChemDraw tools, select the entire
structure or image and delete it.
3. Click OK.
The dialog box closes and the structure or
image is deleted from the table.
CambridgeSoft
Changing Information in a Table Cell
The data type of a cell determines what type of
information you add to a cell. For example, you can
only draw a chemical structure in a cell with a data
type of structure.
Depending upon the data type, you can edit the
information in a cell one of the following ways:
Choose another value from the menu that
appears in the cell use this option when the
cell has enumerated values associated with it.
Enter a value with the keyboard.
Edit a Chemical Structure or change and image
See Working with Structures and Images in
Tables on page 573 for more information.
Certain numerical properties in a table may have
units associated with them.
Working with Numerical Units in Tables
Tables may contain numerical properties, which
may have default units associated with them. Your
system configuration determines the default units
for any given property in a table. See Working with
Numerical Units in Property Lists on page 563 for
the table of default values.
When you are in Search mode, the table query field
allows you to find all equivalent values entered in
various units that share the same unit type. For
example, a search for a volume of 500 mL will
return both 500 mL and 0.5L. The search will
assume the default units for the property if you do
not enter units. Using the same example, if mL were
the default unit for a volume property, and a search
were conducted for a property value of 0.5, no hits
would be returned. A search for 0.5 L would return
both 500 mL and 0.5 L.
Chem & BioOffice 2006 /E-Notebook
Creating a Reference within a Table
Cell
Within a table cell, you can add a link to another
collection/section in E-Notebook or a link to an
external URL. This makes it easy to browse back
and forth between related data.
Adding a Link from a Table to an E-Notebook
Collection
To add a link from a table cell to a collection in
E-Notebook,
1. In the Collection Tree, click the collection
containing the table, then select the section
containing the table.
The section containing the table.
2. Click the table cell to which you wish to add the
reference.
3. In the Collection Tree, click the collection you
would like to reference and, holding the mouse
button down, drag the collection into the
upper-left corner of the table cell, until the
cursor displays a small arrow, as shown .
4. Release the mouse.
5. The reference is created, and a small arrow
appears in the upper-left corner of the table
cell.
6. You can click the arrow in the table cell to navi-
gate to the collection you have referenced, and
click the Back arrow to return to the table.
Alternatively, you may right-click the collection you
wish to reference and select Copy. Then, right-click
within the table cell to which you are adding the
reference, and select Paste Reference.
Working with Data in E-Notebook 575
 Adding a Link from a Table to an E-Notebook
Section
To add a link from a table cell to a section in
E-Notebook:
Administrator
1. In the Collection Tree, click the collection
containing section that you would like to
reference, then select the section.
The section to which you would like to make a
reference appears.
2. Right-click the Section menu icon, and select
Copy Section.
3. In the Collection Tree, click the collection
containing the table to which you are adding
the reference, then click the section that
contains the table.
4. Right-click within a table cell and select Paste
Reference from the menu that appears.
The reference is added to the table cell, and a
small arrow appears in the upper-left corner of
the cell. Clicking the arrow will display the
section you have referenced.
Blocking of References in Tables
You cannot always add links to the tables in the
E-Notebook. You may be blocked from adding a
reference to a specific type of collection that is in a
particular state. If E-Notebook is configured to
block the reference, you will be unable to add the
reference to the table. For example, you can not add
table references to pages/experiments that are in an
archived state.
576 Working with Data in E-Notebook
In the example below, you are prevented from
adding or editing a reference to the Ancillary Data
in a collection that is in the Closed state.
Similarly, you may be prevented from adding
references to several different collection types
and/or several different states of a collection type
depending on your system configuration.
Validation of Values in Tables
Values you enter into a table may be checked against
an external database to ensure that they are valid
values. In this case, if you enter an invalid value, you
will receive an error message, and E-Notebook will
not accept the value.
Actually, your system administrator may have
configured E-Notebook such that the valid and
invalid values for a particular property in the table
are defined and have several qualities. Therefore,
when you attempt to enter a value for the property
that does not match the defined value, you will be
presented with an error message to that effect. For
example, you cannot add text into a field in a table
which is meant for numerical values or structures or
dates.
CambridgeSoft
For example, in a Reaction section, the Reaction
Molarity property cell in a Reaction Conditions table
can only contain numerical values. If you try to
enter text, you will see the following error message:
Working with URL Displays
URL Displays are used to store URLs within
E-Notebook and to display their corresponding
content. A URL may be for either an internal,
intranet site or an external webpage.
To enter a URL and display its corresponding page:
1. Enter the URL address as shown above. In this
example, http://www.cambridgesoft.com was
entered.
2. Click the Go button to the right of the address.
The page corresponding to the URL appears.
You may navigate from within the displayed
page, if desired.
TIP: The URL does not change to reflect your
navigation. If you wish to change the URL that is saved
with the section, you must type in another address.
Chem & BioOffice 2006 /E-Notebook
Rendering in E-Note-
book
E-Notebook provides a number of options for
rendering the contents of your experiments and
other types of collections. You can export to a PDF
file or to an MS Word file.
E-Notebook also offers an E-Signatures feature for
electronically signing your experiments.
See the following topics for more information:
Enterprise Exporting to PDF
Exporting a Collection to MS Word
Exporting a Section to MS Word
Printing Collections
Printing Sections
Enterprise E-Signatures
Exporting
You can export Sections to MS Word, or
Collections containing the sections to PDF or MS
Word, then manage them as you would PDF or MS
Word documents. Rendering to PDF expands the
Standard page size so that the page is sized to set
the contents of the section.
To export a section:
1. In the Collection Tree, click the collection
containing the section(s) you wish to export to
MS Word.
The sections appear in the right frame.
2. Click the Section Menu icon.
Working with Data in E-Notebook 577
Rendering in E-Notebook
 The section menu appears. Sections from X to Y to export a range of
Sections, where X and Y are values you specify.
Current Section to export only the current
Section.
Administrator

6. Click the checkbox Open Document After Export

if you would like the PDF document to be
opened immediately after the export is
complete.
7. Click the Export button.

To export a collection:

1. In the collection tree, right-click the item you

wish to export.
3. Select Export to MS Word. A menu appears.
You are prompted to choose a destination
folder and file name.

4. Choose a folder and file name and click Save.

You are prompted to choose an export range.

5. Select an export range. The options are:

All Sections to export all of the Sections. 2. Select Export to MS Word or Export to PDF.

578 Working with Data in E-Notebook CambridgeSoft

Rendering in E-Notebook
 You are prompted to choose a destination
folder and file name.
3. Continue with step 5 in exporting a Section,
above.
If you chose to open the document after export, the
document is opened, and it displays the Sections
you selected for export. If you chose not to open
the document, the document is saved in the folder
you specified.
Printing
You can print Sections or Collections from
E-Notebook to maintain your hardcopy archives.
To print a collection:
1. From the Collection Tree, right-click the
collection.
The Collection menu appears.
Chem & BioOffice 2006 /E-Notebook
2. Select Print.
The Print dialog box appears, and you are
prompted to enter the information you
normally do when printing, such as page
printer and number of copies, etc.
3. Select the printer options
4. Select the Page Range:
All prints all of the sections in the collection.
Selection prints only the selected section.
Pages allows you to specify a range of
sections to print. For example 1-5 would
print the first, five sections in the collection.
5. Make your selections and click Print.
The collection or the portion of it you selected is
printed.
To print a section:
1. In the right frame, select the section you wish
to print.
2. Click the Section Menu icon.
Working with Data in E-Notebook 579
Rendering in E-Notebook
 The Section menu appears. parties have signed the experiment rendition, it is
stored in a separate database for protection of your
intellectual property.
Administrator

Signing and Closing

When you have completed your experiment, you
can electronically sign it:
1. In the Collection Tree, right-click the
experiment you wish to sign and close.
A menu appears.

3. Continue with step 2 of printing collections,

above.
Note that your system configuration contains
templates that determine exactly how the printed
page appears.
If Visual Display of Changes is enabled, the print
will include the following:
The data as is exists in the current version.
The version history, including the date and the
author for each version after the baseline
version. (The baseline version is the version
that existed when visual display of changes
began).
A list of changes grouped by field.
In some configurations, there is a Final Print
2. Click Sign and Close.
transition that automatically creates a complete
printout of the collection. A dialog appears which asks you to confirm
Sign and Close.
Enterprise E-Signatures
With E-Signatures, you can electronically sign a
PDF version of your completed experiment. This
experiment rendition is then routed to co-authors
(where applicable) and witnesses. Once all required 3. Click Yes.

580 Working with Data in E-Notebook CambridgeSoft

Rendering in E-Notebook
 A dialog appears which contains a list of users
who can be potential witnesses and you are
prompted to select a witness.
4. Select witness(es) and click OK.
The experiment is now rendered to PDF and
the experiment in PDF format appears which
is now ready to submit.
5. Scroll through the entire rendition, enter your
userID and password in the appropriate text
boxes, and click Sign and Store.
Upon Sign and Store, the chosen witness is
given read permission to the experiment so
that s(he) can countersign it.
Chem & BioOffice 2006 /E-Notebook
You can view the record of your submitted
documents in the Display Document List Field at the
bottom of your Home Page.
The field displays two lists:
the first is a list of documents sent to you by
some other author waiting for your action;
the second is a list of documents submitted by
you that are still going through the signature
process.
Reviewing a Document
You can review the documents you have submitted
for electronic signature through your user home
page:
1. In the Collection Tree, select your user
collection.
Your home page appears in the right frame.
You can view the record of your submitted
documents in the Display Document List Field at
the bottom of your Home Page.
2. To review a submitted document, right-click
the document submitted by you from the
second list and click Review...
The PDF rendition is displayed.
3. To make a change in a submitted document:
Click Modify Submission to modify and
resubmit your rendition.
Click Cancel Submission to cancel your
submission. Once a submission has been
cancelled, there is no way to resubmit it.
Countersigning a Document
To countersign a document that has been submitted
to you:
Working with Data in E-Notebook 581
Rendering in E-Notebook
 1. In the Collection Tree, select your user
collection.
Your home page appears in the right frame.
You can view the record of documents
Administrator
The PDF rendition that was submitted to you
is displayed.
3. Click the Countersign button to verify your
approval.

awaiting your signature in the Display Document The document is countersigned and closed,
List Field at the bottom of your Home Page. or...
2. Right-click the document you wish to sign, and
Click Reject to deny your approval.
click Countersign...
The rejected submission can be reviewed by the
primary author and either resubmitted or cancelled.
The rejected submission is highlighted in the list to
distinguish it from the other entries in the list.

582 Working with Data in E-Notebook CambridgeSoft

Rendering in E-Notebook
Chapter 30: Working with Sections
and Collections
Working with Sections
A section is a form for E-Notebook data. Just as
you would use pages in a paper notebook for
recording various types of data, you can use
sections in E-Notebook for recording reactions,
spectra, and other types of information. Sections
are often associated with Experiments or Page
collections. For example, an Experiment may
contain sections for reactions, notes, etc.
You can also use templates to set up sections
automatically and uniformly. See Working with
Templates on page 520 for more information.
Your system configuration determines the types of
sections that are available in E-Notebook.
Creating a Section
You can create a new section within a collection.
To create a section:
1. In the Collection Tree, click the collection to
wish you wish to add the section.
If the collection already contains sections, they
appear in the right frame.
2. Click the icon in the right frame.
A menu appears, listing the types of sections
that you may add.
Chem & BioOffice 2006 /E-Notebook
3. Select the type of section you wish to create.
A new section of that type appears.
Your system configuration determines which types
of sections can be added to which types of
collections. These rules are very flexible, and they
make it possible to tailor the E-Notebook
application to your workflow.
Changing a Section
To modify a section within a collection:
1. Go to the section you wish to change.
2. Edit the data in the section. See the other
portions of the User Guide for information
specific information about how to edit
different types of data in E-Notebook.
It is only possible for one E-Notebook user to edit
the sections in an individual collection at any given
time. If another user is editing a particular
collection and you attempt to edit it, you will be
presented with a message informing you that the
collection is locked for editing by the other user.
In some cases, you will only have Read permission
for a collection, meaning that you may view the
collection but not edit it.
See Changes and Audit Trail on page 601 for
more information about saving your changes.
Working with Sections and Collections 583
Working with Sections
 Removing a Section A menu appears.

To remove a section from a collection:

1. Go to the section you wish to remove.
Administrator

2. With the section displayed, click the

section menu icon.
The Section menu appears.

3. Select Move Up to move the section the left a

single position, or select Move Down to move
the section to the right a single position.
The section is moved in the way you selected.
4. Repeat the process until the section is in the
desired location.
3. Select Delete Section.
Renaming a Section
A message appears, prompting you to confirm
that you wish to remove the section. To rename a section:
4. Click Yes.
1. Go to the section you wish to rename.
The Section is deleted.
2. Click the section menu icon.
NOTE: Your system configuration may prevent you from The Section menu appears.
deleting certain sections. For example, if you are working
3. Select Rename Section.
with a collection that has Visual Display of Changes
enabled, it will not be possible for you to delete a section. A dialog box appears, and you are prompted to
Also, in some cases, it may be possible to delete the sections type in a new name for the section.
only if no data has been added to them.

Moving a Section within a

Collection
4. Type in a new name and click the Rename
You can move a section within a collection. This
button.
allows you to organize sections in the most effective
way. The dialog box closes and the new name of the
section appears.
To move a section:
1. Go to the section you wish to move. TIP: Your system configuration may prevent you from
renaming certain sections.
2. Click the section menu icon.

584 Working with Sections and Collections CambridgeSoft

Working with Sections
Duplicating a Section within 3. Select Copy Section.

a Collection 4. In the Collection Tree, click the collection in

which you would like the copied section to
To duplicate a section within a collection: appear.
5. Click the section menu icon.
1. Go to the section you wish to duplicate.
2. Click the section menu icon. The Section menu appears.
6. Select Paste Section.
The Section menu appears.
A copy of the section appears in the right
frame.

TIP: Note that in some cases, your system configuration

may prevent you from copying the section into a collection.

Exporting Sections to MS
Word
3. Select Duplicate Section. You can export sections to MS Word, then manage
A copy of the section appears. them as you would other MS Word documents. See
Exporting on page 577 for details.
TIP: Note that in some cases, you system configuration may
prevent you from duplicating a particular section within a Printing Sections
collection.
You can print sections from E-Notebook. See
Printing on page 579 for details.
Duplicating a Section
between Collections Working with Collections
All of the information in E-Notebook is organized
To copy a section from one collection to another: into collections, which are the items displayed in the
1. Go to the section you wish to duplicate. Collection Tree. Collections may be notebooks,
folders, experiments, pages, etc. E-Notebook
2. Click the section menu icon. allows you to browse through collections and to
The Section menu appears. search them for important information.
It is possible to manage collections in a number of
ways, as discussed in the following topics:
Creating a Collection
Browsing the Collection Tree (in Ch. 3).
Organizing Collections
Working with Templates
Viewing Collection Properties

Chem & BioOffice 2006 /E-Notebook Working with Sections and Collections 585
Working with Collections
 Changing Collection Security Properties
Performing a Collection Transition
Exporting a Collection or Section to MS
Word
Administrator
Printing Collections
Your system configuration determines the types of
collections that you can create within E-Notebook
and the rules that define their contents. The
permission to view, edit, and create collections can
be set up on a per-collection basis. These rules are
configurable in E-Notebook.
Behaviors of Collections in
E-Notebook
In E-Notebook, there are diverse behaviors
associated with Collectionssuch as the creating,
hiding, renaming, duplicating, and moving
behaviors. Your system configuration determines
the rules to define the traits reflected by a
collection. Therefore, depending on your system
configuration, there may be some additional
behaviors that these collections can show.
Auto-Numbered Collections
The collections in E-Notebook may be configured
to automatically number the collections contained
within a specific collection. Your system
configuration determines the parameters for auto-
numbering the collections.
If the E-Notebook is configured to auto-
numbering of the collections, then the newly
created collections will be automatically named by
appending a serial number to the name of the
collection that contains the newly created
collection.
586 Working with Sections and Collections
For example, if a Notebook collection contains
experiments, and the notebook is named Chemistry
Notebook-01, the experiments within the
collection will be automatically numbered (for
example, Chemistry Notebook-01-001) as shown:
When renaming a collection whose name was
generated according to the auto-numbering, the
collection will check to ensure that the name fits
within the parameters described by your system
administrator for the auto-numbering. For example,
when you rename a Notebook, the names of the
Pages or Experiments within it will change to match
the name of the Notebook. The name must begin
with the name of the parent collection followed by
a dash and a serial number.
Collections that Cannot be Deleted
In E-Notebook, you may be prevented from
deleting the specific collections. Actually, your
system administrator may configure some specific
collections so as to prevent you from deleting them
once they have been created. Therefore, the Delete
command in the Collection menu of such
collections will be grayed out.
CambridgeSoft
Working with Collections
For example, if the Notebook collection has been
configured to avoid deleting, then clicking on it will
show the menu with inactive Delete option as
shown:
Your system configuration determines which types
of collections cannot be deleted. Also, you cannot
delete a collection if references to it exist.
E-Notebook, by default, is configured so that you
can not delete specific collections such as, User
Collection, User Configuration Folder, Notebook
Collections and Offline Folder.
Collections that Cannot be Deleted if
Modified
In E-Notebook, in some cases, it may only be
possible to delete collections if they have not been
modified since they were created. Once the
collection is modified, you are prevented from
deleting such collections.In this case, the Delete
option in the Collection menu is inactive when
collections of that type are selected.
Your system configuration determines which types
of collections cannot be deleted after modification.
Chem & BioOffice 2006 /E-Notebook
Collections that Cannot be Renamed
In E-Notebook, you may be prevented from
renaming specific collections, for example, a
collection whose name is generated by the auto-
numbering feature. If you attempt to rename an
auto-numbered collection, an error message to that
effect appears as shown:
Your system configuration determines which types
of collections cannot be renamed.
Copying Collections that Contain Refer-
ences
It is possible to copy collections that contain
references in the collection tree in the same way as
you would copy normal collections without
references. The copied collection contains
references to all of the collections that are
contained within the collection at the time the copy
is made.
In some cases, your system configuration may
prevent you from copying collections that contain
references to specific types of collections that are in
specific states. This pertains only to references that
exist in property lists and tables. It does not pertain
to references in the collection tree. For example, an
experiment/page collection type may be configured
to prevent you from copying pages/experiments
that contain references to folders that are in a
Closed state.
Your system configuration determines which types
of collections you can copy, and into which types of
container collections you can copy them.
For more information about copying collections,
see Copying a Collection on page 591.
Working with Sections and Collections 587
Working with Collections
 Creating a Collection 3. Select New.

A menu appears, listing all of the type of

Each item displayed in the collection tree represents
collections that may be added to this container
a collection in E-Notebook. In order to create a
collection.
Administrator

new collection, you must first select a container, or

parent, collection for it. The new collection will be
created within the container collection in the tree. NOTE: Your system configuration determines which
For example, you may select a notebook as the options appear).
container collection, and you may create new
experiments or pages within the notebook.

Another example would be creating notebooks

within a user collection. All of the notebooks a user
creates could fall within the container collection
that bears the user's name.

Your system configuration determines where 4. Select the type of collection that you wish to
various types of collections may be added to the create.
Collection Tree.
The new collection appears under the
container collection in the Collection Tree, and
To create a new collection:
you may be prompted to rename it.
1. Be sure you are in browse mode by clicking the 5. Type in a name for the new collection (if
Browse button. prompted).
The Collection Tree appears. The name is saved automatically.
2. Right-click the collection in the Collection Tree
that you would like to be the container for the Organizing Collections
new collection.
You can organize collections in the Collection Tree
A menu appears. to make their order meaningful to you and other
E-Notebook users. Collections can be moved up
and down within a container collection. In some
cases, collections can be moved from one container
collection to another. Your system configuration
determines which items can be moved into which
types of collections.

Moving Collections within a Container

Collection
You can organize collections within a container
collection by moving them up and down.

588 Working with Sections and Collections CambridgeSoft

Working with Collections
To move a collection up or down within its con-
tainer:
1. Click Browse.
The Collection Tree appears.
2. To expand a collection and view the items
within it, either double-click the collection, or
click the plus sign next to the collection.
3. Right-click the collection you wish to move up
or down within the container collection.
The Collection menu appears.
4. Select the appropriate option:
Move Up moves the collection up a single
position in the Collection Tree.
Move Down moves the collection down a
single position in the Collection Tree.
Alternatively you may press CONTROL and the up
arrow key to move a collection up, or CONTROL
and the down arrow key to move a collection down.
Chem & BioOffice 2006 /E-Notebook
Moving Collections between Container
Collections
You can organize collections in the Collection Tree
by moving them from one container collection to
another. Your system configuration defines the
rules that determine which collections can be
moved into which types of container collections.
To move an collection between container collec-
tions:
1. Click Browse.
The Collection Tree appears.
2. In the Collection Tree, click the collection you
wish to move.
The collection you wish to move is highlighted.
3. Drag the collection into the new container
collection using your mouse.
If your system configuration permits the move, the
collection appears in the new location. Depending
upon the rules that define your system
configuration, a copy or a reference may appear
instead. Also, it may not be possible to move the
collection into a particular type of container. If the
new container will not accept the collection you are
attempting to move, you will be unable to highlight
the container when you attempt to drag the
collection into it.
Creating a Reference within the Collec-
tion Tree
Within the collection tree, you can create a
reference to a collection that exists elsewhere in the
tree. The reference acts as a shortcut to the original
collection, and it reflects any changes that are made
to the original. Also, if you have editing privileges to
the original, any changes made to the reference are
reflected in the original.
Working with Sections and Collections 589
Working with Collections
 To create a reference in the collection tree:
1. Click Browse.
The Collection Tree appears.
Administrator
2. Click the collection that you wish to reference.
The collection is highlighted.
3. While holding down the CTRL and SHIFT keys,
drag the item into the Collection where you
would like it to be referenced.
A Reference to the item appears in the
Collection Tree, within the collection you
selected. The icon contains a small arrow,
which indicates that it is a reference.
An alternate method for creating a reference in the
collection tree is the following:
1. Right-click the collection that you wish to
reference.
The Collection menu appears.
2. Select Copy.
3. Right-click the collection into which you wish
to add the reference.
The Collection menu appears.
4. Select Paste Reference.
590 Working with Sections and Collections
The reference appears in the Collection Tree,
within the container collection you selected.
NOTE: Your system configuration determines which
collections can be referenced within which container
collections.
It is also possible to create references to collections
from property lists and tables.
Duplicating a Collection within a
Container Collection
You can duplicate a collection within its container
collection in the Collection Tree. The duplicate you
create contains references to all of the
collections that are contained within the collection
at the time the copy is made.
To duplicate an item within the same container col-
lection:
1. Click Browse.
The Collection Tree appears.
2. Right-click the collection that you wish to
duplicate.
The Collection menu appears.
3. Select Duplicate.
CambridgeSoft
Working with Collections
 A copy of the collection appears within the
same container collection.
NOTE: Your system configuration determines which
collections can be duplicated, and where the duplicates can
reside in the Collection Tree.
Copying a Collection
You can copy a collection in the Collection Tree.
To do this:
1. Click the Browse button.
The Collection Tree appears.
2. Right-click the collection you wish to copy and
select Copy from the menu that appears.
3. Right-click the collection that is to be the
container collection for the copy.
4. Select Paste from the menu that appears.
A copy of the collection appears in the
Collection Tree, within the container you
selected.
Chem & BioOffice 2006 /E-Notebook
Alternatively, you may click the collection you are
copying to select it. Then, while holding down the
CONTROL key, drag it into a container collection to
create a copy.
NOTE: Your system configuration determines which types
of collections you can copy, and into which types of container
collections you can copy them.
Renaming a Collection
You can rename a collection to avoid a duplicate
name, or simply to make the name more meaningful
to you and other E-Notebook users.
To rename a collection:
1. Click the Browse button.
The Collection Tree appears.
2. Right-click the collection you wish to rename
in the Collection Tree.
The Collection menu appears.
3. Select Rename.
You are prompted to enter another name.
4. Enter a name.
The collection is renamed.
Your system configuration determines naming
conventions for various types of collections. If you
enter a name that does not adhere to the naming
conventions, an error message appears and you are
prompted to enter another name. In some cases, a
name may be assigned to a collection automatically,
and it may not be possible to rename the collection
at all.
Deleting a Collection
You can delete a collection from the Collection
Tree so that you manage only the information that
is relevant to your current needs. Your system
configuration determines which types of collections
can be deleted.
Working with Sections and Collections 591
Working with Collections
 To delete a collection from the Collection Tree: The General tab of the Properties dialog box
appears. It contains the following information:
1. Click the Browse button.

The Collection Tree appears.

Administrator

2. Right-click the collection you wish to delete.

The Collection menu appears.

3. Select Delete.

If your system configuration permits it, the

collection is deleted.
You may also delete a collection by clicking it in the
tree to select it, then pressing the DELETE key.

NOTE: You cannot delete a collection if references to it

exist. Also, in some cases, it may only be possible to delete
collections if they have not been modified since they were
created.

Viewing Collection Proper-

ties
Name the name of the collection.
You can see specific information about a collection Owner the user who created the
by viewing the Collection Properties. collection.
Type the type of the Collection or Page.
To view properties of a Collection:
Contents the number of collections
contained in the collection.
1. Click Browse.
Created the date on which the collection
The Collection Tree appears. was created.
2. Right-click the item whose properties you wish Last Modified the date on which the
to view. Collection or Page was last changed.
Status the status of the collection in its
A menu appears.
lifecycle. If no states are defined for the
3. Select Collection Properties. collection, the status is Created.

592 Working with Sections and Collections CambridgeSoft

Working with Collections
 Autosave Interval the time interval after
which the collection is saved automatically.
NOTE: If you wish to view the Collection Security or
Transition Security properties, click the appropriate tab. If
the collection is a user collection, the Region tab appears as
well.
Importing and Exporting
Collections
E-Notebook provides the ability to export and
import collections as XML files. Each XML file
contains all of the data and formatting associated
with the collection.
Importing a Collection
To import a collection,
1. Click the Browse button.
The Collection Tree appears.
2. In the Collection Tree, right-click the collection
into which you would like the collection to be
imported. For example, if you would like to
import an Experiment into a Notebook, you
would right-click the Notebook.
The Collection menu appears.
3. Select Import.
A dialog appears and you are prompted to
select the XML file you wish to import.
4. Select the file and click Open.
5. The collection is imported into E-Notebook.
Chem & BioOffice 2006 /E-Notebook
Exporting a Collection
To export a collection,
1. Click the Browse button.
The Collection Tree appears.
2. In the Collection Tree, right-click the collection
that you wish to export as an XML file.
The Collection menu appears.
3. Select Export.
A dialog appears, and you are prompted to
select a location for the exported file.
4. Select the location for the file and click Save.
5. The collection is exported to the XML file.
TIP: When a collection is exported, the export file does not
include any of the contained collections. Each collection must
be exported separately. For example, if you export a
Notebook that contains Experiments, only the Notebook is
exported; each Experiment must be exported as a separate
XML file.
Changing Collection Security
Properties
You can change the access that other E-Notebook
Users have to a specific Collections. In order to
change the security properties of a Collection, you
must have Full Control privileges to the collection.
Your system administrator determines who has Full
Control privileges for each Collection in
E-Notebook
Working with Sections and Collections 593
Working with Collections
 The default security for any new Collection is 2. Select Collection Properties.
Inherits Security, meaning that a Collection has the The Collection Properties dialog box
same security profile as its parent Collection in the appears.
Collection tree.
3. Click the Collection Security tab.
Administrator

To disable inherited security:
1. Right-click the Collection for which you wish
to disable inherited security.
A menu appears.
The Security tab appears. The Groups and
Users who have permission to access this item
appear in one of the two lists: Inherited
Permissions, Assigned Permissions.

Inherited Permissions are permissions

2. If Inherits Security is checked, select it to clear inherited from the parent collection in the
the checkmark. collection tree. These permissions can not be
changed from this dialog. Only the Assigned
Inherits Security is disabled. Permissions can be changed from this dialog.

Collection Security
To change the Security Properties of a Collection or
Page:

1. Right-click the Collection or Page whose

Security Properties you wish to change.
A menu appears.

594 Working with Sections and Collections CambridgeSoft

Working with Collections
 4. Take the appropriate action:
Desired Action to take
Result
Add a User or 1. Click Add.
Group to the list
2. Select the appropriate user
or group from the tree. You
may either:
a) right-click within a blank
portion of the tree and
select Browse All to see all
of the Users, or
b) click the Search button
and perform a search for a
User or group of Users).
3. Click Add...
4. Select the appropriate
access from the listbox:
Read permits a user to
view the Collection, but
not edit it.
Read and Write permits
a user to view and edit the
Collection.
Full Control permits a
user to view the
Collection, edit it, and
assign or remove security
permissions for it.
Remove a User 1. Highlight the user or group
or Group from in the list.
the list
2. Click Remove.
Chem & BioOffice 2006 /E-Notebook
Desired Action to take
Result
Change the type 1. Highlight the user or group
of access for a in the list of Assigned
Permissions.
user or group
currently in the
list 2. Select the appropriate
access from the listbox:
Read permits a user to
view the Collection, but
not edit it.
Read and Write permits
a user to view and edit the
Collection.
Full Control permits a
user to view the
Collection, edit it, and
assign or remove security
permissions for it.
Transition Security
Transition Security is the security applied to the
collection transitions. For example, some users may
be allowed to close a collection while others can
also reopen the collection.
To change the Transition Security Properties of a
Collection or Page:
1. Right-click the Collection or Page whose
Security Properties you wish to change.
A menu appears.
2. Select Collection Properties.
The Collection Properties dialog box
appears.
3. Click the Transition Security tab.
Working with Sections and Collections 595
Working with Collections
 The Security tab appears. The Groups and 4. Take the appropriate action:
Users who have permission to apply a
transition to this item appear in one of the two Desired Action to take
lists: Inherited Permissions, Assigned Permissions. Result
Administrator

Add a User or 1. Click Add...

Group to the list
The Choose User or
Group dialog appears.

2. Select the appropriate user

or group from the tree. You
may either:

a) right-click within a blank

portion of the tree and
select Browse All to see all
of the Users, or

b) click the Search button

and perform a search for a
User or group of Users.

3. Click Add.

The Choose Transition

Inherited Permissions are permissions
Types dialog appears.
inherited from the parent Collection in the
Collection tree. These permissions can not be 4. Select the appropriate
changed from this dialog. Only the Assigned transition type(s).
Permissions can be changed from this dialog.
5. Click Add.

The User or Group

appears in the Assigned
Permissions list, along
with the transition type(s)
you selected.

Remove a User 1. Highlight the user or group

or Group from in the list.
the list
2. Click Remove.

596 Working with Sections and Collections CambridgeSoft

Working with Collections
Performing a Collection
Transition
Collections may be configured to have states
associated with them. These states define the life
cycle of the collections. For example, a Notebook
may have Open and Closed states; the Open state
may permit editing, and the Closed state may be a
read-only state that does not allow edits. Transitions
are the actions you perform to move a collection
from one state to another, for example, from Open
to Closed.
In order to perform a transition on a collection:
1. Click Browse.
The Collection Tree appears.
2. Right-click the collection in the Collection Tree
that is to undergo the transition.
The Collection menu appears.
3. Select the name of the transition from the
menu, for example Close, Final Print, or Reopen.
(Again, the options will vary based upon your
system configuration).
4. You may be prompted to enter additional
information such as an annotation or addi-
tional data before the transition can
proceed. If so, enter the information to
proceed with the transition.
The transition occurs and the collection enters
the new state. You may always view the state of
the collection by right-clicking it in the
Collection Tree, then selecting Collection
Properties.
Transitions may also perform certain functions,
such as printing a copy of the collection.
Your system configuration determines which
transitions may be performed, and by whom.
Chem & BioOffice 2006 /E-Notebook
Exporting a Collection or
Section to MS Word
You can export Collections and Sections to MS
Word, then manage them as you would MS Word
documents. See Exporting on page 577 for
details.
Printing Collections
You can print collections from E-Notebook to
maintain your hardcopy archives. See Printing on
page 579 for details.
Printing Multiple Collections at Once
Some configurations provide the ability for you to
print multiple contained collections at once.
To do this:
1. Click the container collection in the Collection
Tree. For example, this may be a notebook, and
you may wish to print several
experiments/pages within the notebook.
2. In the right frame, select the section that
contains the Print Multiple tool .
3. Click the tool to select it.
The Print Multiple dialog appears, prompting
you to select the range of contained collections
to print.
4. Select the range by choosing a starting and
ending collection from the dropdown lists.
5. Click the Print button.
Working with Sections and Collections 597
Working with Collections
 Performing a Collection
Transition
Collections may be configured to have states
Administrator
associated with them. These states define the life
cycle of the collections. For example, a Notebook
may have Open and Closed states. The Open state
may permit editing, and the Closed state may be a
read-only state that does not allow edits. Transitions
are the actions you perform to move a collection
from one state to another, for example, from Open
to Closed.
In order to perform a transition on a collection:
1. Log into the E-Notebook.
The Collection Tree appears.
2. Right-click the collection in the Collection Tree
that is to undergo the transition.
The Collection menu appears.
3. Select the name of the transition from the
menu, for example, Close, Final Print, or
Reopen. (Again, the options will vary based
upon your system configuration).
You may be prompted to enter additional
information such as an annotation, or additional
data, before the transition can proceed. If so, enter
the information to proceed with the transition.
The transition occurs and the collection enters the
new state. You may always view the state of the
collection by right-clicking it in the Collection Tree,
then selecting Collection Properties.
598 Working with Sections and Collections
Transitions may also perform certain functions,
such as printing a copy of the collection.
Your system configuration determines which
transitions may be performed, and by whom.
Working with Form Tools
A form tool is used to perform a particular function
in an E-Notebook form/field. There are several
standard form tools in E-Notebook that may be
associated with the section or collection types, for
example, the New Section Form Tool associated
with Notebook collection type or Import/Export
Form Tool, which is present in new section types
you create.
NOTE: Your system configuration determines the
collections to which this form tool can be added.
The New Section Tool
The New Section Tool allows you to add new
sections to a collection, for example, to a page or an
experiment. When you click the tool you will be
presented with a list of the types of sections you
may add.
If you would like to create a new section within a
Page/Experiment:
1. Click the New Section icon,
.
CambridgeSoft
Performing a Collection Transition
 A list of the section types that can be added
appears.
2. Select the section type.
The new section appears within the Page.
The Duplication
Enterprise
Collection Tool
The Duplicate Collection Tool allows you to create
a copy of the selected collection. For example, if
you click the Duplicate Collection Tool/Icon on a
Page/Experiment collection, the Page/Experiment
collection will be copied. The duplicate or new copy
will appear within the same container collection in
the Collection Tree.
To duplicate a collection with Duplication
Collection Tool:
1. Select the experiment/page type you wish to
duplicate.
2. Click the Duplicate icon/tool,
Chem & BioOffice 2006 /E-Notebook
A new copy of the Page or Experiment
collection appears within the same container
Notebook.
1. Alternatively, in the Collection Tree, right-click
the experiment/page which you would like to
duplicate.
A menu appears.
2. Select Duplicate from the menu.
The New Child Collection
Tool
The New Child Collection Tool allows you to add
new contained collections to the selected collection.
For example, you could click this tool on a
notebook in order to create a new page/experiment
within the notebook.
The tool may be used to create a new page within a
notebook. To do this:
1. Click the New Experiment icon/tool,
A list of the experiment/page types appears.
2. Select the experiment/page type.
A new Page or Experiment collection appears
within the Notebook. It is numbered
automatically.
Working with Sections and Collections 599
Working with Form Tools
 1. Alternatively, in the Collection Tree, right-click 1. Click the New Sibling icon,
the Notebook collection to which you would
like to add the Page or Experiment.

A menu appears from which you can select the

Administrator

page to be added to the Notebook Collection.

A list of the collection types that can be created

appears.

The New Sibling

Enterprise

Collection Tool
The New Sibling Collection Tool allows you to
create a new collection of the same type. For 2. Select the collection type.
example, if you click the New Sibling Tool on a A new notebook collection appears within the
notebook, a new notebook will be created. The new same container collection.
sibling will appear within the same container
collection in the Collection Tree. NOTE: Your system configuration determines the
collections to which this form tool can be added.
If you would like to create a new sibling of a
Notebook:

600 Working with Sections and Collections CambridgeSoft

Working with Form Tools
Chapter 31: Changes and Audit Trail
E-Notebook provides auditing and change control
features for compliance with 21 CFR Part 11, which
is part of Title 21 of the Code of Federal
Regulations for the Food and Drug Administration
(FDA). 21 CFR Part 11 sets forth guidelines for
keeping, maintaining and authenticating electronic
records.
For every change made to E-Notebook data, an
audit trail records the logged in identity of the user,
the date, and the time. This is done automatically
when you add, delete, or update data. The audit trail
information is stored in the E-Notebook database.
In addition, E-Notebook may be configured so that
you can annotate the changes you make to
collections by providing reasons for them. See the
following topic for more information:
Annotation of Changes
Working with the Changes Icon
Saving Changes to a Collection
You can also view prior versions of collections and,
if Visual Display of Changes is enabled, you can
view and print the changes that were made to the
data in a collection. See the following topics:
Working with the History Pane
Visual Display of Changes
Working with the Changes
Icon
The changes icon appears in the right frame of
E-Notebook. The appearance of the icon changes
to indicate various conditions:
When you first select a collection in the
collection tree, the changes icon appears as a
key in a keyhole. This indicates that you have
Chem & BioOffice 2006 /E-Notebook
not made unsaved changes to the collection,
and that you have not opened the collection for
editing. The changes icon will always appear in
this form if the collection is in a read-only state.
If you click within one of the sections in
the collection, the key leaves the hole. This
indicates that you have locked the collection
for editing, and other E-Notebook users may
not edit it at this time. The Release state may
also indicate that another user of E-Notebook
has the collection open and locked for editing.
An open book in front of the key indicates
that unsaved changes have been made to the
collection.
If you are viewing a previous version, the save icon
will not appear.
Saving Changes to a Collec-
tion
There are a number of ways in which changes to a
collection may be saved. This topic addresses each
of these items in detail. They are:
Clicking the changes icon.
Selecting Save Changes or Save and Annotate
Changes from the Changes menu.
Browsing to another collection.
Through autosave, which your system adminis-
trator sets up to automatically save the collec-
tion after a set period of time has passed.
Selecting Backup Changes from the Changes
menu. This option would be used in the event
of network failure, to prevent data loss.
Closing the Internet Explorer browser.
Changes and Audit Trail 601
 Clicking the Changes Icon Saving Changes through Autosave

To save your changes using the changes icon: Your system configuration may include the
autosave feature, which defines the set period of
time after which the collection is saved
Administrator

1. Click the changes icon. The open book

indicates that there are unsaved changes. automatically. If autosave occurs and annotation is
required, you will be prompted to enter a reason for
2. If the changes must be annotated, you will be your changes. To view the autosave interval for a
prompted to enter annotation . If no annota- collection, simply right-click the collection and
tion is required, your changes are saved imme- select Collection Properties from the menu.
diately.
The saved version will appear in the History
Pane. The changes icon indicates that your
changes have been saved .

Selecting Annotate Last Change from

the Collection Menu
This allows you to provide an optional annotation
for the last change you made to a collection. To save
your changes using a command in the Changes
menu:

1. Right-click the collection and select Annotate

Last Change... from the menu.

A dialog appears and you are prompted to

enter an annotation for the change.
2. Select or enter an annotation and click the
Annotate button.
Saving Changes by Browsing to
Another Collection
To save changes by browsing to another collection:
1. Click another collection in the Collection Tree.
2. If your changes must be annotated, you will be
prompted to enter annotation . If no annota-
tion is required, your changes are saved imme-
diately.
The version appears in the History Pane.
Saving Changes through Backup and
Restore
In the event of a network failure, you can save your
changes locally, then add them to E-Notebook at a
later time using the Restore command.
To Backup and Restore your changes:
1. When the network goes down, you will be
prompted to save your changes as an XML file.
Select the name and destination for the file and
click OK.
2. When the network comes back up, browse to
the collection and right-click it.
3. Select Restore Changes.

602 Changes and Audit Trail CambridgeSoft

 The Restore Changes dialog appears, and you Providing Required Annotation
are prompted to select the file containing the
changes. With required annotation, you must provide a
reason for your changes each time you save the
4. Select the file you saved as a backup and click
collection or an autosave occurs. You must provide
Open.
the reason before making any further changes. The
Your changes are restored. dialog lists the changes you made to the collection
since the last time the collection was saved.
Annotation of Changes
1. Click the changes icon .
E-Notebook may be configured so that you can
annotate the changes you make to data in The Annotation dialog appears:
collections. There are two possibilities for providing
annotation. They are:
Required Annotation each time you save
the collection, you must provide a reason for
the changes you made. You must also provide
a reason for the changes if autosave has
occurred.
Optional Annotation you may provide a
reason for the changes is you wish, but it is not
required.
Whether annotation is required or optional 2. Either click one of the Predefined Annotations
depends upon 1) the type of collection and 2) its to select it, or type another annotation into the
state. For example, an Experiment or Page may be bottom box.
configured such that it has three states: Open,
Closed, and Reopened. The Save button is enabled.
Open the Open state may have optional 3. Click the Save button.
annotation, so that you may provide a reason
for a change if you wish. The version of the collection is saved, along
with the annotation. The version is listed in the
Closed the Closed state may be read-only. It History Pane.
may not be possible to edit the collection while
it is in this state. Alternatively, you may save your changes by simply
Reopened the Reopened state may permit
browsing to another collection. If you have unsaved
changes, but only if they are annotated each changes, you will be prompted to enter an
time the collection is saved. annotation.

In some configurations, annotation may be required In some configurations, an autosave may occur
when you perform a collection transition. For after a certain time period has elapsed. If autosave
example, it may be necessary to provide a reason for occurs and annotation is required, you will be
moving a collection to the Reopened state. prompted to enter the annotation for your changes.

Chem & BioOffice 2006 /E-Notebook Changes and Audit Trail 603
 Providing Unprompted, Optional Anno-
tation
With Optional Annotation, you may provide a
reason for your changes at any time. You initiate
Administrator
To view the History Pane of a collection:
1. Right-click the collection in the Collection
Tree.
The Collection menu appears:

providing the reason; it is not mandatory. To

provide optional annotation:
1. Click the changes icon .
A menu appears.
2. Select Save and Annotate Changes.

NOTE: This command will only be available if there

are unsaved changes.

3. Click a predefined annotation or type in

another annotation.
4. Click Save.
The version is saved, along with the
annotation. The version is listed in the History
Pane.

Working with the History

Pane
The History Pane indicates whether prior versions 2. Select Show History. The History Pane appears
of a collection exist, and enables you to view those in a pane below the Collection Tree. It displays
versions. A version of the collection is created each all versions and transitions for the collection, in
time the collection is saved. For each version, the reverse chronological order. A save operation is
history pane shows the date, time, and the action
name - which may be save, autosave, or a transition
name.

604 Changes and Audit Trail CambridgeSoft

 denoted with a paper and pencil icon. A collec-
tion transition is denoted with a rubber stamp
icon
.
3. To view a particular version, click the version in
the History Pane. The version is then displayed
in the section frame, to the right.
The changes icon icon is not visible when you
are viewing older versions of a collection.
To view the properties of a version of a collection:
1. Right-click the version in the history pane.
Select Properties from the menu that appears.
The Version Properties dialog appears.
The dialog displays the following information
about the version you selected:
Chem & BioOffice 2006 /E-Notebook
Name the action that created the version
(save, autosave, transition name).
Author the person who performed the
action.
Date the date and time the version was
created.
If there is an annotation associated with the
change, the following information appears as
well:
Person who entered the annotation
Date and time the annotation occurred
Text of the annotation
2. Click the Previous button to view information
about the previous version of the collection, or
the Next button to view information about the
next version of this collection.
3. Click OK to dismiss the Version Properties
dialog.
Specifying an Annotation through the
History Pane
It is only possible to specify an annotation through
the History Pane for the most recent version of the
collection, and only if the state of the collection
does not require that changes be annotated.
To enter an annotation for the most recent version
of the collection:
1. Right-click the version in the History Pane.
2. Select Properties from the menu that appears.
The Properties dialog appears. If the version
displayed in the Properties dialog is
unannotated and requires an annotation, the
Annotate button is visible.
3. To annotate this version, click the Annotate
button and the standard Annotation dialog
box appears.
4.
The standard Annotation dialog appears.
Changes and Audit Trail 605
 5. Enter the reason for the changes, or select a
reason from the predefined list of reasons.
6. Click OK .
The annotation is saved with the version.
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Baseline Version in the version that existed when
the Close transition was performed. A black line
appears under this version.

Visual Display of Changes

Depending upon the type of collection and its state,
it is possible to view a Visual Display of Changes
that have been made to data in the collection. If
Visual Display of Changes is enabled, the changes
that have been made to a collection can be viewed
in E-Notebook, and a record of the changes made
will be shown as footnotes in the printed collection.
In some configurations, Visual Display of Changes If visual display of changes is enabled, there is a
will be possible from the very beginning of the
collection life cycle, when the collection is first paper and pencil icon next to data in the
created. In other cases, Visual Display of Changes section that was changed after the baseline version
will begin when a particular collection transition is was created.
performed; a common example is the transition
from a closed, read-only state to a reopened state in
To view an older version of the data:
which edits are permitted.
The version of the collection that existed when the 1. Click the paper and pencil icon that indicates a
Visual Display of Changes began is called the change was made.
Baseline Version of the collection. It is underlined
in the History Pane. In the example below, the A dropdown menu is displayed. The menu
displays a list of dates and times for every saved
version of this data since the baseline version.
The version currently displayed is denoted with
a checkmark.

2. To view a particular version, select the corre-

sponding date from the dropdown list.

The entire version of the collection as of that

date and time is displayed.

606 Changes and Audit Trail CambridgeSoft

Changes are displayed differently for different types
of data

Type of Data Change Display Example

Chemical Structure The data is displayed as it existed N/A

when the version was created.
Database tables

MS Excel Spreadsheet

Spectrum

Stored Document

Styled Text

URL Displays

MS Word The change tracking features of

MS Word are used: new text is
underlined and displayed in red.
Deleted text is displayed with
red, strikethrough text.

Property Lists Changed Cells display a pencil Changed or new property:

icon.
Tables
New cells display a pencil icon.
Deleted property:
Deleted cells display an X
through them.

If Visual Display of Changes is enabled, the printed
output will include three main portions:
The data as is exists in the current version.
The version history, including the date and the
author for each version after the baseline
version.
A list of changes grouped by field.
NOTE: Even when the visual display of changes is not
enabled, the audit trail still captures the history, and the
history pane displays a list of the saved versions and
transitions for the collection.

Chem & BioOffice 2006 /E-Notebook Changes and Audit Trail 607
Administrator

608 Changes and Audit Trail CambridgeSoft

Chapter 32: Searching
Searching allows you to find information in
E-Notebook that meets the criteria you specify.
E-Notebook makes it possible to search for:
Chemical structures
Strings of text
Values in Property Lists and Tables
Collections and sections that meet specific
criteria, such as creation date or owner's name
or state.
Unannotated versions of collections
Conducting a Search
You can search for information in E-Notebook that
meets the criteria you specify. You can then save
your queries and the results lists.
To conduct a search:
1. Click the Search button.
Search mode appears.
2. From the Search for drop-down list, select the
type of search you would like to conduct.
3. Click the New Query Section icon.
A menu appears.
The options in the menu depend on both the
type of search chosen in step 2 and your
configuration.
Chem & BioOffice 2006 /E-Notebook
4. Select the type of query you would like to run.
An empty query form is displayed. An example
is shown below:
5. Specify the parameters that will determine the
search results.
The parameters you can specify are determined
by the type of query you are conducting.
6. Do one of the following:
Click Search Now to execute the query.
A results list appears.
Click Save Query to save the query.
The Collection Tree appears with a new
search, and you are prompted to give the
search a name.
Working with Query Results
When you conduct a Search in E-Notebook, the
results are displayed in a list. You can save the
results list, and/or view any item on the list.
Viewing Items in a Results List
To view an item on the results list:
Searching 609
Conducting a Search
 Click the arrow in the upper left corner of the
name of the item, as shown below.
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The Collection Tree appears, with the item
displayed.
Saving a Results List
To save the results list:
1. Click Save Results.
A dialog appears, prompting you to browse to
the location in the Collection Tree where you
would like the results to be saved.
2. Click a collection to select it in the tree, and
click the Save button.
The Collection Tree appears, showing the
search results as a new collection. The links are
maintained so that you may browse to any of
the items.
Customizing the Display of Search
Results
You can customize the display of a hitlist, just as
you can customize a table of contents. To do this:
Right-click a column in the hitlist.
A menu appears.
You may hide the selected column or sort the
results list. You may also specify which columns are
displayed, using the Show command. See Working
with Table of Contents on page 519 for a more
detailed description of these options.
610 Searching
Saving a Query
When you create a query in E-Notebook, you may
save the query in the Collection Tree.
To save a query:
1. Click the Save Query... button to the left of the
query form.
A dialog appears, and you are prompted to
select the location where you wish to save the
search.
2. Click a collection to select it as the location,
and click the Save button.
The Collection Tree appears, and the query
appears in the tree. You are prompted to
rename the query.
3. Enter a name for the query
TIP: The last query you created will appear by default
when you enter Search mode again.
Running a Saved Query
To run a query that is saved in the collection tree:
1. Click the Browse button at the top of the
screen.
The Collection Tree appears.
2. Select the query in the collection tree by
clicking it.
The query form appears in the right frame.
3. Right-click the section menu icon, and select
Copy Section.
4. Click the Search button at the top of the screen.
Search mode appears.
5. From the Search For dropdown list, select the
type of query that corresponds to the query
form you are copying.
6. Right-click the Section menu icon, and select
Paste Section.
CambridgeSoft
Conducting a Search
 The query form appears.
NOTE: It may be necessary to delete one of the query
forms if you do not want to use multiple query forms.
See Removing a Section on page 584 for more
information.
Refining a Search
Once you have conducted a search, you can further
refine it, performing a search that is:
An intersection of two searches
A union of two searches
The exclusion of one set of search results from
another
It is possible to refine both section searches and
collection searches.
To do this:
1. From the dropdown list at the top of the query
form, choose any of the following options:
Create a New Set of Search Results
deletes the previous search results and
replaces them with the search results
generated by the new query.
Refine the Previous Search By
Collection uses the previous search
results to limit the collections in which a
search is done. The stored hit list will
contain the intersection of the previous
search results and the results specified by the
new query.
Refine the Previous Search By Section
uses the previous search results to limit the
sections in which the search is done. The
stored hit list will contain the intersection of
the previous search results and the results
specified by the new query. If the current
search engine is a collection search engine,
then this option is not present.
Chem & BioOffice 2006 /E-Notebook
Exclude Collections from the Previous
Search excludes collections from the
stored hit list that are part of the previous
search results. The stored hit list is
completely replaced.
Exclude Sections from the Previous
Search excludes sections from the stored
hit list that are part of the previous search
results. The stored hit list is completely
replaced. If the current search engine is a
collection search engine, then this option is
not present.
Add to the Previous Search adds the
results specified in the search query to the
previous search results. Duplicate
collections and/or sections will not be
added.
Remove from the Previous Search
removes the results specified in the search
query from the previous search results.
2. Fill in the new search criteria.
3. Click the Search Now button.
The hitlist appears, modified according to the
option you chose in step 1.
If you wish, you may refine your search further, by
selecting another option from the dropdown list.
Using the E-Notebook
Search Types
E-Notebook offers an extensive array of searching
features. You can search for:
Chemical structures
Strings of text
Values in property lists and tables
Collections and sections that meet specific
criteria, such as creation date or owner's name.
You can search for sections that meet the criteria
you specify. Similarly, you can search for collections
based on specific attributes. The Chemical
Searching 611
Conducting a Search
 Structure search will find structures in chemical
structure fields and tables in E-Notebook. The
results of the search are grouped by structure for
easy analysis and organization. You can also search
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for collections that require annotation, but for
which no annotation was provided when changes
were made. You can save queries and the results lists
of the searches made to the E-Notebook Collection
Tree.
Searching for Sections
You can search for sections that meet the criteria
you specify. You can then refine your search, or save
your queries and the results lists.
To conduct a search for sections:
1. While in Search mode, select Sections from the
Search for drop-down list. If no form appears
in the right frame, click the New Query icon.
A menu appears.
2. Select the new query form you wish to create.
The options are: Basic Query and Advanced
Query.
An empty query form appears.
3. Enter your search criteria into the form, using
the instructions below.
Do one of the following:
Click Search Now to execute the query.
A results list appears, displaying the sections
for which all of the parameters you specified
apply.
Click the Save Query button to save the
query.
612 Searching
A dialog appears, prompting you to choose
a location for waving your search.
Select a location and click the Save button.
The Collection Tree appears with a new
Section Search, and you are prompted to
name the search
When you conduct a search for sections, all of the
search criteria you enter into the query form must
exist in a section in order for the section to be
considered a match. In other words, the search is an
AND search. If you add an additional search
form, you can conduct an OR search. The search
results will contain the sections that match 1) all of
the criteria in the first search form and 2) all of the
criteria in the second search form. After running a
search you may refine it, adding additional criteria,
etc. See Refining a Search on page 611.
Searches are not case sensitive. A search for
Benzene will find both Benzene and
benzene.
Your section search form may include the following
search fields:
Query Text Field
The Query Text field may be used to search for the
following text:
Text in MS Word fields
Text in Styled Text fields
Text in MS Excel spreadsheets
Text in Chemical Structure fields
Properties in Property Lists
Properties in Tables
Text in several types of stored document files
MS Word, MS Excel, MS PowerPoint
See Searching for Text with the Query Text Field
on page 626 for a description of the search
capabilities.
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Conducting a Search
Chemical Structure Field
If you wish, draw a structure or reaction using the
ChemDraw Toolbar. (Alternatively, you may open
a structure file of a supported file type). See
Chemical Structure Search on page 614 for
information about performing a structure search.
The section search differs from the chemical
structure search in that the results of a section
search are not organized by substructure.
Search Location Field
The Search Location field allows you specify the
branch of the collection tree for your search. To
select a search location, simply click the Search In
checkbox to select it, and browse to or search for
the root collection for your search. The search will
cover the root you select and any collections within
it.
Chem & BioOffice 2006 /E-Notebook
Collection (Metadata) Properties
Metadata Properties describe the collections that
contain the sections for which you are searching.
For Selecting, a checkbox makes visible an area that
allows you to enter criteria. See Searching with
Collection Attributes on page 623 for more
instructions on entering these criteria.
Property Query and Table Query Fields
These fields are included in the Advanced Section
Query. The Property Query Field is used to search
over Property Lists, and the Table Query field is
used to search over Tables. See Searching with the
Property Query and Table Query Fields on page
624.
Collections Search
The collection search allows you to search for
collections, such as notebooks, folder, or
experiments. You may conduct a search based for
specific content or for metadata, such as owners
name and creation date. You can save your queries
and the results lists in the Collection Tree.
To conduct a search for collections:
1. While in Search mode, select Collections from
the Search for drop-down list. If no form
appears in the right frame, click the New Query
icon.
A menu appears.
2. Select Basic Query or Advanced Query.
An empty query form appears.
3. Enter your search criteria, as described below.
Searching 613
Conducting a Search
 Do one of the following: by structure for easy analysis and organization. You
Click Search Now to execute the query.
can save queries and the results lists to the
E-Notebook Collection Tree.
A results list appears, listing the Collections
that match the criteria you specified. Note that you may also search for chemical
Administrator

structures with the Section Search and Collection

Click the Save Query button to save the Search. These searches allow you to combine the
query. structure search with other search criteria. The
A dialog appears, prompting you to choose results of the Section Search and Collection Search,
a location for waving your search. however, will present the search results in a list,
rather than ordering them by structure.
Select a location and click the Save button.
The Collection Tree appears with a new To conduct a search for structures:
Collection Search, and you are prompted to 1. While in Search mode, select Chemical Structure
name the search. from the Search for drop-down list.
Your search for collections may include the 2. Click the New Query icon.
following search fields:
An empty query form appears.
Query Text Field see Query Text Field on
page 612.
Chemical Structure Field see Chemical
Structure Field on page 613.
Search Location Field see Search Location
Field on page 613.
Collection (Metadata) Properties see
Collection (Metadata) Properties on page 613.
Property Query and Table Query Fields see
Property Query and Table Query Fields on page
613.

Chemical Structure Search

Substructure searching finds structures that contain
the query and any additional attachments at the
open positions. Using the ChemDraw toolbar, you
can attach different features, such as atom lists and
variable bond types, to a query to perform a
narrower or broader search.
The Chemical Structure search will find structures
in chemical structure fields and tables in
E-Notebook. The results of the search are grouped
3. Within the chemical structure box, draw the
structure or substructure for which you wish to
search, or right click within the structure box to
import a file. (For more information about the
structure drawing capabilities of ChemDraw,
please consult the ChemDraw Users Manual.)
4. Do one of the following:
Click Search Now to execute the query.
A results list appears.

614 Searching CambridgeSoft

Conducting a Search
 Click the Save Query button to save the
query.
The Collection tree appears with a new
Structure Search, and you are prompted to
give the Structure Search a name.
An example of substructure searching of
Cyclopentane. The substructure query:
Will hit the following (and other molecules):
O
HO
O below.
Chem & BioOffice 2006 /E-Notebook
In searching substructures, E-Notebook finds the
substructure query regardless of its orientation or
drawing presentation in the targeted molecules.
E-Notebook does its best to follow your
instructions even if those instructions are
contradictory. For example, you can create a query
such as the following:
This indicates that the bond
must NOT be in a ring
Chn
That bond is already in a ring, so no hits are
returned for this query.
General Query Properties
E-Notebook allows the following general
properties to be assigned to a query:
Atom
Bond
Substituents
Charges and radicals
Isotopes
Atoms
Atom types specified in the query must match
atoms at corresponding positions in the target.
Hydrogen is an exception see Substituents,
Searching 615
Conducting a Search
 Bonds
Bond Type Description
All bonds explicitly drawn in the query must match
in the target. E-Notebook recognizes the following Triple target must have triple bond
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standard bond types: here

Bond Type Description Substituents

In E-Notebook, a substituent is defined as a non-
Single target must have single bond hydrogen atom connected by a bond of any order.
here For example, a carbonyl oxygen is a substituent of
the carbonyl carbon.
Dashed same as Single
All unfilled valences in the query may be filled by
hydrogen atoms or by non-hydrogen substituents.
Hashed same as Single The normal valence of an atom is determined from
data in the periodic table. For example, carbon has
Thick same as Single a valence of 4, while sulfur has valences of 2, 4, and
6. Any explicit charges, radicals, or query properties
Wedged Hashed specifies stereochemistry down modify the normal valence. For example, a
from the point end to the wide carbocation has a valence of 3.
end Hydrogen atoms in the query may match non-
hydrogen substituents in the target if the hydrogen
Wedged specifies stereochemistry up in the query is implicit on an unlabeled carbon atom
from the point end to the wide or heteroatom.
end Hydrogen atoms in the query must match
hydrogens in the target when the query hydrogen is
Wavy specifies stereochemistry at the end of an explicit bond. The matched
either at both ends hydrogen in the target may be implicit in an
unlabeled carbon.
Hollow Wedged same as Wedged
Figure 32-1Query Figure 32-2

Dative same as Single H O

Double target must have double bond; H N

stereo dictated by geometry

Double Either target must have double bond;

any stereochemistry ok

Double Bold same as Double

616 Searching CambridgeSoft

Conducting a Search
Figure 32-3Finds: Figure 32-4Does not Isotopes
find: Isotopic labels specified in the query must match
Cl OH
the target. Unlabeled atoms in the query match
O
HN O
unlabeled or isotopically labeled atoms in the target.
NH2
Additionally, D is treated interchangeably with 2H,
Br
and T is treated the same as 3H. With a
H OH
O Substructure Search:
NH2
OH
Figure 32-9Query Figure 32-10:
H OH
H N
1
3
O C
Br
D
H NH2

Charges and Radicals

Figure 32-11Finds Figure 32-12Does not
Charges or radicals specified on atoms in the query find:
must match those in the target. The valence of a HO 13
CH 3
charged atom is taken to be the valence of the 13
C O
isoelectronic neutral atom With a Substructure D
T
Search: O
13
CH 3

13
O CH 3
Figure 32-5Query Figure 32-6: D
HO
D D
N
D
13
O C

Atom Properties
E-Notebook allows special atom properties to be
Figure 32-7Finds Figure 32-8Does not find: assigned to an atom in a query. They generally serve
to broaden or narrow the scope of the search.
N H 3 N H

Special Atom Types

H 2
E-Notebook recognizes six special atom types that
N N
can match any one of a predefined set of elements:
A matches any non-hydrogen atom.

N N
Q matches any heteroatom (non-hydrogen,
non-carbon).
O H
R matches any atom, including hydrogen.
X matches any halogen (F, Cl, Br, I, At).

Chem & BioOffice 2006 /E-Notebook Searching 617

Conducting a Search
 M matches any metal atom: With a substructure search, the query:

Figure 32-13Query: Figure 32-14

This atom is marked

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X3
with the atom property
Substituents Exactly:3

Figure 32-15Finds: Figure 32-16Does not

Cl
find:

Atom Lists
As with the predefined special atom types, an atom
list is a list of atoms, one of which must match the O
target atom. HO

O
For example: O

[Cl,Ag,N] atom must be Cl or Ag or N

Atom lists may contain only elements. Special atom

types, nicknames (Ph), and structural fragments
(NH2, OCH2CH3) may not be included in an atom
list. E-Notebook recognizes a maximum of five Substituents: Up To
atoms in an atom list. This property specifies a maximum value for the
number of substituents on an atom, including those
Atom Not-Lists explicitly drawn. This property is only meaningful
in a substructure search.
The opposite of an atom list is a list of atoms, none
of which must match the target atom. For example: Figure 32-17Query: Figure 32-18
This atom is marked
[NOT O,S,Se] atom must not be O or S or Se (but U2
with the atom property
may be any of the 100 other elements) Substituents Up to:2

Atom not-lists have the same restrictions as atom

lists.

Substituents: Exactly
This property specifies a precise value for the
number of substituents on an atom, including those
explicitly drawn.

618 Searching CambridgeSoft

Conducting a Search
Figure 32-19Finds: Figure 32-20Does not Figure 32-23Finds: Figure 32-24Does not
Cl
find: find:

HO
O HO
O

O
O
O
CH3

Substituents: Free Sites
The Substituents: Free Sites property specifies the
maximum number of additional substituents that
may be present on an atom. This property is only
meaningful in a substructure search.
TIP: Specifying Free Sites: 0 is a quick way to indicate that
you want no further substitution at a site. Target structures
will match the query structure as drawn, with no additional
ligands.
Unsaturation
Sometimes it is useful to specify that an atom must
or must not be attached to unsaturated (aromatic,
double, or triple) bonds. E-Notebook allows
searches for atoms whose unsaturation Must Be
Absent (all bonds to the atom are single). It also
allows searches for atoms with at least one multiple
(double, triple, or aromatic) bond. The default
value, Undefined, finds targets without regard to
the hybridization of the atom. With a substructure
search, the query:

Figure 32-25Query: Figure 32-26

Figure 32-21Query: Figure 32-22
O
This atom is marked
2 with the atom property
Substituents Free sites:2 OH
S

This atom is marked

with the atom property
Unsaturation: must be present

Chem & BioOffice 2006 /E-Notebook Searching 619

Conducting a Search
 Figure 32-27Finds: Figure 32-28Does not
O
find: Bond Type Description
O

OH
D/A target must have a double bond
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OH
O or an aromatic bond here

HO
HO
S/A target must have a single bond
or an aromatic bond here
O

Topology
OH
OH
If Ring or Chain is chosen, the target bond must or
OH
O
O must not be in a ring, respectively.

Bond Properties Reaction Center

E-Notebook allows special properties to be
assigned to bonds in a query. These properties
usually will only be meaningful during a search.
They generally serve to broaden or narrow the
scope of the query.
The reaction center refers to those bonds that are
directly affected by a reaction. This property allows
you to specify just how a given bond is affected.
Property Description

Special Bond Types Unspecified target must have a bond here,

The table below describes the special bond types but the bond can participate in
that E-Notebook allows. the reaction in any fashion, or
not at all

Bond Type Description

Center target must have a bond here
that directly participates in the
Aromatic target bond must be aromatic reaction in some way
as defined by the Hckel 4n+2
rule
Make/Break target must have a bond here
that is either made (if in a
Any target can have any bond type product) or broken (if in a reac-
here tant)

S/D target must have a single bond Change target must have a bond here
or a double bond here whose bond order changes
over the course of the reaction,
Tautomeric same as S/D but is not made or broken

620 Searching CambridgeSoft

Conducting a Search
 two atoms on either side) and the two atoms on
Property Description either side) is part of the reaction center. The rest of
the structure is unchanged from the reactant to the
Make&Change target must have a bond here product:
that is either made (if in a
O OH
product) or broken (if in a reac-
tant) or whose bond order
changes over the course of the
reaction
F Cl F Cl
Not Center target must have a bond here,
By default, E-Notebook does not consider reaction
and that bond must not partici-
centers in the search. In order to include the
pate in the reaction
reaction center in the search, you must select the
Map Reaction Centers checkbox before running the
Not Modified target must have a bond here, search.
and regardless of whether it is
part of the reaction center or For example:
not, its order must not change
F Cl
over the course of the reaction
will only hit the reaction shown above if the Map
Reaction Searching Reaction Centers option is not selected. The reason
for this is that, although there is a C-F bond in the
The chemical structure search in E-Notebook
target reactant and a C-Cl bond in the target
allows you to search for reactions. In a reaction, one
product, these bonds do not participate in the
or several compounds (reactants) are transformed
reaction, which affects another part of the
into other compounds (products). Individual
compound.
reactants (or products) are separated from each
other with plus signs. The reactants are separated When creating reaction queries, it is important to
from the products with an arrow. consider what sort of information you really wish to
find. Suppose you want to convert n-decanal to n-
Reaction Centers decanol:
The most important part of a reaction is that part
O
that actually changes from the reactants to the
products. This part, which normally includes a
number of atoms and bonds, is called the reaction
center. For example, only the bond below (and the OH

Chem & BioOffice 2006 /E-Notebook Searching 621

Conducting a Search
 Are you really interested in these two compounds
exclusively? You might be interested in any reaction
that converts a straight-chain aldehyde to the
alcohol:
Administrator
H H
H H
O OH
H H
Since the corresponding n-octanol -> n-octanol
reaction would probably occur under very similar
conditions, it is a reasonable reaction to look at.
Generally, you want to use substructure queries that
include little beyond the reaction center in question
when you are searching for reactions.
Atom-to-Atom Mapping
In chemical structure fields, you can specify atom
maps. These maps can be used during searching to
resolve certain type of structure hits.
Consider a simple esterification reaction:
O O
OH
H2 O
OH O
Does the ester oxygen come from the acid or the
alcohol? You specify the fate of individual atoms
through an atom-to atom map. In reality, the ester
oxygen in this reaction originates in the alcohol, so
the atom-to-atom map looks like this:
3 3
O O
OH 6 reactions in which maleic anhydride or a compound
2
Rxn
5 2
5 H2O 4
OH 4 O
1 1 Rxn
6
622 Searching
By matching numbers across the arrow, you can see
where atoms move during the course of the
reaction. The other reaction (not observed
experimentally) in which the ester oxygen comes
from the acid, would be mapped like this:
3 3
O O
6
Rxn OH
5 H2O 6
2 5 2
1 OH 4 1 O Rxn
4
E-Notebook uses atom-to-atom map information
to determine the reacting centers for reactions. If
only some atoms are mapped, E-Notebook uses
that information and does not worry about the
specific fates of other atoms. Foe example, if you do
not know (or do not care) about the mapping of
certain atoms, you can leave them unspecified in
the-atom-to-atom map.
Searching for Reactants
If you know what starting materials you are
interested in but do not know their products, you
might perform a reactants query. A reactants query
is very similar to a reaction search, except that there
is nothing to the right of the arrow. For example,
consider the query:
O
O
O
If you are doing a substructure search, this finds any
containing a maleic anhydride substructure is
consumed or transformed.
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Conducting a Search
Searching for Products
If you know the desired end product but not how
to get there, you can do a products query. A
products query is similar to a reaction search,
except that there is nothing to the left of the arrow.
For example, consider the query:
If you are doing a substructure search, this finds any
reactions in which bicyclo[2.2.1]heptane or a
compound containing its substructure is produced.
Searching with the
Search Location Field
The search location field makes it possible for you
to select the specific branch of the collection tree
over which your search is conducted.
To use the search location field:
1. While in Search mode with a search form
displayed, click the Search In... checkbox to
activate the field.
The Collection Tree appears.
Chem & BioOffice 2006 /E-Notebook
2. Then, either:
Browse to the root collection over which
you wish to select OR
Click the Search button inside the search
location field to search for the root
collection.
The collection that appears at the top of the
Collection Tree in the search location field is
the collection over which your search will be
run. This root collection, all of its contained
collections, and all of the collections
referenced within it in the collection
hierarchy will be included in the search.
Searching with Collec-
tion Attributes
You may search for collections and sections in
E-Notebook based on specific attributes, such as
owner's name and creation date.
To conduct a search for collections:
1. While in Search mode, select Collections or
Sections from the Search for drop-down list.
2. If no form appears in the right frame, click the
New Query icon.
A menu appears.
3. Select Basic Query or Advanced Query.
An empty query form appears.
4. If you would like to search by collection
attributes, select the checkboxes next to any
items you would like to include in the query.
Selecting a checkbox makes visible an area that
allows you to enter criteria.
Searching 623
Searching with the Search Location Field
 Specify the collection attributes that will determine
the search results. The parameters you may enter Parameter Options
are:
State Name the contains
Administrator

Parameter Options name of the current

state of the Collec- is
tion. Examples are
Collection's contains starts with
Open and Closed.
Name the name
of the Collection is ends with.

starts with Each of these options can

be specified as of a certain
ends with date. For example, Closed
as of 2/1/2003 would return
Owner's Name contains the Collections that were in
the name of the the Closed state on
User who created is 2/1/2003.
the Collection.
starts with
Searching with the Prop-
ends with
erty Query and Table
Type the Collec- is Query Fields
tion type. Examples
is not The Property Query Field is used to search over
are Notebook,
property lists, and the Table Query field is used to
Folder, Experiment,
search over E-Notebook tables. These search fields
or Page.
are normally found in Advanced Section Query
forms.
Creation Date is
the date the Collec-
tion was created. is before

is after

Last Modified is
Date the date the is before
Collection was last is after
modified.

624 Searching CambridgeSoft

Searching with the Property Query and Table Query Fields
Adding Properties to the Removing Properties from
Field the Field
To remove a property from the field:
To add properties to a Property Query or Table
Query field: 1. Right-click the property you wish to remove.
A menu appears.
1. Right-click within the field.

A menu appears.

2. Select Remove Property.

You are prompted to confirm that you wish to
delete the property.
2. Select Add Property. 3. Click Yes.

The Add Property dialog appears, listing the The property is removed from the query field.
properties that appear in E-Notebook. If Search Options
properties are already present in the field, the
You may either search for an exact match, or use
list is filtered to display only those properties
one of the following options:
that share the same section type:
Wildcard searches for text properties:
Property Query field the properties that
If a property has a Data Type of text, you can
appear in E-Notebook property lists are conduct a contains search. Use the
displayed. percentage symbol as the wildcard. In the
example below, all of the Spectrum sections
Table Query field the properties that
where the Analyst name ends in Smith will be
appear in E-Notebook tables are displayed. returned.
3. Select the properties you wish to include in the
search. You may use SHIFT+click and
CTRL+click to select multiple properties.
If a property has a numerical Data Type, you
Make sure that all of the properties exist in the
can search for a range, as shown below:
same section type, or your search will return no
hits.

4. Click the Add button.

Other search options may be used with numerical
The properties appear in the search form. properties as well:

Chem & BioOffice 2006 /E-Notebook Searching 625

Searching with the Property Query and Table Query Fields
 Greater than >30 returns all sections in
which the property is greater than 30
Less than <30 returns all sections in which
the property is less than 30
Administrator
Greater than or equal to >=30 returns all
sections in which the property is greater than
or equal to 30
Less than or equal to <=30 returns all
sections in which the property is less than or
equal to 30.
If you enter units, the search will return all of the
equivalent values entered in other units of the same
type. For example, a search for a volume of 500 mL
will return both 500 mL and 0.5L.
The search will assume the default units for the
property if you do not enter units. Using the same
example, if mL were the default unit for a volume
property, and a search were conducted for a
property value of 0.5, no hits would be returned. A
search for 0.5 L would return both 500 mL and
0.5 L.
Searching for Text with
the Query Text Field
With the Query Text field, you can search for text
that is contained in the following E-Notebook
fields:
Styled Text fields
MS Word fields
MS Excel fields
Stored document fields that are MS Word, MS
Excel, or MS PowerPoint
E-Notebook property lists
E-Notebook tables
Text in chemical structure fields
626 Searching
If you enter text into the Query Text field and you
have specified no other search criteria in the search
form, all of the E-Notebook sections you have read
access to will be searched.
The searches are not case sensitive.
A number of basic and advanced text searching
options are available to you:
Basic Text Searching
Advanced Text Searching
Numerical properties in Property Lists and Tables
can be searched, but only as text; that is, if you
perform a search for 500* you will find 500 g, 500
atm, etc.; you cannot search for a numerical range or
perform a greater/less than search with the Query
Text field. Also, the advanced text searching
options do not apply to Property Lists and Tables.
Depending upon your database settings, text
entered into MS Word fields and Styled Text
fields may not be available for searching
immediately after it is entered. There may be a delay
of several hours.
Basic Text Searching
You can use basic text searching, or querying, to
find information in MS Word and Notes portions
of E-Notebook. There are a number of special
characters used in basic text searching which will
help narrow or increase search results.
Normally, the more narrow a search, the more
precise the search results become, making it easier
to find the information you need. As a search
becomes broader, the number of hits in the search
results list becomes greater.
Different types of basic text searching are available.
See the following topics for more information:
Exact Phrase Matching
CambridgeSoft
Searching for Text with the Query Text Field
 Wildcard Searching
Exact Phrase Matching
If a search is meant to find only exact matches for
the text entered, exact word or phrase matching
should be used. This is the most simple search, or
query, that returns exactly the information
requested.
For example, the following searches really mean:
Searching For ... Returns ...
thymidine synthesis the words thymidine
synthesis in that order, with
no words between them in
the text of a document.
cyclohexane the word cyclohexane in
the text of a document.
Wildcard Searching
If a prefix or a suffix for a word is either unknown
or variable, wildcard characters become useful in a
free test search to return all words with the same
word root. Wildcard characters can be used in a
basic text search when searching for all documents
that contain a part of a word. This kind of search
typically returns more matches to search criteria
than the exact phrase search.
For example, the following searches really mean:
Searching For ... Returns ...
Searching For ... Returns ...
*ethane any word with ethane as
the last 6 letters in a docu-
ments text. Matches
include ethane, and
methane.
Advanced Text Searching
E-Notebook offers a number of advanced text
searching options for searching Notes and MS
Word documents in the application. Using specific
operators in an advanced search allows you to
narrow search parameters dramatically.
Escape Characters
In order to perform a query over words or symbols
that have special meaning to query expressions,
such as & or |, you must escape them. There are two
ways to escape characters in a query expression,
using curly brackets {} or a backslash \.
Curly Brackets {}
Use braces to escape a string of characters or
symbols. Everything within a set of braces in
considered part of the escape sequence. When you
use braces to escape a single character, the escaped
character becomes a separate token in the query.
The following table has examples of how to use
curly brackets to escape an ampersand (&) and
a dash (-).

Instead of Use
synth* any word with synth as the
first 5 letters in a docu-
ments text. Matches AT&T {AT&T}
include synthesis,
synthetic, and syntheses. high-voltage {high-voltage}

Chem & BioOffice 2006 /E-Notebook Searching 627

Searching for Text with the Query Text Field
 Backslash \
Use the backslash character to escape a single
character or symbol. Only the character
immediately following the backslash is escaped.
Administrator
The ABOUT operator becomes very powerful when
coupled with other operators, such as AND or NOT.
For example, the following searches really mean:

The following table has examples of how to use a

Searching For ... Returns ...
backslash to escape an ampersand (&) and a dash (-
).
ABOUT (carbon) any word with words
AND diamond related to carbon as well as
Instead of Use
the word diamond in the
documents text.
AT&T AT\&T
ABOUT (carbon) any word with words
high-voltage high\-voltage NOT ABOUT related to carbon but
(diamond) excluding the word
diamond in the docu-
ABOUT
ments text.
The ABOUT operator, when used in an advanced
text search, retrieves documents that contain
information related to a word or phrase. NOTE: For advanced Oracle users: The word or phrase
specified in an ABOUT query does not have to exactly
Use the ABOUT operator by entering the word
match the themes stored in the index. Oracle automatically
ABOUT in all capital letters followed by the word or
normalizes the word or phrase before performing lookup in
phrase on which to search in parentheses.
the Text index.
ABOUT searches are always case-sensitive. The text
string inside the parentheses is interpreted with
respect to case. AND (&)
The AND operator used in an advanced text search
For example, the following searches really mean:
finds documents that contain more than one word
or phrase. The AND operator is used to search for
Searching For ... Returns ... documents that contain at least one occurrence of
each of the query terms.
ABOUT (carbon) any word with words The AND operator is used by entering the first term,
related to carbon in the then the word AND in all capital letters (or entering
documents text. Matches the ampersand (& symbol)) followed by another
include coal and diamond. word or phrase on which to perform a search.

ABOUT (carbon by- any phrases with words

products from related to carbon by-
syntheses at 25 products from syntheses at
degrees Celsius) 25 degrees Celsius in the
documents text.

628 Searching CambridgeSoft

Searching for Text with the Query Text Field
For example, the following searches really mean: For example, the following searches really mean:

Searching For ... Returns ... Searching For ... Returns ...

carbon AND diamond both the words carbon, graphite EQUIV the words graphite or
and diamond, found diamond diamond found anywhere
anywhere within a docu- within a documents text.
ments text.
graphite = diamond the words graphite or
carbon & diamond both the words carbon, diamond found anywhere
and diamond, found within a documents text.
anywhere within a docu-
ments text. carbon the words carbon dioxide,
dioxide=monoxide carbon monoxide, or both
carbon & diamond & all the words carbon, terms found anywhere
graphite diamond, and graphite, within a documents text.
found anywhere within
a documents text.
NOTE: The EQUIValent operator has higher precedence
thymidine synthesis both the phrases thymi- than all other operators except the expansion operators
AND carbon dioxide dine synthesis, and (fuzzy, soundex, stem).
carbon dioxide, found
anywhere within a docu-
ments text. Fuzzy (?)
The fuzzy operator used in an advanced text search,
EQUIValence (=)
or query, will find documents that contain words
The EQUIValence operator used in an advanced text similar to the word used in a search. For example,
search, or query, will allow the user to find the fuzzy operator can be used to expand queries to
documents that contain information about words include words that are spelled similarly to the
that can be used in place of each other, alone or in specified term. This type of expansion is helpful for
a phrase. The EQUIValence operator is used to finding more accurate results when there are
specify an acceptable substitution for a word in a
frequent misspellings, or alternate spellings in the
query.
documents in the database.
The EQUIValence operator is used by, entering
EQUIV in all capital letters (or enter the equals sign The fuzzy operator is used by entering a question
(=)), followed by the phrase on which the search is mark (?), followed by the word on which to perform
to be performed. a search.

Chem & BioOffice 2006 /E-Notebook Searching 629

Searching for Text with the Query Text Field
 For example, the following searches really mean: For example, the following searches really mean:

Searching For ... Returns ... Searching For ... Returns ...
Administrator

?boron any word spelled similarly carbon - diamond the words carbon and
to boron found anywhere diamond in them, but
within a documents text. documents with diamond
Matches include baron. are listed last.

?read any words spelled similarly carbon MINUS the words carbon and
to read found anywhere diamond diamond in them, but
within a documents text. documents with diamond
Matches include read, lead, are listed last.
and real.
diamond -carbon the words diamond and
?chemist any words spelled similarly carbon in them, but docu-
to chemist found anywhere ments with carbon are
within a documents text. listed last.
Matches include chemists
and chemistry.
NEAR
MINUS (-) The NEAR operator is used in an advanced text
The MINUS operator can be used in an advanced search, or query, to find documents that contain
text search, or query, to find documents that two phrases that are close together. The maximum
contain two phrases, with the first phrase taking distance between the two terms can be specified.
precedence. The MINUS operator is used to search
for documents that contain two query terms, but The NEAR operator is used by entering the first
documents containing the second term will ranked term, followed by NEAR in all capital letters (or
lower than documents without the second term. enter a semicolon (;)), followed by the second term
The MINUS operator is useful for lowering the on which the search is to be performed.
score of documents that contain a certain term,
without eliminating those documents. Use the NEAR operator to return documents based
The MINUS operator is used by, entering the first on the proximity of two or more query terms.
term, then MINUS in all capital letters (or enter the
minus sign or hyphen (-)), followed by another term NOTE: NEAR cannot be used in ABOUT queries.
on which to perform a search.

630 Searching CambridgeSoft

Searching for Text with the Query Text Field
For example, the following searches really mean:
Searching For ... Returns ...
Searching For ... Returns ...
NEAR ((carbon, the words carbon,
diamond), 10) AND diamond, and benzene in
carbon NEAR the words carbon and
benzene them, but only when
diamond diamond in them, but
carbon and diamond
only when they appear
appear less than 10 words
less than 100 words apart
apart and in no specific
and in no specific order.
order.
NEAR uses the following defaults:
NEAR ((carbon, the words carbon,
Search terms are found if they are 100 words diamond = diamond, and graphite in
apart or less, unless specified otherwise. Use graphite), 10) them, but only when
whole numbers between 1 and 100. carbon and diamond or
Search terms are found in any order, specified carbon and graphite appear
otherwise. Use TRUE or FALSE. less than 10 words apart
The NEAR operator can be used with other and in no specific order.
operators, such as AND, OR, and EQUIValence.
For example, the following searches really mean: NOT (~)
The NOT operator can be used in an advanced text
Searching For ... Returns ... search, or query, to find documents that contain a
word or phrase, but only when it appears without a
second word or phrase. The NOT operator is used
NEAR ((carbon, the words carbon and by, entering the term to be found, followed by the
diamond), 20, diamond in them, less than word NOT in all capital letters (or enter a tilde (~)),
FALSE) 20 words apart, in no followed by the term to be excluded in the search.
specific order.
Use the NOT operator to search for documents that
contain one query term and not another.
NEAR ((carbon, the words carbon and
diamond), 20, diamond in them, less than
TRUE) 20 words apart, in this
specific order.

Chem & BioOffice 2006 /E-Notebook Searching 631

Searching for Text with the Query Text Field
 For example, the following searches really mean: For example, the following searches really mean:

Searching For ... Returns ... Searching For ... Returns ...
Administrator

carbon NOT the word carbon, but not
diamond the word diamond
anywhere in the docu-
ments text.
carbon ~ diamond the word carbon, but not
the word diamond
anywhere in the docu-
ments text.
carbon NOT the word carbon, but not
(diamond OR the word diamond or
graphite) graphite anywhere in the
documents text.
NOTE: The NOT operator does not affect other logical
operators.
carbon OR diamond the words carbon,
diamond, or both anywhere
in the documents text.
carbon | diamond the words carbon,
diamond, or both anywhere
in the documents text.
carbon OR diamond the words carbon,
OR graphite diamond, graphite, or any
combination of the terms
anywhere in the docu-
ments text
thymidine synthesis the words thymidine
OR carbon dioxide synthesis, carbon dioxide,
or both terms anywhere in
the documents text.

OR (|) Soundex (!)

The OR operator can be used in an advanced text
search, or query, to find documents that contain
information about any words in the query, but not
necessarily all words in the query. The OR operator
is used by, entering the first term, followed by the
word OR in all capital letters (or enter the pipe (|)),
followed by another term on which the search is to
be performed.
Use the OR operator to search for documents that
contain at least one occurrence of any of the query
terms.
The soundex operator is used in an advanced text
search, or query, to find documents that contain
words that sound like the word used in a search.
The soundex operator is used by, entering an
exclamation point (!), followed by the word on
which to perform a search.
Use the soundex (!) operator to expand queries to
include words that have similar sounds; that is,
words that sound like other words. This function
allows comparison of words that are spelled
differently, but sound alike in English.

632 Searching CambridgeSoft

Searching for Text with the Query Text Field
For example, the following searches really mean:
Searching For ... Returns ...
!carben any words that sound like
the word carben in a docu-
ments text. Matches
include carbon and
carboxylic.
?read any words that sound like
the word read in a docu-
ments text. Matches
include read and lead.
Use the stem operator to search for terms that have
the same linguistic root as the query term. Stem
expands a query to include all terms with the same
stem or root word as the search term.
For example, the following searches really mean:
Searching For ... Returns ...
$commit any words with the root
commit found in the docu-
ments text. Matches
include commits, commit-
ting, committee, and
committed.

$chemist any words with the root

Stem ($)
chemist found in the docu-
The stem operator is used in an advanced text ments text. Matches
search, or query, to find documents that contain include chemist, chemistry,
words similar to the word used in a search. When and chemists in them.
the stem operator is used, enter a dollar sign ($),
followed by the word on which to perform a search.

Chem & BioOffice 2006 /E-Notebook Searching 633

Searching for Text with the Query Text Field
Administrator

634 Searching CambridgeSoft

Searching for Text with the Query Text Field
Chapter 33: Introducing Enterprise
CombiChem for E-Notebook
With the introduction of CombiChem, it is now
possible for you to set up and manage
combinatorial chemistry libraries in E-Notebook.
You can set up a generic reaction, add reactants, and
automatically enumerate the products.
Features include:
Data import/export import reactants from
an SD file or other chemical database, and
CombiChem will scan the database for reac-
tants that match generic
components. CombiChem also allows you to
export enumerated products to an SD file.
Select reaction sites when more than one
reaction site is possible, you can select which
reaction sites you would like to include in the
product enumeration process.
Automatic stoichiometry calculations
When you enumerate products in
CombiChem, you can automatically populate
the stoichiometry grid for each individual reac-
tion.
Flexible plate handling you can determine
the plate size, location of blanks, and grouping
order of reactants in the plate.
Navigator and structure palettes you can
browse through CombiChem easily. Clicking a
location in the CombiChem Navigator
displays the reaction components in that loca-
tion. With the structure palette, you can scroll
through the corresponding structures of reac-
tants and products.
Chem & BioOffice 2006 /E-Notebook
Configurable data sections as with all
E-Notebook sections, the configuration of
CombiChem sections may be modified easily
so that your data is presented in the most effec-
tive manner.
See the following topics:
Setting up the Generic Reaction
Managing CombiChem Reactants
Enumerating and Managing CombiChem
Products
Using the CombiChem Navigator and Struc-
ture Window
Managing Plate Layout and Structure Palette
Settings
CombiChem is sold as a separate, E-Notebook add-
in feature, and may not be available in your
configuration of E-Notebook.
Setting up the Generic
Reaction
In a CombiChem Library, you may either add a new
generic reaction, or prepare a reaction from an
existing experiment.
Adding a Generic Reaction
CombiChem is a reaction-based combinatorial
product. You first enter a reaction template with R-
groups at the variable sites in your starting
materials, then search for reactants based on these
structures. CombiChem puts your final product
structures together and creates a virtual library. All
sites of variability require unique R-group
designations.
Introducing CombiChem for E-Notebook 635
Setting up the Generic Reaction
 An example of a reaction that CombiChem To view the generic components of the reaction,
supports is shown below: click the Components tab.

H2 N
R4 R3 R4 The display changes to show one of the generic
NH R3
components of the reaction.
Administrator

R3 NH
R2 NH

R4 R2

R2

R1
R1 R1

To add a generic reaction to a CombiChem Library:

1. From a CombiChem Library section, click
Reaction in the CombiChem menu.
2. Select Edit Reaction.
The Edit Structure window, a ChemDraw
window, appears.
3. Either draw the reaction in the window, or
right-click within the window and select File,
then Open, to open an existing reaction file.
4. Click OK when you have finished editing the
reaction.
The Edit Structure window closes and the
reaction appears in E-Notebook.
To view a particular component, select it from the
dropdown list.
To return to the generic reaction, click the Reaction
tab that is next to the Components tab.
Preparing a Reaction from
an Existing Experiment
CombiChem makes it possible for you to prepare a
generic reaction from an existing experiment.
When you select this option, the generic products
of the existing reaction become the generic
reactants of the new experiment.
To prepare a generic reaction from an existing
experiment:
1. From a CombiChem Library section, click
Reaction in the CombiChem menu.

2. Select Prepare from Existing Experiment.

636 Introducing CombiChem for E-Notebook CambridgeSoft

Setting up the Generic Reaction
 The Select Experiment dialog appears, with Importing Reactants from a Chemical
the Collection Tree displayed in the left frame. Database
To add reactants to a CombiChem Library from a
chemical database:

1. From a CombiChem Library section, click

Reactants in the CombiChem menu.

The Reactants menu appears

3. Click the experiment to select it in the Collec-
tion Tree, then click the Select button. 2. Select Import Reactants.

The generic products of the reaction you
selected appear in the reaction field.
See Adding a Generic Reaction on page 635 for
instructions on how to edit the reaction.
The Import Reactants dialog appears, and
you are prompted to select the generic
component that will be matched against the
chemical database.

Managing CombiChem
Reactants
This portion of the CombiChem guide provides
instructions for managing reactants in CombiChem O
- adding and editing reactants, and specifying
reaction sites for the product enumeration process.
R1

Adding Reactants from a

Chemical Database
After you have added a generic reaction, you may
either add reactants from a chemical database, or
draw them using the ChemDraw tools. The source 3. Select the component to be matched from the
of the reactants can be a ChemFinder database or dropdown list, and click OK.
any other datasource that can export MDL SDFiles.
The Open Chemical Structures dialog
(To create an SDFile from ChemFinder, you can
appears, and you are prompted to select the
simply select the Export command from the File
database file to be scanned for matches.
menu after you have run a ChemFinder query to
find the reactants you wish to include in the file). 4. Select the file and click Open.

Chem & BioOffice 2006 /E-Notebook Introducing CombiChem for E-Notebook 637
Managing CombiChem Reactants
 The file you selected is scanned for structures The Add Reactant dialog appears, as shown
that match the generic reactant. The matches below.
are imported into E-Notebook. Each imported
reactant appears as a subsection within the
Administrator

Reactants section.

5. Use the scroll bar to scroll through the reac-

tants:

displays the first reactant

3. In the left frame, select a generic reactant from

displays the previous reactant the dropdown list.
The correct generic reactant appears in the left
displays the next reactant frame.
4. Using the navigator to the right, click a location
displays the last reactant for the reactant to select that location.
5. Select an Add Option:
You may also browse to a particular reactant by
right-clicking the scroll bar and selecting Go To Insert After inserts the reactant after the
Section. selected reactant (to the the right of the
selected reactant in the plate).
Insert Before inserts the reactant before
the selected reactant (to the left of the
selected reactant in the plate).
Overwrite replaces the reactant in the
selected location.
6. Click OK.
Adding Reactants Manually
The Edit Reactant Structure dialog appears.
In addition to adding reactants from a chemical 7. Draw the reactant or open a structure file.
database, you may add the reactants manually.
8. Click OK.
To add reactants manually: CombiChem performs a check to ensure that the
reactant matches the generic component you
1. From a CombiChem Library section, click
selected. If it does not match, a message is displayed
Reactants in the CombiChem menu.
to that effect, and you are prompted to change the
The Reactants menu appears. drawing. If it does match, the Add Reactant dialog
closes, and the reactant appears as a new subsection
2. Select Add Reactant. in the CombiChem library.

638 Introducing CombiChem for E-Notebook CambridgeSoft

Managing CombiChem Reactants
Checking Reaction Sites
When a reactant has more than one possible
reaction site, CombiChem makes it possible to
choose which site(s) participate in the product
enumeration process, and which do not.
To check and select reaction sites:
1. From a CombiChem Library section, click
Reactants in the CombiChem menu.
The Reactants menu appears.
2. Select Check Reaction Sites.
The Check Reactants dialog appears. If there
are multiple matching reaction sites, a message
appears to that effect. The different reaction
sites appear in tabs.
3. Click the numbered tabs to the right in order to
view the different reaction sites.
Chem & BioOffice 2006 /E-Notebook
By default, all of the possible reaction sites will
be used in the product enumeration process. If
there are certain reaction sites you do not want
to use in the enumeration process, click the Use
checkbox to deselect the site.
4. Click OK to close the Check Reactants dialog.
Editing Reactants
Once you have added reactants to a CombiChem
Library, either manually or from a chemical
database, you may edit their structures.
To edit the structure of a reactant in a CombiChem
Library:
1. In a a CombiChem Library section, click the
Reactants tab.
2. Use the scroll bar or the Navigator to select the
reactant you wish to modify.
The reactant section you wish to modify
appears.
3. Click Reactants in the CombiChem menu.
The Reactants menu appears.
4. Select Edit Current Reactant.
The Edit Structure dialog appears, and you
may use the ChemDraw toolbar to edit the
structure.
5. Make your edits, and click OK.
CombiChem performs a check to ensure that the
reactant matches the generic component you
selected. If it does not match, a message is displayed
to that effect, and you are prompted to change the
drawing. If it does match, the Edit Structure dialog
closes, and the modified structure appears in the
CombiChem library.
Introducing CombiChem for E-Notebook 639
Managing CombiChem Reactants
 Removing Reactants from a
CombiChem Library
After you have added reactants to a CombiChem
Administrator
Library, you may delete them. You have the option
to remove a selected reactant from the CombiChem
Library or to remove all of the reactants at once.
Removing a Selected Reactant
To remove a selected reactant from the
CombiChem Library:
1. In a CombiChem Library section, browse to
the reactant you wish to remove.
The reactant appears.
2. Click Reactants in the CombiChem menu.
The Reactants menu appears.
3. Select Remove Current Reactant.
A message appears, prompting you to confirm
that you wish to remove the reactant.
4. Click OK to confirm.
The reactant is removed from the CombiChem
Library,
Removing All Reactants from a
CombiChem Library
To remove all of the reactants from a CombiChem
Library:
640 Introducing CombiChem for E-Notebook
Enumerating and Managing CombiChem Products
1. Click Reactants in the CombiChem menu.
The Reactants menu appears.
2. Select Remove All Reactants.
A message appears, stating that the action will
remove all reactants and invalidate all products
already enumerated.
3. Click OK to proceed.
All of the reactants are removed from the
CombiChem Library.
Enumerating and
Managing CombiChem
Products
Once you have added reactants to a CombiChem
library, you can set up a template to be used for the
enumerated products. Then, you can enumerate the
products, either enumerating all possible products,
or only selected products.
Working with the Enumera-
tion Template
Before enumerating the products of a generic
reaction, you must create an Enumeration
Template, which specifies the layout and content of
the form for each enumerated product. You may
either create a template to display the reactions and
their corresponding stoichiometry grids, or you
may create a template to display the structure and
properties of the product.
Creating an Enumeration Template
To create the enumeration template:
1. From a CombiChem Library section, click the
Products section.
The Products section appears
2. From a CombiChem Library section, click
Products in the CombiChem menu.
CambridgeSoft
 The Products menu appears.
3. Select Create Enumeration Template.
The Select Product Template Type dialog
appears, and prompts you to select the type of
template. In the example below, you may select
either:
Parallel or Small Array displays each
enumerated product in a reaction that also
shows the reactants.
Larger Array displays each enumerated
product as a structure; the output structure
template does not display the reactants in
the drawing.
4. Click the type of template you desire to select,
and click OK.
The template appears in the Products section
of the CombiChem Library.
5. Add any information you wish to the template.
This may be reaction properties, etc. The infor-
mation you enter will appear in the output
section for each product you enumerate with
this template.
Chem & BioOffice 2006 /E-Notebook
Enumerating and Managing CombiChem Products
Once you have created the enumeration template,
you may enumerate products of the reaction. If you
would like to apply different settings to different
wells, you can set up an enumeration template, then
use the Enumerate Selection feature to enumerate
only selected wells. Then, you can set up another
enumeration template, and enumerate a different
selection of wells. Each time you enumerate a
selection, the template settings will be applied to
each product that is enumerated.
Showing an Enumeration Template
To view the current enumeration template:
1. From a CombiChem Library section, click
Products in the CombiChem menu.
The Products menu appears
2. Select Show Enumeration Template.
The Enumeration Template appears.
Updating an Enumeration Template
If you wish to edit the current Enumeration
Template:
1. From a CombiChem Library section, click
Products in the CombiChem menu.
The Products menu appears.
2. Select Update Enumeration Template.
The Enumeration Template appears, and you
may edit it as desired.
Removing an Enumeration Template
If you wish to remove the current Enumeration
Template to, for example, replace it with a new
Enumeration Template:
1. From a CombiChem Library section, click
Products in the CombiChem menu.
The Products menu appears.
2. Select Remove Enumeration Template.
Introducing CombiChem for E-Notebook 641
 The Enumeration Template is removed from
the CombiChem Library.
Enumerating Products
Administrator
When you enumerate the products of the generic
reaction, you may either enumerate all possible
products, or only a selection of the products.
Enumerating All of the Products of a
Generic Reaction
To enumerate all of the products for a reaction:
1. From a CombiChem Library section, click
Products in the CombiChem menu.
The Products menu appears
2. Select Enumerate All.
The Enumerating Products dialog appears,
showing the progress of the enumeration.
When the enumeration is complete, each product
appears as a subsection in the Products tab.
You may scroll through the products to view them.
Depending upon your enumeration template, the
products will either be displayed as structures or
displayed in reactions. If they are displayed in
reactions, the stoichiometry grid will be populated
for each individual reaction.
If, in the enumeration process, the number of
products exceeds the number of wells in the
product plate, additional plates will be generated.
Enumerating Selected Products of a
Generic Reaction
To enumerate only selected products of the
reaction:
642 Introducing CombiChem for E-Notebook
Enumerating and Managing CombiChem Products
1. Click the Navigator button.
The navigator appears.
2. Using your mouse, highlight the locations
representing the products you wish to
enumerate. You do this by clicking the first
location in the range, then dragging your
mouse to select the entire range. Or, you may
use Ctrl+click to select multiple locations that
are not contiguous.
3. Right-click your selection, and choose
Enumerate Selection from the menu that
appears.
The selected products are enumerated, and
appear in the Products section. (In this
example, the products corresponding to
columns 1 and 2 will be enumerated).
Exporting Products to an SD
File
CombiChem makes it possible for you to export
products to an SD file, which you may then import
into ChemFinder.
To export products to an SD file:
1. From a CombiChem Library section, click the
Products tab to select it.
The Products tab appears.
2. Click Products in the CombiChem menu.
CambridgeSoft
 The Products menu appears. A message appears, stating that the action will
irrevocably remove all enumerated products,
and asking you to confirm that you wish to
remove them.
4. Click Yes to confirm.
The products are removed from the
CombiChem Library.

Using the CombiChem

Navigator and Structure
Window
The CombiChem Navigator represents a plate, and
can be used as a tool to browse through the
3. Select Export to SD File. reactants and products in CombiChem. When a
location is selected in the CombiChem Navigator,
A dialog appears, and you are prompted to the CombiChem Structure Window displays the
enter a name and location for the file. components of the reaction in that location.
4. Enter the name and location and click Save.
The products are exported to the SD File. The
file may be opened with ChemFinder.
You may also open the file with ChemFinder for
Excel, which is useful for viewing and printing the
products.

Removing Products from a Both the Navigator and the Structure Window can
CombiChem Library be viewed either in a docked position on the screen
or as floating palettes.
After you have enumerated products in a
CombiChem Library, you may remove them from Using the CombiChem Navi-
the library.
gator
To remove the products from a CombiChem
Library: CombiChem offers a color-coded Navigator palette
that represents a plate. When you are viewing the
1. In a CombiChem Library section, click the Products portion of a CombiChem library, each
Products tab to select it. location or well in the Navigator represents an
The products tab appears. individual reaction. Selecting a well makes it
possible for you to view the reaction components
2. Click Products in the CombiChem menu.
that correspond to that well. Thus, by clicking
The Products menu appears. locations in the Navigator, you can browse through
3. Select Remove Products. the reactions/products in the CombiChem library.

Chem & BioOffice 2006 /E-Notebook Introducing CombiChem for E-Notebook 643
Using the CombiChem Navigator and Structure Window
 At the base of the navigator, there is a tab for each
generic reactant, and a tab for enumerated
products. Clicking a tab displays the locations of the
corresponding component in the plate. Each
Administrator
there are seven, individual structures corresponding
to the second generic component. Again, each
structure is denoted with a unique color.

unique reactant or product is denoted with a unique

color.

In addition to the Navigator, CombiChem provides

a structure palette, which displays the structures of
the reactants and products in a well. When you click
a particular well in the navigator and the structure
palette is displayed, the structure palette will change Clicking the P1 tab displays the enumerated
to display the structures in the well you selected. See products of the reaction. In this example, there are
Using the Structure Window on page 646 for ninety one(13 C1 * 7 C2)one for each unique
more information. combination of the reactants.
When you are viewing the Reactants portion of a
CombiChem library, the Navigator changes to
display the reactants plate, and allows you to browse
through the individual reactants.

Using the Navigator when in Products

Mode
Below, the Products section of a CombiChem
Library is shown. The products have already been
enumerated. Clicking the C1 tab in the Navigator
displays the plate locations of the reactants that
match C1, the first generic component of the
reaction. In this example, you can see that there are
thirteen separate structures corresponding to the
first generic component. Each structure is denoted
with a unique color.
To display any one of the enumerated
products/reactions, simply click the well
corresponding to the reaction in the Navigator.
The displayed section changes to reflect your
choice.
Using the Navigator in Reactants Mode
In addition to using the Navigator to browse
through products/reactions when in Products
mode, you may use the Navigator when in
Reactants mode. The plate in this case may
represent the locations of the reactant stocks that
are used to fill the product/reaction plate.

Below, the Reactants section of the same

Clicking the C2 tab in the Navigator displays the CombiChem library is shown. The tab for C1,
locations of the reactants that match C2, the second corresponding to the first generic reactant, is
generic component of the reaction. In this example, displayed. Click any of the locations in the

644 Introducing CombiChem for E-Notebook CambridgeSoft

Using the CombiChem Navigator and Structure Window
Navigator to view the corresponding structure that
matches C1. For example, clicking position A2 in
the Navigator displays the second C1 reactant.
Clicking the location A7 in the navigator displays
the second structure that matches C1:
To view the reactants that match the second generic
component of the reaction, click the C2 tab. Then,
click any of the locations in the Navigator to view
the corresponding structure that matches generic
component C2.
Viewing and Hiding the Docked
CombiChem Navigator
You have the option to either view the navigator
palette in a docked position or in a floating position,
depending upon your viewing preference. Initially,
the Navigator is docked, but you may remove it
from its dock and relocate it to any area on the
CombiChem screen. This allows you to customize
the appearance of your CombiChem library.
Chem & BioOffice 2006 /E-Notebook
Using the CombiChem Navigator and Structure Window
When the CombiChem Navigator is docked, you
use the Navigator button to display it. To view the
CombiChem Navigator when it is docked,
From the Reactants or Products section in a
CombiChem Library, move your cursor until it is
over the Navigator button.
The Navigator appears, sliding out from its dock.
To hide the docked the navigator, simply move your
cursor to an area of the screen that is outside of the
Navigator, and the Navigator will slide into its dock
again.
Viewing the Navigator as a Floating
Palette
To remove the Navigator from its dock and view it
as a floating palette, as shown below.
1. If the Navigator is not already visible, move
your cursor over the Navigator button, so that
the Navigator becomes visible and slides out
from its dock.
2. Click the docking button in the upper
right corner of the Navigator palette.
The appearance of the docking button changes
to indicate that the Navigator is no longer
docked.
3. Drag the Navigator to any place on the screen.
The Navigator appears in the new location
You may also resize the Navigator for more
favorable viewing. (To do this, move your cursor to
the edge of the Navigator until it appears as a
double-headed arrow, then drag your mouse to
resize the Navigator).
Docking the Navigator at Another Loca-
tion
You may also dock the navigator elsewhere, such as
at the top or bottom of the section. To do this
Introducing CombiChem for E-Notebook 645
 1. View the Navigator as a floating palette. This 1. From the Products section in a CombiChem
may require releasing the Navigator from its Library, click a location in the Navigator to
dock, as described above. select it.

The reaction or product corresponding to that

Administrator

2. Drag the Navigator toward a boundary of the

section. well is displayed.

2. Move your cursor until it is over the Structure

As you drag the Navigator a gray rectangle
appears to show you what the new location will
be if you release the mouse at that point.
3. Drag the Navigator until the gray rectangle
expands to the width or length of the section.
This should happen when your cursor is posi-
tion over an edge or corner of the section.
4. Release the mouse.
The Navigator is docked at the new location.
If you copy the Structure palette on top of the
Navigator, a button for each palette will appear,
allowing you to switch back and forth between the
two palettes.
Using the Structure Window
When you select a location in the CombiChem
Navigator, the CombiChem Structure Window
displays the structures that participate in that
reaction. You may use the scroll bar to scroll
through the reactants and enumerated products in
that well.
button. (The button may be either vertically or
horizontally oriented).
The Structure Window appears, sliding out
from its dock.
3. Use the scrollbar at the base of the Structure
Window to scroll through the reactants and
product in the well.
4. To hide the docked Structure Window, simply
move your cursor to an area of the screen that
is outside of the Structure Window, and the
Structure Window will slide into its dock again.
In the example shown below, the Navigator is
displayed in the upper left. The well at location C 4
is selected. The reaction corresponding to this well
is shown to the right. In the lower left, the Structure
Window displays the structure that matches the first
generic component of this reaction.
TIP: The color of the reactant in the Navigator and the
Structure Window are the same.

Viewing and Hiding the Docked

CombiChem Structure Window
When the CombiChem Structure Window is
docked, you use the Structure button to display it.

To view the CombiChem Structure Window when

it is docked:

646 Introducing CombiChem for E-Notebook CambridgeSoft

Using the CombiChem Navigator and Structure Window
Scrolling one position to the right using the scroll
bar at the base on the Structure Window displays
the reactant in this well that matches C2, the second
generic component of the reaction.
Scrolling to the right once more displays the
product of the reaction in this well.
NOTE: The selected tab in the Navigator does not change
automatically to reflect the component you are viewing in the
Structure Window.
Chem & BioOffice 2006 /E-Notebook
Using the CombiChem Navigator and Structure Window
Viewing the Structure Window as a
Floating Palette
As with the Navigator palette, you have the option
to either view the Structure Window in a docked
position or in a floating position, depending upon
your preference. Initially, the Structure Window is
docked, but you may remove it from its dock and
relocate it to any area on the CombiChem screen.
This allows you to customize the appearance of
your CombiChem library.
To remove the Structure Window from its dock and
view it as a floating palette, as shown below.
1. If the Structure Window is not already visible,
move your cursor over the Structure Window
button, so that the Structure Window becomes
visible and slides out from its dock.
2. Click the docking button in the upper
right corner of the Structure Window.
The appearance of the docking button changes
to indicate that the Structure Window is
no longer docked.
3. Drag the Structure Window to any place on the
screen.
The Structure Window appears in the new
location
You may also resize the Structure Window for more
favorable viewing. To do this:
1. Move your cursor to the edge of the Structure
Window until it appears as a double-headed
arrow,.
2. Drag your mouse to resize the Structure
Window.
Docking the Structure Window at
Another Location
You may also dock the Structure Window
elsewhere, such as at the top or bottom of the
section. To do this:
Introducing CombiChem for E-Notebook 647
 1. View the Structure Window as a floating
palette. This may require releasing the
Structure Window from its dock, as described
above.
Administrator
2. Drag the Structure Window toward a boundary
of the section.
As you drag the Structure Window, a gray
rectangle appears to show you what the new
location will be if you release the mouse at that
point.
3. Drag the Structure Window until the gray rect-
angle expands to the width or length of the
section. This should happen when your cursor
is positioned over the edge or corner of the
section.
4. Release the mouse.
The Structure Window is docked at the new
location.
If you drag the Structure Window on top of the
Navigator, a button for each palette will appear,
allowing you to switch back and forth between the
two palettes.
Managing Plate Layout
and Structure Palette
Settings
The CombiChem library has a number of settings
that you can modify in order to present your data
accurately and effectively. You can modify the
layout of reactants and products in a plate. You can
also modify the naming and numbering schemes for
enumerated products. In addition, CombiChem
makes it possible for you to modify the way that
structures are displayed in the library.
648 Introducing CombiChem for E-Notebook
Managing Plate Layout and Structure Palette Settings
Editing Structure Palette
Display Settings
You can modify the settings for the structure palette
that is used in a CombiChem library. The settings
you apply will only be visible in the structure
window of the CombiChem Navigator.
To do this:
1. From a CombiChem library, click Tools in the
menu.
The Tools menu appears.
2. Select Edit Structure Palette Display Settings.
The Edit Display Settings dialog appears. It
contains a ChemDraw field.
3. Right-click within the ChemDraw field to
display the ChemDraw menu.
The menu is displayed.
4. Select File, and Apply Document Settings From.
5. Select the source for the settings from the list
that appears, or select Other to choose another
file.
6. Click OK to close the Edit Display Setting
dialog.
Editing Reactant Layout
Settings
You can modify the layout of reactant plates in
CombiChem. When the Reactants tab is selected in
the CombiChem Library, the Navigator will display
the layout that you have configured.
To do this:
CambridgeSoft
 1. From a CombiChem Library, click Tools in the
menu.
The Tools menu appears.
2. Select Edit Reactant Layout Settings.
The Reactant Layout dialog appears.
Columns the number of columns in the
plate.
Rows the number of rows in the plate.
Fill Direction the direction in which the
plate is populated with the structures that
match this component.
5. Click another tab if you wish to modify the
layout of another component.
6. Click OK to close the dialog.

Editing Product Layout

Settings
You can modify the layout of the product/reaction
plate in CombiChem, changing the size of the plate,
the grouping order of components, and specifying
which wells are to remain empty.
When the Products tab is selected in the
CombiChem Library, the Navigator will display the
layout that you have configured.
To edit the product layout settings:
1. From a CombiChem library, click Tools in the
menu.
The Tools menu appears.

3. Click the tab corresponding to the generic

reactant whose layout you wish to change. In
this example, C1 is selected.
4. You may modify the following information: 2. Select Edit Product Layout Settings.

Chem & BioOffice 2006 /E-Notebook Introducing CombiChem for E-Notebook 649
Managing Plate Layout and Structure Palette Settings
 The Product Layout dialog appears, open to 2. Right-click your selection, and select Disable
the Design tab. Selection from the context menu.
Administrator

Specifying Empty Wells in the Plate The Xs are removed from the wells, leaving the
wells blank:
You can specify which wells are to be left blank in
the plate. To do this,
1. Use your mouse to select the wells you would
like to be empty. You may do this by:
Clicking the first well you are selecting and
dragging your mouse to the last well, OR
Clicking a column header or row number to
select an entire column or row. You may use
CTRL+click to select multiple columns or
rows.

Alternatively, you may click each well individually to

disable it.

Changing the Size of the Plate

To change the size of the product/reaction plate:

In the Product Layout dialog, type in new

values for the Column Count and Row Count.

650 Introducing CombiChem for E-Notebook CambridgeSoft

Managing Plate Layout and Structure Palette Settings
 The plate layout changes to reflect the new
values.
Changing the Grouping Order
You can change the order in which components are
laid out in the product/reaction plate. By default,
the first generic component is filled into the plate
with a horizontal fill direction, from left to right; the
second generic component is laid out vertically,
within the array of the first component.
3. Mouse over any of the values to view its
1. In the Product Layout dialog, select the first
component to be laid out in the plate from the
dropdown list.
2. Select the Fill Direction for the component
from the dropdown list.
The next component will automatically assume the
fill direction that is perpendicular to your selection.
Setting Product Grid Options
You can modify the settings that determine how
products are named and numbered in a
CombiChem Library.
1. To do this:
From a CombiChem library, click Tools in the menu.
The Tools menu appears.
2. Select Set Product Grid Options.
Chem & BioOffice 2006 /E-Notebook
Managing Plate Layout and Structure Palette Settings
The Set Product Grid Options dialog
appears.
description. You may modify any of the
following:
Grid First Serial Number the number that
is assigned to the first product/reaction plate.
The default value is 0001. (Note that there may
be multiple plates in a library if, during the
enumeration process, the number of products
exceeds the number of locations in the grid).
Grid Name Format the format for the
name of the grid.
&P represents the collection name
&S represents the serial number
In the example above, the name of the
collection is CombiChem-Notebook-009
and the serial number is 0001. Hence, the
grid name is CombiChem Notebook-009-
0001
Product Location ID Format the format
for the ID of the product location.
&R row number
&c column number. Use a lower case
letter for this value.
In the example above, the product location is
row number followed by column number.
So, the product in the first column and
second row would be B1; the product in the
Introducing CombiChem for E-Notebook 651
 fourth column and third row would be C4,
etc. (This assumes that the rows and columns
have not been rearranged in the plate).
Product Name Format the format for the
Administrator
In the example above, the product name is
the grid name followed by the product
location ID. Thus, the name for the product
in location A1 is CombiChem Notebook-

name of the product. 009-0001-A1.

&G grid name (as specified in the grid
4. Click OK to close the dialog and save your
name format)
changes.
&W product location ID (as specified in
the product location ID format).

652 Introducing CombiChem for E-Notebook CambridgeSoft

Managing Plate Layout and Structure Palette Settings
Chapter 34: Miscellaneous Topics
This portion of the guide provides a description of Alternatively, click Tools from the menu bar at
the following features:. the top in the window and select Session
Manager.....
Using the Session Manager

Refreshing E-Notebook

Viewing User Information

Using the Session

Manager The Session Manager appears.

In certain situations, an E-Notebook session may

be left open. With the Session Manager, you can
end your old session, and release any collection that
may be locked by it.

To access the Session Manager,

1. Right-click within a blank portion of the

Collection Tree.

A menu appears:

This dialog shows the Users, Session numbers,

and Start Times for each current session.

Ending a Session
If you wish to end a session:

1. Click the session in the list.

The session is highlighted.

2. Select Session Manager.... 2. Click the End Session button.

Chem & BioOffice 2006 /E-Notebook Miscellaneous Topics 653

Using the Session Manager
 A message appears, asking you to confirm that To do this:
you wish to end the session.
1. Click Browse.
2. Right-click a blank space in the Collection Tree.
Administrator

3. Click Yes.

The session is ended. Any record that was

locked by the session is released.

NOTE: You must have Full Control permission over

your home collection (your user collection) to end your
sessions. A menu appears.
3. Select User Info....

Refreshing E-Notebook The User Properties dialog box appears. It

contains the following information:
If other users add information to E-Notebook, you
may need to refresh your view of E-Notebook so
that you can see their changes. To refresh
E-Notebook:

1. Click Browse.

The Collection Tree appears.

2. Right-click any blank area in the Collections

Tree. Login ID the Login ID of the user who is
currently logged into E-Notebook.
A menu appears.
Password Depending upon the type of login
3. Select Refresh. authentication your system uses, this field may
be used to change the password for the logged-
E-Notebook information is updated. in user.
Administrator a checkbox that indicates
Viewing User Informa- whether the user has administrative privileges.
tion NOTE: This checkbox is only visible if the logged-in
user is an administrator.
You can see specific information about the
user who is currently logged into E-Notebook.

654 Miscellaneous Topics CambridgeSoft

Refreshing E-Notebook
Chapter 35: Managing Section Types
and Forms
Section types are used for displaying and managing
data in E-Notebook. Each section type has a
single form associated with it; this form appears in
the right frame when a section type is selected in the
Collection Tree.
To set up a section type, you add fields, form tools,
and section listeners. Then, you configure the fields
and form tools to create the form. You may also
specify a summary field for a table of contents. The
Section Type Configuration dialog is shown
below.
Chem & BioOffice 2006 /E-Notebook
Once you have configured the form, you create an
export template, which allows users to print
sections of this type, and to export them to MS
Word.
See the following topics for more information:
Creating a New Section Type on page 655.
Managing Fields within a Section Type on
page 656.
Managing Form Tools on page 658.
Managing Section Listeners on page 663.
Configuring a Form on page 666.
Managing Export Templates for Section
Types on page 677.
Managing Summary Fields in a Table of
Contents on page 657.
Creating a New Section
Type
A section type defines an E-Notebook data section
or search section. A section type is composed of
fields, form tools, section listeners, and an export
template.
To create a new section type,
1. In the Collection Tree, right-click the folder or
collection into which you are adding the
section type.
The Collection menu appears.
Managing Section Types and Forms 655
Creating a New Section Type
 2. Select New, then Section Type.
Administrator
A new section type appears in the Collection Tree;
its blank form appears to the right. You are
prompted to enter a new name for the section type.
3. Type in a new name for the section type.
4. Right-click the new section type in the Collec-
tion Tree and select Section Type Configuration
from the menu that appears.
The Section Type Configuration dialog
appears. This is the dialog through which you
add the following components:
Fields
Form Tools
Section Listeners
See the following topics for information
Adding a Field to a Section Type on page
656.
Managing Form Tools on page 658.
Managing Section Listeners on page 663.
Configuring a Form on page 666.
656 Managing Section Types and Forms
Managing Summary Fields in a Table of
Contents on page 657.
Managing Fields within
a Section Type
You can add fields to a section type, and use them
to create a form and an export template. You can
also specify which field will appear in the table of
contents of a container collection. See the following
topics for more information:
Adding a Field to a Section Type on page
656.
Managing Summary Fields in a Table of
Contents on page 657.
For information about the individual fields and
their properties, see Managing Fields on page
697.
Adding a Field to a Section
Type
In order to configure a form for E-Notebook, you
must first add fields to the section type.
To add a field to a section type:
1. Right-click the section type in the collection
tree.
The Collection menu appears.
2. Select Section Type Configuration from the
menu.
The Section Type Configuration dialog
appears:
CambridgeSoft
Managing Fields within a Section Type
 3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the field and select a Field
Type.
Each type of field has its own, special
characteristics and configuration options. See
Managing Fields on page 697 for a
description of each field type, and instructions
for configuring the field.
5. Click Add.
The new field appears in the list of fields.
6. Repeat steps 3 through 5 to add multiple fields
to the section type.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Chem & BioOffice 2006 /E-Notebook
Managing Summary Fields
in a Table of Contents
For each section type, you can specify a summary
field that will appear in the table of contents of a
parent collection. The summary field is displayed in
the table of contents if that section is the first
section in a collection.
For example, if the chemical structure field is the
summary field of a reaction section type, and the
reaction section is the first section in a
page/experiment, then the reaction drawing
will appear in the table of contents for the the
notebook, as shown below:
To set the summary field for a section type,
1. Right-click the section type in the Collection
Tree.
The Collection menu appears.
2. Select Section Type Configuration from the
menu.
The Section Type Configuration dialog
appears:
3. In the right frame, click the field that you wish
to be the summary field for this section type.
Managing Section Types and Forms 657
Managing Fields within a Section Type
 You may only select one of the following types 2. Select Section Type Configuration from the
of fields as a summary field: menu.
a styled text field The Section Type Configuration dialog
a chemical structure field appears:
Administrator

a spectrum field
4. Close the dialog.
If you do not specify a summary field, the name of
the first section will appear in the table of contents.

Managing Form Tools

If you would like to perform data analysis or
messaging within a particular E-Notebook section,
3. Right-click Form Tools, and select New Form
you can associate a form tool with that section type.
Tool.
E-Notebook provides several standard form tools.
See the following topics for more information:
Adding a Form Tool to a Section Type on
page 658.
Viewing and Editing the Properties of a Form
Tool on page 659. 4. A new form tool appears in the tree, and you
Removing a Form Tool from a Section Type prompted to name it.
on page 660.
Managing the Standard Form Tools on page
660.
You can also develop your own, customized form
tools.

Adding a Form Tool to a 5. Enter a name, and fill in the IENFormTool

Section Type ProgID.

A form tool is used to perform a particular function
in an E-Notebook form. E-Notebook provides a
number of form tools, such as the Reaction Form
Tool, which you can add to new section types you
create.
To add a form tool to a section type:
1. Right-click the section type in the Collection
Tree.
The Collection menu appears.
This is the programmatic identifier that the
Windows registry uses to uniquely identify the
object that implements the corresponding
interface. The format is
OleServerName.ObjectName.
For the ProgID's of the standard, E-Notebook
form tools, see Managing the Standard Form
Tools on page 660.
6. To associate an Enabled icon with the form
tool, click the Import... button.

658 Managing Section Types and Forms CambridgeSoft

Managing Form Tools
 A dialog appears, prompting you to select the To view and edit the properties of a form tool:
file icon file.
1. Right-click the section type in the Collection
7. Select the file and click Open. Tree.
The icon is associated with the form tool, and The Collection menu appears.
appears in the Enabled Icon box. 2. Select Section Type Configuration from the
8. Associate a disabled icon with the form tool, menu.
(following steps 6 and 7, above). This icon will The Section Type Configuration dialog
appear when the form tool is disabled. appears:
9. If the form tool has properties to configure,
click the Custom Properties button.
The Form Tool Properties dialog appears,
and you may configure the custom properties
of the form tool.
10. Click OK to dismiss the Form Tool Properties
properties dialog.
The dialog closes.
3. If necessary, click the plus sign next to Form
11. To close the Section Type Configuration Tools to expand the list and view the form tools
dialog, click the close button in the upper right that are associated with the section type. Click
corner. the form tool whose properties you wish to
The dialog closes. The form refreshes, and view or change.
displays the icon associated with the form tool.

Viewing and Editing the

Properties of a Form Tool
You can view and edit the custom properties that
are associated with a form tool. For example, you
may want to associate the form tool with a different
field in an E-Notebook form. Or, if you had The ProgID's and license key information
developed a form tool to conduct calculations, you appears to the right. You may edit this
may want to change a property that defines the information if you wish.
precision of the calculated results. 4. Click the Custom Properties button.

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 659
Managing Form Tools
 If the form tool has properties associated with
it, the Form Tool Properties dialog appears.
This example shows the dialog associated with
the Next Step Form Tool:
Administrator
NOTE: If the form tool has no custom properties, a
message to that effect is presented, and no properties dialog is
displayed.
5. Edit the custom properties if desired, and click
OK to close the dialog.
6. To close the Section Type Configuration
dialog, click the close button in the upper right
corner.
The dialog closes. The form refreshes.
Removing a Form Tool from
a Section Type
If you no longer want a particular form tool to be
associated with a form, you can remove it from the
section type.
To remove a form tool from a section type:
1. Right-click the section type in the Collection
Tree.
The Collection menu appears.
2. Select Section Type Configuration from the
menu.
The Section Type Configuration dialog
appears.
660 Managing Section Types and Forms
3. If necessary, click the plus sign next to Form
Tools to expand the list and view the form tools
that are associated with the section type. Right-
click the form tool you wish to remove from
the form. A menu appears:
4. Select Delete Form Tool.
A message appears, asking you to confirm that
you wish to delete the form tool from the
section type.
5. Click Yes.
The form tool is deleted.
6. To close the Section Type Configuration
dialog, click the close button in the upper right
corner.
The dialog closes. The form refreshes. If there
was an icon associated with the form tool, it no
longer appears in the form.
Managing the Standard
Form Tools
E-Notebook provides a number of standard form
tools. The form tools listed below may only be
associated with section types. There are several
form tools that may only be associated with
collection types, for example, the New Section
Form Tool. See Managing Collection Type Form
Tools on page 762 for more information.
See the following topics for more information
about the functions and attributes of the section
form tools:
CambridgeSoft
Managing Form Tools
 Managing the Next Step Form Tool When you add a Reaction Form Tool to a form, you
creates a new collection with a reaction section must configure the following custom properties.
containing the products of the selected reac-
tion.
Managing the New Subsection Section
Form Tool creates a new subsection when
clicked.
Managing the Spectrum Form Tool
enables the import of various spectra files, and
The E-Notebook User Guide provides more
allows users to copy, paste, import, and export
information about the tool and the calculations in
those files.
the stoichiometry grid. The stoichiometric grid is
Managing the Active Document Form the combination of the Reactants and Products
Tool allows the import and export of MS Fields.
Word documents and stored document Fields.
Managing the New Section Form Tool
Managing the Insert Reference Form
Tool allows a user to reference to a specific The New Section Form Tool allows users to add
collection type in a target property of a prop- new sections to a collection, for example, to a page
erty list. or an experiment. When users click the form tool
they will be presented with a list of the types of
Managing the Print Multiple Form Tool sections they may add.
allows a user to print multiple collections
with a single action.
Form Tool Form Tool Control ProgID

Managing the Next Step Form Tool

The Next Step Form Tool is used to create a new
page or experiment containing the products of the
associated chemical reaction.
In order to use the Next Step Form Tool in an
E-Notebook form, one of each of the following
types of fields must be present in the form:
Chemical Structure Field
New Section ENStandardCtl9.NewSectionForm
Tool
Managing the New Subsection Section
Form Tool
The New Subsection Form Tool allows users to
add new subsections to a section. For example, a
user may add new spectrum subsections to a

Table Field with Reactants Listener

Table Field with Products Listener

Form Tool Form Tool Control ProgID

Next Step ENStandardCtl9.ReactionFormTool

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 661
Managing Form Tools
 spectra section. When users click the form tool they
will be presented with a list of the types of sections
they may add.
Administrator
Managing the Active Document Form
Tool
The Active Document Form Tool is used in to

import and export documents to and from an

Form Tool Form Tool Control ProgID
E-Notebook Section. When the form tool can also
compute the checksum for the uploaded file and
New Subsec- ENStandardCtl9.NewSubsection- display it in a property list.
tion FormTool
Form Tool Form Tool Control ProgID
Managing the Spectrum Form Tool
The Spectrum Form Tool is used in conjunction Active Docu- ENStandardCtl9.ActiveDoc-
with a spectrum field to import and export spectral ment FormTool
data from a file into an E-Notebook section.
In order to use the Active Document Form Tool in
Form Tool Form Tool Control ProgID an E-Notebook form, the following types of fields
must be present in the form:
Spectrum ENStandardCtl9.Spectrum-
FormTool Active Document Field OR
Stored Document Field OR
In order to use the Spectrum Form Tool in a form,
a Spectrum Field must be present in the form. Excel OLE Control Field

When you add a Spectrum Form Tool to a form, If you wish to display the checksum, source file
you must configure the following custom path, and source file name, the section type must
properties: also contain a property list with the following
properties:

Source File Name

Source Path
Checksum

When you add an Active Document Form Tool to

a form, you must configure the following custom
properties:

662 Managing Section Types and Forms CambridgeSoft

Managing Form Tools
Managing the Insert Reference Form
Tool
The Insert Reference Form Tool makes it possible
for users to insert references to a specific collection
type into a target property in a property list.
Form Tool Form Tool Control ProgID
Insert Refer- ENStandardCtl9.InsertRefer-
ence enceFormTool
In order to use the Insert Reference Form Tool in
an E-Notebook form, a Property List field must be
present in the form.
When you add a Insert Reference Form Tool to a
form, you must configure several custom
properties.
Source Collection Type the type of collec-
tion that a user may reference in the target
property.
Source State the state that the collection
must be in when the reference to it is created.
Target Field the property list field in which
the user may create the reference.
Target Property the specific property in the
property list to which the user may add the
reference.
Chem & BioOffice 2006 /E-Notebook
In this example, a user may add a reference to a
collection of type Page. The collection must be in
an Open state when the reference is created.
Note that if you wish to prevent users from adding
references to other collection types, you must make
the target property read-only in the property list.
This will prevent users from dragging or copying
other references into the property, and force them
to use the Insert Reference Form Tool.
Managing the Print Multiple Form Tool
The Print Multiple Form Tool allows a user to print
multiple collections with a single action. .
Form Tool Form Tool Control ProgID
Print Multiple ENStandardCtl9.PrintMultiple-
FormTool
If the collection containing the section in which the
form tool appears has contained collections or
references, a dialog box appears when the user
selects the Print Multiple form tool. The dialog
allows the user to specify the range of contained
collections to be printed.
The Print Multiple Form Tool has no custom
properties.
Managing Section
Listeners
A Section Listener modifies the behaviors of
sectionssuch as the add, duplicate, remove, move
and rename behaviors. E-Notebook provides
several, standard section listeners, which you may
add to section types.
See the following topics for more information:
Adding a Section Listener to a Section Type
on page 664.
Managing Section Types and Forms 663
Managing Section Listeners
 Viewing and Editing the Properties of a 3. Right-click Section Listeners, and select New
Section Listener on page 664. Section Listener.
Removing a Section Listener from a Section
Type on page 665.
Administrator

Managing the Standard Section Listeners on

page 666.
You may also develop your own section listeners to
further customize the behavior of sections in
E-Notebook. 4. A new Section Listener appears in the tree, and
you are prompted to name it.
Adding a Section Listener to
a Section Type
A section listener modifies the behaviors of
sections such as the add, duplicate, remove,
move and rename behaviors. 5. Enter a name for the section listener
To add a section listener to a section type: 6. Fill in the following information:

1. Right-click the section type in the Collection IENSectionListener ProgID the

Tree. programmatic identifier that the Windows
registry uses to uniquely identify the object
The Collection menu appears. that implements the corresponding
2. Select Section Type Configuration from the interface. The format is:
menu. OleServerName.ObjectName.
The Section Type Configuration dialog
For the ProgID's of the standard, E-Notebook
appears:
section listeners, see Managing the Standard
Section Listeners on page 666.
7. If the section listener has properties to
configure, click the Custom Properties button.
The Section Listener Properties dialog
appears. and you are prompted to configure the
custom properties.
8. Click OK to dismiss the dialog.
The dialog box closes and the form refreshes.

Viewing and Editing the

Properties of a Section
Listener
You can view and edit the properties that are
associated with a section listener.

664 Managing Section Types and Forms CambridgeSoft

Managing Section Listeners
To view and edit the properties of a section listener:
1. Right-click the section type in the Collection
Tree.
The Collection menu appears.
2. Select Section Type Configuration from the
menu.
The Section Type Configuration dialog
appears.
3. If necessary, click the plus sign next to Section
Listeners to expand the list and view the section
listeners are associated with the section type.
Click the section listener whose properties you
wish to view or change.
Removing a Section Listener
from a Section Type
If you no longer want a particular section listener to
be associated with a section type, you can remove it
from the section type.
To remove a section listener from a section type:
1. Right-click the section type in the Collection
Tree.
The Collection menu appears.
2. Select Section Type Configuration from the
menu.
The Section Type Configuration dialog
appears.
3. If necessary, click the plus sign next to Section
Listeners to expand the list and view the section
listeners are associated with the section type.

The ProgID's and license key information

appears to the right. You may edit this
information if you wish.
4. Right-click the section listener you wish to
4. Click the Custom Properties button. remove and select Delete Section Listener from
the menu that appears.
If the section listener has custom properties
associated with it, the Section Listener
Properties dialog appears.

Note that if the section listener has no custom

properties, a message to that effect is presented,
and no dialog is displayed.

5. Edit the custom properties if desired, and click

OK to close the dialog.
6. To close the Section Type Configuration
dialog, click the close button in the upper right
corner.
The dialog closes. The form refreshes.
A message appears, asking you to confirm that
you wish to delete the section listener.
5. Click Yes.
The section listener is removed from the
section type.

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 665
Managing Section Listeners
 Managing the Standard
Section Listeners
E-Notebook provides a number of standard
Administrator
Section Listeners, which you may add to section
types.
See the following topics for more information
about their functions and attributes:
Managing the Fixed Section Name
Listener prevents the user from renaming
the section.
Managing the Required Section Listener
prevents the user from deleting the section at
any time.
Managing the Audit Section Listener
prevents a user from deleting the section only
if it has been modified since it was created.
Managing the Required Section Listener
The Required Section Listener prevents users from
deleting sections of this type. For example, you may
have a Results section that is mandatory with each
Experiment/Page.
Section IENSectionListener ProgID
Listener
Required ENStandard9.RequiredSection-
Section Listener
666 Managing Section Types and Forms
Managing the Fixed Section Name
Listener
The Fixed Section Name Listener prevents users
from renaming sections of this type. For example,
you may have a procedure section associated with
each experiment/page, and you may always want
the section to bear the name Procedure. .
Section IENSectionListener ProgID
Listener
Fixed Section ENStandard9.FixedSection-
Name NameListener
Managing the Audit Section Listener
The Audit Section Listener prevents a user from
deleting a section of this type if it has been modified
since it was created.
Section IENSectionListener ProgID
Listener
Audit ENStandard9.AuditSectionListener
Configuring a Form
Each section type in E-Notebook has a single form
associated with it. The form is what users see when
they create sections of this type.
You can configure a form to display data in the
most effective way. Boxes are the building blocks of
forms. You can add boxes to forms, delete them
from forms, and manipulate their sizes and
properties. You insert the fields you wish to appear
in a form into the boxes.
See the following topics for more information
about manipulating boxes in a form:
Configuring a New Form on page 667.
CambridgeSoft
Configuring a Form
 Reconfiguring an Existing Form on page 3. Right-click within the inner box, and select
669. Insert Box Above from the menu that appears.
Showing and Hiding the Max Button for a
Box on page 671.
Showing and Hiding the Name of a Box on
page 672.
Resizing Boxes in a Form on page 673.
Clearing Fields when Configuring a Form on
page 675.
Hiding Fields and Boxes when Configuring a A box appears on top of the box you selected.
Form on page 675. There are now two boxes, one on top of the
Changing Box Orientation on page 676. other, within the root box, as shown below:

NOTE: Prior to configuring the form, the section type must

contain the fields that are to be added to the form.

Configuring a New Form

When you create a new section type, you must
configure its form. Initially, the form has a single,
root box. You configure the form by adding
additional boxes, then inserting fields into those
boxes.
The configuration created in the steps below is an
example. There are many ways in which boxes may
The next step you take depends upon the form
be organized within the form.
layout you seek. In this example, we will configure
To configure a new form, the form so that there are two fields in a row on top
of another field, for a total of three fields in the
1. Right-click within the root box. form.
A menu appears.
4. Right-click within the top box, and select Insert
Box Within.

2. Select Insert Box Within.

A box appears within the root box. The hashed
lines indicate that there is a box behind the top
box.

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 667
Configuring a Form
 5. Right-click within the new box, and select Insert A dialog box appears, listing the fields that you
Box to the Right. have added to the section type.
Administrator

3. Click the field you wish to insert into the box,

and click Insert.
A box appears to the right of the box you The field appears in the box. Any edits you
selected, as shown below. make to the field will appear in E-Notebook
when a user creates a section of this type.

4. Repeat steps 1 through 3 for the other boxes.

Setting the Fields in Boxes Once a field has been set in a box, you may
access the Box menu by right-clicking the
To set the field within a box,
frame of the box.
1. Right-click within the box.
NOTE: The orientation of a box is determined by the
A menu appears. orientation of its container. For example, say that Insert Box
2. Choose Set Field. Above and Insert Box Below are menu options for Box X.
Then, you insert Box Y within Box X, by using the Insert
Box Within command. The menu options for Box Y will
include Insert Box to the Right and Insert Box to the
Left. If you inserted Box Z into Box Y, the menu options for
Box Z would include Insert Box Above and Insert Box
Below. By default, the orientation of the container box is
opposite the orientation of the contained box.

668 Managing Section Types and Forms CambridgeSoft

Configuring a Form
Reconfiguring an Existing The new box appears in the form:
Form
In some cases, you may want to reconfigure a
particular form, adding new fields, removing
existing fields, or changing the layout of the fields in
the form. For audit reasons, it is not possible to
remove a field from a form if that form is in use.

Adding a Field to an Existing Form

1. Click the section type of interest in the
Collection Tree.
The form for the section type appears in the 4. Right-click within the new box, and select Set
right frame. Field from the menu that appears.
2. Right-click the frame of the box that is to be
adjacent to the new box you are adding.
The Box menu appears.
3. Select a menu option to add a new box to the
form.
In this example we are selecting Insert Box
Above to add a box above the Metadata
Properties box.

The Insert Field dialog appears, listing the

Fields that have been added to the section type.

5. Select the field to be insert, and click Insert .

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 669
Configuring a Form
 The field appears in the form. In the example The box is moved according to the selection
below, a query text field has been inserted. you made.
Administrator

Deleting a Box from a Form

If you no longer want a particular box to be part of
a form, you may delete it. If you delete a box that
contains a field, there must be an empty box for the
field elsewhere in the form.
Rearranging Boxes in a Form To delete a box from a form:

You may rearrange the boxes in a form to change 1. Right-click the frame of the box you wish
the layout of the form. delete.
A menu appears.
1. Right-click the frame of the box that you wish
to move.
The Box menu appears.
2. Select one of the options for moving the box.

(Depending upon the orientation the box,

either 1) Move Box Left and Move Box Right, or
2) Move Box Up and Move Box Down will
appear in the menu). In this example, we are
moving a box to the left.

2. Select Delete Box.

The box is deleted from the form. (Note that if
the box contained a field, and you had
customized the field for this form, you can add
the field to another box in the form and your
changes to the field will be maintained).

670 Managing Section Types and Forms CambridgeSoft

Configuring a Form
Showing and Hiding the 3. Click the Show Max Button checkbox to clear it.

Max Button for a Box

In a form, each box may have a max button

associated with it. The button appears in the upper
right corner of the box. When a user clicks the
button, the field expands to fill the entire section
display. (Clicking the max button again returns the
field to its original size). The field below displays
the max button in the upper right corner:

4. Click OK .
The dialog closes, and the max button is no
longer visible in the box.

Hiding the Max Button

To hide the max button for a box, Showing the Max Button
1. Right-click the frame of the box. To show the max button for a box:
The Box menu appears. 1. Right-click the frame of the box.
The Box menu appears.
2. Select Box Properties.
2. Select Box Properties.

The Box Properties dialog appears. The Box Properties dialog appears.

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 671
Configuring a Form
 3. Click the Show Max Button checkbox so that a 2. Select Box Properties.
checkmark appears:
Administrator

The Box Properties dialog appears.

3. Click the Show Name checkbox to clear it.

4. Click OK .
The dialog closes, and the max button appears.

Showing and Hiding the

Name of a Box
36 .
In a form, each box has a title bar associated with it.
4. Click OK .
You may choose to either hide of this bar or have it
appear above the box in the form: The dialog closes, and the name of the box is
no longer visible in the form.
Hiding the Box Name
To hide the name of a box,
1. Right-click the frame of the box.
The Box menu appears.

672 Managing Section Types and Forms CambridgeSoft

Configuring a Form
Showing the Name of a Box 4. Click the Show Name checkbox so that a
checkmark appears:
To show the name of a box:

1. Right-click the section menu tool on the tab,

and select Hide Fields.

5. If you wish, edit the name for the box.

6. Click OK .
The fields in the form are hidden. The dialog closes, and the box name appears in
2. Right-click within the box whose name you the upper left corner of the box.
wish to display in the form.
The Box menu appears.
3. Select Box Properties.

Resizing Boxes in a Form

You can change the size of a box to make it appear
larger or smaller in a form. You can set the
maximum dimensions, minimum dimensions, and
proportional size of a box relative to other boxes in
the same container.

Changing the Weight of a Box

To change the size of a box relative to other boxes
in the same container, you may change the weight
The Box properties dialog appears. of the box.

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 673
Configuring a Form
 To do this, The dialog closes, and the box sizes change to
reflect your change.
1. Right-click the frame of the box whose weight
you wish to change. In this example, the weight
of the Structure box will change.
Administrator

The Box menu appears.

2. Select Box Properties.

Changing the Dimensions of a Box

Manually
1. Right-click the frame of the box whose size you
wish to change.
The Box Properties dialog appears.
The Box menu appears.
3. Change the value of the Weight. In this
2. Select Box Properties.
example, we are changing the value to 3 (three
times greater than the default box weight of 1).

The Box Properties dialog appears.

3. Click the checkboxes to apply the options you
4. Click OK
desire to the box.
The sizes of the boxes will change according to
the options you select.
Minimum Height and Minimum Width
The minimum height and width,
respectively, to which the box can shrink
when the E-Notebook window is resized or
the form is further configured in a way that
would shrink the box (for example, by
adding a box next to it).

674 Managing Section Types and Forms CambridgeSoft

Configuring a Form
 Preferred Height and Preferred Width
The starting height and width, respectively,
of the box relative to other boxes in the same
container. To calculate the actual height of a
box within a container, begin with the
preferred height of the contained boxes.
Then,
if the preferred dimensions would leave
extra space in the container box, add the
extra space in the container to each
contained box according to its Weight
relative to the other boxes, ensuring that
each box does not exceed its maximum
dimensions.
Clearing Fields when Config-
uring a Form
When you are configuring a form, you may remove
a field after adding it to the form. It is only possible
to clear the field if the form is not yet in use. If the
form is in use, the field will move to an empty box.
(This prevents the possibility of obscuring data that
a user has entered in a form).
To clear a field from a box,
1. Right-click the frame of the box.
The Box menu appears.
2. Select Clear Field.

if the preferred dimensions would cause the

contained boxes to overflow the container,
subtract space from each box according to
its Weight relative to the other contained
boxes, ensuring that each box is no smaller
than its minimum dimension.

Maximum Height and Width The

maximum height and width, respectively, a
box can attain when the E-Notebook
window is resized or as the form is further
configured in a way that would increase the
size of the box (for example, by deleting a
box next it). A scroll bar appears within the
box if the field within it requires more space
than the maximum dimension allows.
Box dimensions are expressed in twips, with 20
twips equalling one pixel.
The field is removed from the form.
Hiding Fields and Boxes
when Configuring a Form
When you are configuring a form, hiding fields and
boxes makes it easier for you to access box menus.
Hiding a Box
You may wish to hide a box if, for example, you
wish to access the box that contains it in a form.

NOTE: If you would like a box to simply conform to the To hide a box,
sizes of the boxes it contains, you can deselect all of the sizing
1. Right-click the frame of the box.
options for that box.
The Box menu appears.

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 675
Configuring a Form
 2. Select Hide Box. To hide the fields in a form:
1. Right-click the section menu icon that appears
in the form.
Administrator

The Section menu appears.

2. Select Hide Fields.

The Box is no longer visible in the form, as

shown below. (In this case, the root box of the
form is visible. The root box does not display
the hash marks).
The fields in the form are hidden.
3. To see the field in a particular box again, right-
click within the box, and select Show Contents
from the menu that appears.
This menu option will only appear if 1) the box
contains a field or 2) a contained box is hidden.
3. To access the box that contains the hidden box,
right-click within the hidden box, and select
Box Properties .

The Box Properties dialog for the container

of the hidden box appears.

Hiding Fields in a Form Changing Box Orientation

You may wish to hide the fields in a form while you You may wish to change the orientation for a box,
are configuring it, so that it is easier to access the so that the stacking of its contained boxes will
box menus. This may become especially important change from horizontal to vertical, or from vertical
if you have hidden the frames of the boxes. to horizontal.

676 Managing Section Types and Forms CambridgeSoft

Configuring a Form
In this example, we will change the orientation of 3. Change the Sub Box Layout to Vertical (i.e., the
contained boxes from a horizontal arrangement to opposite of the current layout).
a vertical arrangement.
In the form we are shown below, there are three,
horizontally arranged boxes within a single
container box.

1. Right-click the frame of the box that contains

the three boxes (making sure you select the
correct box the one that is directly outside
of the three boxes; in this example, Container
Box 1 is selected). 4. Click OK.
The Box menu appears. The Box Properties dialog closes. The three
boxes are now arranged vertically, as shown
below.

2. Select Box Properties. Managing Export

The Box Properties dialog appears.
Templates for Section
Types
Export templates for section types allow users to
print E-Notebook sections and export sections to
Microsoft Word. You create export templates with
MS Word sections, using tags to refer to
E-Notebook fields.

An export template must be set up for each, new

section type you create.

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 677
Managing Export Templates for Section Types
 To view the export template: 3. Click the New Default Section button in
the right frame.
1. Right-click the section type in the Collection
Tree. A menu appears, listing all of the E-Notebook
section types.
Administrator

A menu appears.
2. Select Show, then Export Templates.

If the section type has an export template, the

template appears in the right frame. If not, the
right frame is blank, and you must create a new
template.
4. Select Export Template.
See the following topics:
A new export template appears.
Creating the Export Template for a Section
See Editing the Export Template for a Section
Type on page 678.
Type on page 678 for instructions on setting up
Editing the Export Template for a Section the template.
Type on page 678
Editing the Export Template
Creating the Export
for a Section Type
Template for a Section Type
This topic provides instructions for setting up or
Export templates allow users to print E-Notebook modifying an export template.
sections and to export sections to Microsoft Word.
To do this:
To create an export template:
1. Right-click the section type in the Collection
1. Right-click the section type in the Collection
Tree.
Tree.
A menu appears.
A menu appears.
2. Select Show, then Export Templates.
2. Select Show, then Export Templates.

The right frame is blank if there is no export
template associated with the section type. (For
information about configuring an existing
export template, see Editing the Export
Template for a Section Type on page 678).
The export template appears in the right frame.
If no template appears, you must first create
the template.
You can then edit the template in one of two
ways:

678 Managing Section Types and Forms CambridgeSoft

Managing Export Templates for Section Types
 You can edit it within E-Notebook, using
the MS Word tools that E-Notebook
provides.
You can export it to MS Word and edit it
within MS Word to make use of the full, MS
Word feature set. You can then import it
back into E-Notebook. See Working with
MS Word Documents in the User Guide if
you would like more information about how
to import and export MS Word documents)
The body of each export template contains tags that
mark the locations for the content within the
exported section. The format of a tag consists of a
left bracket, the name of a field, and a right bracket.
For example, if there is a field named Reaction it
will replace the first instance of <Reaction> in
the export template.
Each field type determines how it will replace the
tag with its data (within the IENFieldCtl_Export
method).
When a user prints a section, the printed header and
footer are pulled from the collection type export
template that corresponds to the user's region. See
Creating and Editing the Export Templates for a
Collection Type on page 780 for information
about headers, footers, and setting up templates for
users from different geographical regions.
Section Metadata Tags
Within the contents of the section type export
template, the following tags can be inserted. Each
of these tags will be replaced by the corresponding
information at the time of export or printout.
Tag Replacement
<sectionName> The name of the section.
Chem & BioOffice 2006 /E-Notebook
Tag Replacement
<sectionIndex> The numerical position of the
section within its containing set
of sections.
<sectionCount> The number of sections that
are contained within the set of
sections.
Standard Field Types
This section describes how each of the standard
add-in field types replaces the tags in an export
document with the field type.
Active Document field type The Active
Document field type replaces the export tag
with the body of the Word document.
ChemDraw Structure field type The
ChemDraw Structure field type substitutes a
ChemDraw OLE object into the Microsoft
Word document. As a result, the ChemDraw
application is required to render the OLE
object, either for display on the client machine,
or for printing.
Collection Query field type The Collection
Query field type replaces the export tag with
tab-separated descriptions of the selected
collection query options.
Collection Type Query field type The
Collection Type Query field type replaces the
export tag with tab-separated description of
the collection type query.
Database Table field type Normally, the
Database Table field type creates a Word table
to replace the contents of the tag. Each column
of the Database Table data corresponds to a
column in the Word table; each row of the
Database Table data corresponds to a row in
the Word table. If the tag appears within a
Managing Section Types and Forms 679
Managing Export Templates for Section Types
 Word table, then, instead of creating a new
Word table, the Word table that contains the
tag is used to contain the Database Table data.
Any formatting within the Word table is
Administrator
applied to the content.
Property List field type In the export
template, the tag for the Property List field type
should appear in an MS Word table; then, the
Word table that contains the tag is used to
contain the data. The first column of the table
contains the names of the properties, and the
second column contains the values of the prop-
erties. Any formatting within the Word table is
applied to the content.
Property Query field type Normally, the
Property List field type creates a Word table to
replace the contents of the tag. creates a Word
table to replace the contents of the tag. The
first column of the data corresponds to the
property name, and the second column corre-
sponds to the value. a column in the Word
table; each row of the data corresponds to a
row in the Word table. If the tag appears within
a Word table, then, instead of creating a new
Word table, the Word table that contains the
tag is used to contain the data. Any formatting
within the Word table is applied to the content.
Query Text field type The Query Text field
type replaces the tag with the text stored in the
section.
Search Location field type The field
marker within the template is either deleted (if
the Search In check box is unchecked) or
replaced by the name of the selected collection
(if the Search In check box is checked
Spectrum field type The Spectrum field
type substitutes an image of the spectrum for
the tag.
680 Managing Section Types and Forms
Managing Export Templates for Section Types
State Query field type The Collection Type
Query field type replaces the export tag with
tab-separated description of the collection type
query.
Stored Document field type The Stored
Document field type replaces the export tag
with tab-separated description of the stored
document: its type and its size in bytes.
Styled Text field type The Styled Text field
type replaces the tag with the formatted text
stored in the section.
Subsection field type The Subsection field
type replaces the tag with the contents of a
Word document that is created by exporting all
of the sections contained in the subsection.
Table field type Normally, the Table field
type creates a Word table to replace the
contents of the tag. Each column of the Table
data corresponds to a column in the Word
table; each row of the Table data corresponds
to a row in the Word table. If the tag appears
within a Word table, then, instead of creating a
new Word table, the Word table that contains
the tag is used to contain the Table data. Any
formatting within the Word table is applied to
the content.
Table Query field type creates a Word table
to replace the contents of the tag. Each column
of the data corresponds to a column in the
Word table; each row of the data corresponds
to a row in the Word table. If the tag appears
within a Word table, then, instead of creating a
new Word table, the Word table that contains
the tag is used to contain the data. Any format-
ting within the Word table is applied to the
content.
URL Display field type The URL Display
field type replaces the export tag with the
contents of the web page specified in the
section.
CambridgeSoft
Page Breaks for the first paragraph of the corresponding export
template. This is an MS Word setting. If this
By default, if a user prints a range of sections in a
paragraph setting is not checked, then the sections
collection, the sections will print contiguously,
will appear continuously on the word page.
without page breaks. You may however, insert a
page break at the end of the section type export
template if you do not want sections to print on the
same page. To add a page break before a section,
check the Page Break Before paragraph setting

Chem & BioOffice 2006 /E-Notebook Managing Section Types and Forms 681
Managing Export Templates for Section Types
Administrator

682 Managing Section Types and Forms CambridgeSoft

Managing Export Templates for Section Types
Chapter 36: Managing Commands
Commands can be associated with a collection To add commands to a collection type:
types and sections types to render content in:
1. Right-click the collection type in the Collection
exporting to MS Word, PDF, or printing. The
results of renderings can be stored in files, printed Tree, and select Collection Type Configuration
on paper, or stored in databases. For example, users from the menu that appears.
may export a collection to MS Word or PDF and
save it at some location outside E-Notebook.

Managing Collection
Commands
You can associate commands with a collection type
to render the contents of collections in various
formats i.e. MS Word or PDF. The results of
renderings can be stored in files, printed on paper,
or stored in databases. For example, users may
export a collection to MS Word or PDF and save it
The Collection Type Configuration dialog
at some location outside E-Notebook.
appears.
This section describes how to set up an 2. Right-click Commands and select New
E-Notebook application to render the contents of Command from the menu that appears:
collection in a specific format. E-Notebook can be
configured to render the contents of a collection in
several contexts, such as in response to a menu
command or as part of a transition.

Adding a Command to a
Collection Type
You can associate commands with a collection type
if you wish the users to allow to render the contents
of collections in specific formats i.e. MS Word or
PDF.

Chem & BioOffice 2006 /E-Notebook Managing Commands 683

Managing Collection Commands
 A new command appears and you are 2. If necessary, click the plus sign next to
prompted to rename it. Commands to view the commands that are
associated with this collection type. Click the
command whose properties you wish to view
Administrator

or edit.
3. Click the Custom Properties button.
The Command Properties dialog appears.
4. Edit the properties, if you wish. For example,
3. Type in a name for the command.
you may wish to add section types to be
4. Enter the IENCommandProgID for the rendered. For this,
Command you wish to add.
Click the Set Rendered Section Types button
5. To close the Collection Type Configuration to add section types. A dialog appears
dialog, click the close button in the upper right displaying the list of section types and
corner. checkboxes before their names.
The dialog closes. Checkmark the boxes to select the section
types and click OK to close the dialog.
6. To add another command to the Collection
Type, repeat steps 2 and 3. 5. Click OK to close the dialog.
6. To close the Collection Type Configuration
Viewing and Editing the dialog, click the close button in the upper right
Properties of a Collection corner.
Command The dialog closes and your changes are saved.

You can view and edit the custom properties that
may be associated with a collection command. To
do this:
1. Right-click the collection type that contains the
command in the Collection Tree, and select
Collection Type Configuration from the menu
that appears.
The Collection Type Configuration dialog
appears.
Removing a Command from
a Collection Type
If you no longer want a particular command to be
associated with a collection type, you can remove it
from the collection type. To do this:
1. Right-click the collection type that contains the
command in the Collection Tree, and select
Collection Type Configuration from the menu
that appears.
The Collection Type Configuration dialog
appears.
2. If necessary, click the plus sign next to
Commands to view the commands that are
associated with this collection type.
3. Right-click the command you wish to remove
from the collection type.

684 Managing Commands CambridgeSoft

Managing Collection Commands
 A menu appears.
4. Select Delete Command.
A message appears, asking you to confirm that
you wish to delete the command.
5. Click Yes.
The command is removed from the collection
type.
6. To close the Collection Type Configuration
dialog, click the close button in the upper right
corner.
The dialog closes.
Managing the Standard
Collection Commands
There are some standard commands that you may
associate with collection types in E-Notebook. The
commands are used to render the contents of
collections in various formats i.e. MS Word or PDF
and the results of these renderings can be stored in
files, printed on paper, or stored in databases.
Printing and Exporting operations are configured
and executed in similar ways. Because of these
similarities, the term Render is used throughout Export to PDF
here when it refers to either Printing or Exporting,
depending on a specific configuration.
Chem & BioOffice 2006 /E-Notebook
Managing the Export to MS Word
Collection Command
You can associate the Export to MS Word
command to allow users to render or export the
contents of a collection to an MS Word document
type thereby storing the results of these renderings
in files or databases.
For example, users may wish to export a collection
to MS Word and save it at some location outside
E-Notebook.
Command Command ProgID
Export to MS Word ENRenderWord9.ExportC
Command
Managing the Export to PDF Collection
Command
E-Notebook can be configured to allow users to
render the contents of a collection to PDF
document which is managed by associating Export
to PDF Collection Command with that collection
type.
For example, users may want to export a collection
and save it in PDF format at some location outside
E-Notebook.
Command Command ProgID
ENRenderWord9.Export-
PDFCCommand
Managing Commands 685
Managing Collection Commands
 Managing the Print Collection 1. Right-click the section type in the Collection
Command Tree, and select Section Type Configuration
from the menu that appears.
If the Print Collection Command is associated with
a collection type, users can print collections of that
Administrator

type.

Command Command ProgID

Print Collection ENRenderWord9.PrintC-

Command
The Section Type Configuration dialog appears.
Managing Section 2. Right-click Commands and select New
Commands Command from the menu that appears:
A new command appears and you are
You can associate commands with a section type to
prompted to rename it.
render the contents of sections to MS Word, or to
print sections. 3. Type in a name for the command.
4. Enter the IENCommandProgID for the
This section describes how to set up an
Command you wish to add.
E-Notebook application to render the contents of a
section. 5. To close the Section Type Configuration
dialog, click the close button in the upper right
Adding Commands to a corner.
Section Type 6. The dialog closes.

You can associate commands with a section type if
you wish the users to allow to render the contents,
either printing or exporting to MS Word.
To add commands to a section type:
To add another command to the Section Type,
repeat steps 2 and 3.
Viewing and Editing the
Properties of a Section
Command
You can view and edit the custom properties that
may be associated with a section command. To do
this:
1. Right-click the section type that contains the
command in the Collection Tree, and select
Section Type Configuration from the menu that
appears.
The Section Type Configuration dialog
appears.

686 Managing Commands CambridgeSoft

Managing Section Commands
 2. If necessary, click the plus sign next to
Commands to view the commands that are
associated with this collection type. Click the
command whose properties you wish to view
or edit.
3. Click the Custom Properties button.
4. Edit the properties, if you wish. For example,
you may wish to add section types to be
rendered. For this,
Click the Set Rendered Section Types button
to add section types. A dialog appears
displaying the list of section types and
checkboxes before their names.
Checkmark the boxes to select the section
types and click OK to close the dialog.
5. Click OK to close the dialog.
6. To close the Section Type Configuration
dialog, click the close button in the upper right
corner.
The dialog closes and your changes are saved.
Removing a Command from
a Section Type
If you no longer want a particular command to be
associated with a section type, you can remove it
from the section type. To do this:
1. Right-click the section type that contains the
command in the Collection Tree, and select
Section Type Configuration from the menu that
appears.
The Section Type Configuration dialog
appears.
2. If necessary, click the plus sign next to
Commands to view the commands that are
associated with this section type.
Chem & BioOffice 2006 /E-Notebook
3. Right-click the command you wish to remove
from the section type.
A menu appears.
4. Select Delete Command.
A message appears, asking you to confirm that
you wish to delete the command.
5. Click Yes.
The command is removed from the section
type.
6. To close the Section Type Configuration
dialog, click the close button in the upper right
corner.
The dialog closes.
Managing the Standard
Section Commands
You can associate some standard commands with
section types in E-Notebook. These commands are
described here. The commands are used to render
the contents of sections in MS Word format and the
results of these renderings can be stored in files,
printed on paper, or stored in databases.
The term Render is used throughout here when
it refers to either Printing or Exporting, depending
on a specific configuration. This is because of the
fact that Printing and Exporting operations are
configured and executed in similar ways.
Managing the Export to MS Word
Section Command
Export to MS Word command allows users to
render the contents of a section to an MS Word
document if it is associated with the section type.
Thus, the results of these renderings are stored in
files or databases.
Managing Commands 687
Managing Section Commands
 For example, users can export a section to MS For example, users can export a section to MS
Word and store at some location outside Word and store at some location outside
E-Notebook. E-Notebook.
Administrator

Command Command ProgID Command Command ProgID

Export to MS Word ENRenderWord9.ExportS Print Section ENRenderWord9.Print-

Command SCommand

Managing the Print Section Command

If the Print Section command is associated with a
section type, users can print the contents of a
section of that type by selecting the command from
the Section menu.

688 Managing Commands CambridgeSoft

Managing Section Commands
Chapter 37: Managing Rendering in
E-Notebook
This portion of the guide describes the
configuration of printing and exporting in
E-Notebook. Printing and Exporting operations
are configured and executed in similar ways.
Because of these similarities, the term Render is
used throughout to refer to either Printing or
Exporting.
An E-Notebook system can be configured to
render the contents of a collection in several
contexts, such as in response to a menu command,
as part of a transition, or the operation of a form
tool. Different rendering add-ins support different
workflows. For each use of a rendering add-in, the
add-in is configured with one or more rendering
templates that determine how the information in a
collection or section is laid out within the Microsoft
Word document. For add-ins that render
collections, templates are created that specify paper
sizes, styles, headers, footers and the layout of data
for each type of section to be rendered.
During the rendering operation for collections, the
rendering add-in instantiates an instance of
Microsoft Word and uses a template associated with
the rendering add-in to lay out the document. Each
section in the collection whose type has a rendering
template associated with the rendering add-in is
then incorporated into the new document. For each
field in each section, a tag is located in the rendering
template that contains the name of the field
associated with that section cell surrounded by
brackets, such as <FieldName>. This tag is
replaced by a rendition of the field's data. Once the
document is rendered, it is either printed or saved
to a file, depending on the behavior of the rendering
add-in
Chem & BioOffice 2006 /E-Notebook
Configuring a Rendering
Template
Many rendering operations require a template in the
form of a Microsoft Word document that describes
the layout of data to be rendered. When a rendering
add-in requires a rendering template as part of its
configuration, that rendering template can reside in
one of two places. It can either be associated
directly with the rendering add-in or it can be
located in users user configuration folders and
referenced by name from the add-in.
For rendering templates located in users user
configuration folders, the rendering templates must
be stored in a Microsoft Word field in a section that
is contained in a configuration collection. This
configuration collection is contained within a
configuration folder. The configuration folder and
the configuration collection may be referenced
within the user configuration folder (if you want
several users to have the same rendering
configuration) or contained directly in the
configuration folder (if you want users to be able to
customize their rendering templates).
To associate a rendering template for a section type
with an Export to MS Word command:
1. Right-click the collection type that contains the
section for which the rendering template has to
be associated.
2. Select Collection Type Configuration from the
menu that appears.
The Collection Type Configuration dialog
appears.
Managing Rendering in E-Notebook 689
Configuring a Rendering Template
 3. Click the plus sign next to Commands to view
the commands that are associated with this
collection type. In this example, click the
command for Export to MS Word.
Administrator
b. Checkmark the boxes to select the section
types and click to close the dialog.
6. Click the section type, for MS Word document
in this case, then the From Configuration button

4. Click the Custom Properties button. in the dialog.

7. Select the properties as shown:

The Command Properties dialog appears.

This example shows the dialog for the Export to In this example, the rendering template is
MS Word command, which is one of the located in the each users User Configuration
standard E-Notebook commands. Folder within a folder named Rendering
5. Add the section type for which the rendering Folder that contains a collection named Page
template has to be associated. For this, Section Types.
a. Click the button to add 8. Click OK to close the dialog.
section types. A dialog appears displaying 9. To close the Collection Type Configuration
the list of section types and checkboxes dialog, click the close button in the upper right
before their names as: corner.
The dialog closes and your changes are saved.
Similarly, you can configure the rendering templates
for other sections and with other commands.

Designing a Rendering
Template
Export templates allow users to print and export
from E-Notebook. You can insert various tags in
the export templates to pull different types of
information into a rendition.

690 Managing Rendering in E-Notebook CambridgeSoft

Designing a Rendering Template
Rendering Tags
The following tags can be inserted into headers,
footers and section rendering templates and
replaced with the corresponding data
Tag Replacement
<collectionStatus> The state of the collection.
(Note that if you are using
the Final Print Transition
Listener, the state will print
as the initial state of the
transition, and not as the
target state. In this specific
case, if you would like the
name of the target state to
print, simply type the text
name of the state into the
header or footer.)
<dateCreated> The timestamp of creation
of the collection
Tag Replacement
<collectionType> The type of the collection
Templates for Headers and
Footers
Headers and Footers are described using templates
that are separate from the document settings
template used to implement page sizes and styles.
This allows multi-section Word documents to be
included in rendered documents and the headers
and footers to be included in all sections of the
rendered documents.
The header and footer is printed on every page
when a user prints the collection or a portion of the
collection. The header and footer of a collection
type export template can contain standard
replacement tags above.
The Rendering Template for a header looks as
shown below:

<dateModified> The timestamp of last

modification

<dateToday> The timestamp of the

creation of the export
document or printout

<collectionOwner> The name of the owner of

the collection

<collectionName> The name of the collection

To edit this data:

Chem & BioOffice 2006 /E-Notebook Managing Rendering in E-Notebook 691

Designing a Rendering Template
 1. While viewing the export template in
E-Notebook, click the print layout view button
in the lower left corner of the MS Word field.
It is the third button in the row.
Administrator
The export template appears in print layout
view, and the header is visible
2. Double-click the header or footer.
Section Metadata Tags
Within the contents of a section type export
template, the following tags can be inserted. Each
of these tags will be replaced by the corresponding
information at the time of export or printout.
Tag Replacement
<sectionName> The name of the section
<sectionIndex> The numerical position
of the section within its
containing set of sections
<sectionCount> The number of sections
that are contained within
the set of sections
692 Managing Rendering in E-Notebook
The Rendering Template for an Ancillary Data
Section looks as shown below:
Managing the MS Word
Section Renderers
The word sections renderers can be associated with
commands (as a command listener) or transitions
(as a transition listener) to modify the behavior of
rendering commands and transitions. If more than
one Word section renderer is associated with a
rendering operation, then the Word section
renderers insert their contents in the order they are
associated with the rendering operation.
For example, a transition type contains three
transition listeners in the following order:
PrintTListener, Full History Renderer and Fixed
Text After Renderer. In this case, the document
produced by the PrintTListener will contain all of
the sections to be printed, followed by the full
history of the collection being printed, followed by
the fixed text that is associated with the Fixed Text
After Renderer.
Managing the Fixed Text
After Word Renderer
The Fixed Text After Word Renderer renders some
fixed text at the end of a collection when rendering
the collection. This renderer is configured with a
word document whose contents are inserted into
the main story of the rendered output after all of the
CambridgeSoft
Managing the MS Word Section Renderers
sections that are rendered as part of a print or Select the custom properties as shown below:
export operation. For example, the rendered
document might contain a signature block.

Word Renderer Word Renderer

ProgID

Fixed Text After ENRenderWord9.Fixed-

TextAfterRenderer

Select the custom properties as shown below: Managing the Tracked

History Word Renderer
The Tracked History renderer is configured with a
word document that may contain other text and the
tag <History> which indicates where the history is
to be inserted. If a collection to be rendered has
visual display of changes turned on, then this
renderer inserts the collection history of the
collection since visual display of changes is turned
on

Managing the Full History Word Renderer Word Renderer

Word Renderer ProgID

The Full History Word renderer may be associated Tracked History ENRenderWord9.Tracke-
with a collection type. This renderer inserts the full dHistoryRenderer
collection history of a collection after all of the
sections that are rendered as part of a print or Select the custom properties as shown below:
export operation.

Word Renderer Word Renderer

ProgID

Full History ENRenderWord9.FullHis-

toryRenderer

Chem & BioOffice 2006 /E-Notebook Managing Rendering in E-Notebook 693

Managing the MS Word Section Renderers
 Managing the Standard property list field, the label and the data are only
printed for properties that do not have blank values.
Field Renderers The label is printed with a Bold typeface.
Rendering of section cell data can be overridden by
Administrator

a Field Renderer that is associated with a particular

section type in a particular add-in command. Field Renderer Field Renderer
ProgID
Managing the Fixed Table
Field Renderer NonBlank Property ENReaction9.NonBlank-
PropertyRenderer
The Fixed Table Renderer renders the contents of a
table according to the tags in a Word table. When
The renderer has no custom properties associated
this renderer is associated with a table field, the
with it.
columns in the table are positioned using tags that
appear in the second row of a word table. The tags
are of the form <FieldName><PropertyName>.
Managing the One Property
Value Field Renderer
The One Property Value Field Renderer renders the
Field Renderer Field Renderer
value of a single property according to the tags in a
ProgID
Word table. When this renderer is associated with a
property list field, the data for one property in the
Fixed Table ENReaction9.Fixed- property list is positioned using tags that appear in
TableRenderer the Word template. The tags are of the form
<FieldName><PropertyName>.
The renderer has no custom properties associated
with it.

Managing the NonBlank Field Renderer Field Renderer

ProgID
Property Field Renderer
The NonBlank Property Renderer renders the One Property Value ENReaction9.OneProper-
name and value of a property if the property is not tyValueRenderer
blank. When this renderer is associated with a
The renderer has no custom properties associated
with it.

Managing the One Table

Value Field Renderer
The One table Value renderer renders the value of
a single table cell according to the tags in a Word
table. When this renderer is associated with a table
field, the data for one property in the first row of

694 Managing Rendering in E-Notebook CambridgeSoft

Managing the Standard Field Renderers
the table is positioned using tags that appear in the associated with a property list field, the data for
Word template. The tags are of the form each property in the property list is rendered
<FieldName><PropertyName>. without its label. This is typically used for property
lists that have only one property.

Field Renderer Field Renderer

ProgID Field Renderer Field Renderer
ProgID
One Table Value ENReaction9.OneTabl-
eValueRenderer Property Value ENReaction9.PropertyVal-
ueRenderer
The renderer has no custom properties associated
with it. The renderer has no custom properties associated
with it.
Managing the Property
Value Field Renderer
The Property Value Field renderer renders the
values of all the properties in a property list without
their corresponding names. When this renderer is

Chem & BioOffice 2006 /E-Notebook Managing Rendering in E-Notebook 695

Managing the Standard Field Renderers
Administrator

696 Managing Rendering in E-Notebook CambridgeSoft

Managing the Standard Field Renderers
Chapter 38: Managing Fields
Fields are the basis for the forms in E-Notebook.
Each field is based on an add-in field type.
E-Notebook provides many standard field types,
which you can use to configure your own data
forms, searches, and analysis tools. You may also
develop addition add-in field types for your own,
custom data types.
The field types in E-Notebook span many, diverse
types of data. They make it possible to customize
E-Notebook to match your workflow and manage
your information in the most effective way possible.
The following field types are designed for use in
data forms, for data entry, analysis, and display:
Active Document Fields (MS Word fields)
AutoText Fields
Chemical Structure Fields
Context Sensitive Help Fields
Captured Image Fields
Database Table Fields
Database Value Fields
PowerPoint Fields
Excel Fields
Property List Fields
Spectrum Fields
Stored Document Fields
Subsection Fields
Table Fields
URL Display Fields
Several Fields Types are designed for use
exclusively within search forms, to search for data
in E-Notebook. They are:
Chemical Query Fields
Collection Query Fields
Collection Type Query Fields
Query Text Fields
State Query Fields
Property Query Fields
Table Query Fields
Unannotated Version Query Fields
Search Location Fields
Join Type Fields
For information about adding custom field types
that you have developed, see Managing the Add-
In Configuration on page 739.
Other topics in this portion of the documentation
are:
Managing Field Listeners provides instruc-
tions for associating a field listener with a field
in order to modify its behavior.
Time Settings
Managing Units in Property Lists and Tables
Managing Field Listeners
Field listeners modify the behavior of various types
of E-Notebook fields. E-Notebook provides many
standard field listeners that you can use in your
configuration.
You may also develop your own listeners to further
customize the behavior of fields in E-Notebook.
Adding a Field Listener
To add a field listener to a field,

Chem & BioOffice 2006 /E-Notebook Managing Fields 697

Managing Field Listeners
 1. From the Section Type Configuration
dialog, right-click the field to which you wish to
add the listener.
2. Select New Field Listener from the menu that
Administrator
If the listener has properties associate with it,
they are displayed, and may be edited.
Managing Generic Field

appears. Listeners
The following field listeners are not limited to any
particular type of E-Notebook field. (Most
E-Notebook field listeners were created for a
specific field type).

Managing the Block User Edit Field

Listener
A dialog appears, prompting you to enter the
The Block User Edit Field Listener may be used to
ProgID for the listener.
prevent users from editing a particular field within
a section. If this listener is associated with the field,
the field will be read-only to users. This listener still
enables administrators to edit the field.

Table Listener IENTableListener

ProgID
3. Enter the ProgID and click the OK button.

The listener appears in the left frame and you Block User Edit ENStandardCtl9.Block-
are prompted to rename it. UserEditlFEListener

4. Enter a name for the listener.

To view and edit the properties of the property list Managing the Block Edit Cell Field
listener: Listener
1. Click the listener. The Block Edit Cell Field Listener may be used to
prevent users from editing a particular field within
The Prog ID and properties button appear to
a section. If this listener is associated with the field,
the right.
the field will be read-only within that section.

Table Listener IENTableListener

ProgID

Block Edit Cell ENStandardCtl9.BlockEdi

tCelllFEListener
2. Click the Custom Properties button.

698 Managing Fields CambridgeSoft

Managing Field Listeners
Managing the Copy Default Managing Active Document
Field Listener Fields
The Copy Default Field Listener removes the
Active Document Fields allow users to view and
content of a field when a user copies the collection
that contains the field. edit MS Word documents within E-Notebook
sections. If you associate the Active Document
Form Tool with an active document field, users can
Table Listener IENTableListener import MS Word documents from external sources,
ProgID or export MS Word documents and edit them in MS
Word.
Copy Default ENStandardCtl9.CopyDe-
faultFCListener To add an Active Document field:
1. In the Collection Tree, right-click the section
type to which you wish to add the property list.
Managing Data Fields
2. Select Section Type Configuration from the
The following E-Notebook field types are designed menu that appears.
for use in data forms, for data entry, analysis, and
display: The Section Type Configuration dialog
appears.
Active Document Fields (MS Word fields)
3. Right-click Fields, and select New Field.
AutoText Fields
Chemical Structure Fields
Context Sensitive Help Fields
Captured Image Fields
Database Table Fields The Add Field dialog appears.
Database Value Fields
Excel Fields
PowerPoint Fields
Property List Fields
Spectrum Fields
4. Enter a name for the field and select Active
Stored Document Fields
Document from the drop-down list of field
Subsection Fields types.
Table Fields 5. Click the Add button.
URL Display Fields The new field appears in the list of fields.
Several fields types are designed for use exclusively 6. In order for users to be able to import and
within search forms, to search for data in export the MS Word documents, you must
E-Notebook. See Managing Search Fields on associate the Active Document Form Tool
page 733 for information about these fields. with the field.

Chem & BioOffice 2006 /E-Notebook Managing Fields 699

Managing Data Fields
 Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Administrator
Managing the Extract Links Document
Listener
The Extract Links Document Listener may be

associated with active document (MS Word) fields

Managing Active Document Field
Listeners
An Active Document Field Listener modifies the
behavior of an MS Word field in E-Notebook.
E-Notebook provides an active document listener
that prevents users from adding hyperlinks to
external URLs. See Managing the Prevent
External Link Active Document Field Listener on
page 700.
You may also develop your own Active Document
Field Listeners to further customize the behavior of
active document fields in E-Notebook.
See Managing Field Listeners for instructions on
associating a field listener with a field.
Managing the Prevent External Link
Active Document Field Listener
to extract the links from the Word document into a
property list.
Active IENActiveDocListener
Document ProgID
Listener
Extract Links ENStandardCtl9.ExtractLinks-
DListener
Managing AutoText Fields
With AutoText Fields, users can enter text that is
related to other data in a form. Users can add
predefined fragments of text automatically, and
values from other fields in a section may be pulled
in as well. The E-Notebook User's Guide provides
instructions for configuring AutoText. Note that
for the AutoText features to function, the AutoText
collection type name, section type name, and field
names in the section type must not be changed.

The Prevent External Link Active Document Field If you configure the Styled Text Field to display the
Listener may be associated with active document toolbar, users may alter any of the following
fields to prevent users from adding hyperlinks to formatting options.
external URL's. If links are present in the field, they
Font
will be stripped from the document when the user
browses away. Font Size

Bold
Active IENActiveDocListener
Document ProgID Italics
Listener
Underline

Prevent External ENStandardCtl9.RequireENU Superscript

Link RLDListener
Subscript

700 Managing Fields CambridgeSoft

Managing Data Fields
An example of a Styled Text Field is shown below.
To add a Styled Text field:
1. In the Collection tree, right-click the Section
Type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name, and select AutoText from the
drop-down list of field types.
5. Click Add.
The new field appears in the list of fields.
Chem & BioOffice 2006 /E-Notebook
6. Right-click the styled text field, and select Field
Properties from the menu that appears.
7. You may edit the following properties, if
desired:
Default Font you may select another font
from the drop-down list to change the
default to something other than Times
Roman.
Default Font Size you may select a larger
or smaller font size from the drop-down list.
Show Tool Bar if you clear the
checkmark, the toolbar will not appear
above the styled text field in the form.
Not Blank If you select this option, the
styled text field must contain text when a
user performs a specific transition on a
collection. This option must be used in
conjunction with the Required Properties
Transition Listener.
Read Only the styled text field is for
display only, and only administrators may
edit it.
Managing Fields 701
Managing Data Fields
 Once you have added a field to the section type, you Users may dismiss the ChemDraw toolbar at any
may add it to the form for the section type. See time. For more information about using the
Configuring a Form on page 666 for more ChemDraw Toolbar, please see the ChemDraw
information. User's Guide.
Administrator

Managing AutoText Field It is possible to associate a listener with a chemical

Listeners
An AutoText Field Listener modifies the behavior
of an AutoText field in E-Notebook.
Managing the AutoText Color Field
Listener
The AutoText Color Field Listener allows you to
configure the color of AutoText items within an
AutoText field.
structure field to perform a specialized function.
E-Notebook offers a listener that automatically
updates the stoichiometry grid when a user
modifies a reaction drawing. See Managing the
Analyze Reaction Chemical Structure Listener on
page 703 for more information.

Table IENTableListener ProgID

Listener

AutoText Color ENStyledTextPlus9.AutoText-

ConfigFLstnr

You select the color you desire through the custom

properties of the listener. To add a chemical structure field to a section type:

Managing Chemical Struc- 1. In the Collection Tree, right-click the section

type to which you wish to add the field.
ture Fields
2. Select Section Type Configuration from the
Chemical Structure Fields make it possible for users
menu that appears.
to draw or import drawings of chemical structures
and reactions. These fields make use of the The Section Type Configuration dialog
ChemDraw ActiveX Control. An example of a appears.
Chemical Structure Field is shown below. These
fields may also be used for images. Users can paste 3. Right-click Fields, and select New Field.
in standard images, such as GIFs and JPEGs.

Users can access a ChemDraw menu by right-

clicking within the structure window. This menu
allows a user to, among other things, copy and paste
structures.

702 Managing Fields CambridgeSoft

Managing Data Fields
 4. The Add Field dialog appears. a user edits a reaction drawing. For automatic
analysis to occur, you must also associate the
Analyze Reaction Table Listener with both the
reactants and products table fields.

Active Document IENActiveDocListener

Listener ProgID
5. Enter a name, and select Chemical Structure
from the drop-down list of field types.
Analyze Reaction ENStandardCtl9.Analyz-
6. Click the Add button. eRxnCSListener
The new field appears in the list of fields.
This listener has custom properties associated with
NOTE: Anything that you draw in the Chemical Structure it. You must select the reactants field and the
Field will appear with the new sections of this type that users products field in the stoichiometry grid.
create.
Managing the Chemical Property Chemical
Once you have added a field to the section type, you Structure Listener
may add it to the form for the section type. See The Chemical Property Chemical Structure
Configuring a Form on page 666 for more Listener calculates chemical structure properties of
information. molecular weight and molecular formula, and
You may also develop your own Chemical Structure inserts them into a property list when the contents
Field Listeners to further customize the behavior of of the chemical structure change.
chemical structure fields in E-Notebook.
Active Document IENActiveDocListener
Managing Chemical Structure Field Listener ProgID
Listeners
A Chemical Structure Field Listener modifies the Chemical Property ENStandardCtl9.ChemP-
behavior of a chemical structure field in ropertiesCSListener
E-Notebook.
The following are required in the section type in
Managing the Analyze Reaction Chemical
Structure Listener
order to use this listener.

The Analyze Reaction Chemical Structure Listener A chemical structure field.

may be associated with chemical structure fields to A property list with the following properties:
update a stoichiometry grid automatically when Molecular Weight and Molecular Formula.

Chem & BioOffice 2006 /E-Notebook Managing Fields 703

Managing Data Fields
 Configuring E-Notebook with ISIS Draw 3. Right-click Field Listener, and the following
Tool dialog follows:
This topic provides instructions for administrators
who are adding the ISIS/Draw tool to the
Administrator

E-Notebook configuration. .

Tool Tool ProgID

ISIS Draw ENISISDraw9.ISIS- 4. Replace the Analyze Reaction field listener, with
DrawCSListener a new field listener. For this, click New Field
Listener. Enter a name and type
ENISISDraw9.ISISDrawCSListener in the
To add the form tool to a section type:
ProgID of the Reaction field listener, as shown
1. Browse to the Section type in the Collection above. This listener implements ISIS Draw
tree and right-click on it to display the editing.
following menu:

Click OK, and following dialog appears:

2. Select Reaction and right click it to select

Section Type Configuration from the menu that
appears.
The Section Type Configuration dialog
To countercheck that the configuration is done
appears as:
properly, click Custom Properties, and the
following dialog should appear:

5. Click OK, to dismiss the dialog.

6. Close the Section Type Configuration dialog.

704 Managing Fields CambridgeSoft

Managing Data Fields
Managing Database Table The Add Field dialog appears.
Fields
Database table fields display the results of a SQL
SELECT statement (represented as an ADO
record set). These fields are for display only, and
users may not edit them.
4. Enter a name, and select Database Table from
A Database Table Field may exist independently in
the drop-down list of field types.
a section. Or, you may set up the field such that its
value(s) are determined by a value in a separate 5. Click Add.
property list field that is part of the same section.
The new Field appears in the list of Fields.
See the following topics:
See Configuring a Database Table Field on page
Creating a Database Table Field on page 705. 705 for instructions on defining the data to be
displayed in the Field.
Configuring a Database Table Field on page
705. Once you have added a field to the section type, you
may add it to the form for the section type. See
Creating a Database Table Field Configuring a Form on page 666 for more
information.
Database Table Fields are used to display data that
is pulled in from an external database. Configuring a Database Table Field
To create a Database Table Field: Database Table Fields are used to display data that
is pulled in from a database.
1. In the Collection tree, right-click the Section
Type to which you wish to add the Property To configure a Database Table Field:
List.
1. Right-click the Database Table Field in the
2. Select Section Type Configuration from the
Section Type Configuration dialog, and
menu that appears.
select Field Properties from the menu that
The Section Type Configuration dialog appears.
appears.

3. Right-click Fields, and select New Field.

Chem & BioOffice 2006 /E-Notebook Managing Fields 705

Managing Data Fields
 The Properties dialog appears.
Administrator
2. Enter the following information. (See below
for examples).
Connection String A string used to
define a connection to a database. If this
string is 0-length (Null in the database), then
it is assumed to be a connection to the
primary schema of the E-Notebook
database. If the string is a path to an MDB
file, then a connection is made to that file
using the Microsoft Access OLEDB
provider. Otherwise, the string is treated as a
valid string that can be assigned to an
ADODB.Connection objects
ConnectionString property.
Username An optional string used to
specify the logon identification required to
connect to the specified database. If the
Username is 0-length and the Connection
String is 0-length, then the owner of the
primary schema of the E-Notebook
database is used as the username.
Password An optional string used to
identify the logon ID required to connect to
the specified database. If the UserName is
0-length and the Connection String is
0-length, then the password is ignored.
SQL String A required string that starts
with the text SELECT . This string is used
to specify the record set that appears within
706 Managing Fields
the E-Notebook section. The SQL String
can have the following special phrases that
are dynamically replaced based on the
location of the section cell.
%%section_key%% The unique
identifier for the section containing the
section cell in which the record set appears.
This datum corresponds to a value in the
primary_key column for a row in the
ELN_sections table.
%%field_key%% The unique identifier
for the field that describes the section cell in
which the record set appears. This datums
corresponds to a value in the primary_key
column for a row in the ELN_fields table.
%%collection_key%% The unique
identifier for the collection that contains the
section containing the section cell in which
the record set appears. This datum
corresponds to a value in the
section_set_key column for a row in the
ELN_collections table.
%%session_key%% The unique
identifier for the database session in which
the record set is retrieved. This datum
corresponds to a value in the primary_key
column for a row in the ELN_sessions table.
%% logged_in_user_key%% The
unique identifier for the person record for
the user that initiated the database session in
which the record set is retrieved. This datum
corresponds to a value in the primary_key
column for a row in the ELN_people table.
%%home_collection_key%% The
unique identifier for the home collection of
the user that initiated the database session in
which the record set is retrieved. This datum
corresponds to a value in the
section_set_key column for a row in the
ELN_collections table.
CambridgeSoft
Managing Data Fields
 %%access_view%% The name of the
table used to validate security privileges for
the logged in user.
In addition, a SQL string may contain the
name of a property that appears in a property
field in the same section as the DBTable
section cell. This property field is identified
using the property field name property of the
SQL section cell, below. For example, a
property could appear in the WHERE clause
of the SQL statement to determine which
records in the database table appear
Property List Field An optional name of
a property list field that contains properties
which are used to parameterize the SQL
statement, above .
3. Click OK .
Several examples are given below. Note that the
syntax of the query may vary depending upon the
type of database you are querying.
Example 1
In this example, all of the values for suppliername
are pulled in from the external database table
Suppliers.
suppliername value to be displayed in Data-
base Lookup Table.
Suppliers name of external database table.
Chem & BioOffice 2006 /E-Notebook
Example 2
In this example, the value suppliername is pulled
from the external database table Suppliers. The
suppliername displayed in the database table field
corresponds to the value that a user has entered into
a property list. A user enters SupplierID into the
Supplier ID property, which exists in a Property
List named ID Number.
suppliername value to be displayed in Data-
base Lookup Table.
Suppliers name of external database table.
SupplierID the supplier ID field in the
external database table.
ID Number name of the E-Notebook prop-
erty list containing the Supplier ID property.
Supplier ID name of the E-Notebook prop-
erty into which a user enters the value for
SupplierID.
Managing Database Value
Fields
Database Value Fields are used to pull in and display
values that are the results of SQL query from an
external database.
To create a Database Value Field:
1. In the Collection tree, right-click the Section
Type to which you wish to add the Property
Value.
2. Select Section Type Configuration from the
menu that appears.
Managing Fields 707
Managing Data Fields
 The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
Administrator
Field is shown below. If the Active Doc Form Tool
is associated with the section, a user may import or
export the document.

4. Enter a name, and select Database Value from

the dropdown list of field types.
5. Click Add.
The new Field appears in the list of Fields.
See Configuring a Database Value Field for
instructions on defining the data to be displayed in To add an Excel Field section type:
the Field.
1. In the Collection Tree, right-click the section
Once you have added a field to the section type, you type to which you wish to add the field.
may add it to the form for the section type. See
Configuring a Form on page 666 for more 2. Select Section Type Configuration from the
information. menu that appears.
The Section Type Configuration dialog
Configuring a Database Value Field
appears.
To configure a Database Value Field:
3. Right-click Fields, and select New Field.
1. Right-click the Database Value Field in the
Section Type Configuration dialog, and
select Field Properties from the menu that
appears.
The Properties dialog appears.
2. Enter the properties. See step 2 in Creating a
The Add Field dialog appears.
Database Table Field on page 705 for details.
3. Click OK.
Note that the syntax of the query may vary
depending upon the type of database you are
querying.
Once you have added a field to the section type, you
may add it to the form for the section type. See 4. Type in a name, and select Excel Spreadsheet
Configuring a Form on page 666 for more from the drop-down list of field types.
information.
5. Click Add.

Managing Excel Fields The new field appears in the list of fields.
Excel Fields make it possible for users to embed In order for users to be able to import and export
and edit Microsoft Excel documents in the MS Excel spreadsheet, you must associate the
E-Notebook sections. An example of an Excel Active Document Form Tool with the field.

708 Managing Fields CambridgeSoft

Managing Data Fields
Once you have added a field to the section type, you 1. Click the Custom Properties button in the right
may add it to the form for the section type. See panel to configure the properties associated
Configuring a Form on page 666 for more with it:
information.

Managing Break Link Excel Listener

The Break Link Excel Listener may be associated
with the Excel fields to break the links to external
data sources in Excel documents when the
document is saved. If links are present in the field,
they will be stripped from the document when the
user browses away and the user will be warned
when saving the file that the link will be broken
once the document is saved in E-Notebook. A dialog to configure the field listener opens. It
contains a box to list the Disabled Addins, an
enabled Add button, and a disabled Remove
Listener IENListener ProgID button.
2. Click Add. A dialog opens that allows you to
Break Link ENStandardCtl9.Break- enter the name of the Add-In you want to
LinksOListener disable.

The listener has no custom properties associated

with it.

Managing Hide Addins Excel Listener

The Hide Addins Excel Listener may be associated 3. Enter name of an Add-In in the text box and
with the Excel fields and disables and enables click OK. The dialog closes. The name you
specified Excel Add-ins associated with the Excel entered is added to the Disabled Addins box,
below the text you added previously.
field.
4. Similarly, to remove a previously added Add-In
from the disabled list, select one of the items in
Listener IENListener ProgID
the Disabled Addins box. The Remove button
gets enabled.
Hide Addins ENStandardCtl9.HideAd-
5. Click Remove. The selected item is removed
dinsOListener
from the list in the Disabled Addins box.
6. Click OK. The dialog to configure the field
With the field listener selected in the tree, listener closes.

Chem & BioOffice 2006 /E-Notebook Managing Fields 709

Managing Data Fields
 Managing Remove Macros Field 1. In the Collection Tree, right-click the section
Listener type to which you wish to add the field.
2. Select Section Type Configuration from the
The Remove Macros Field Listener may be
menu that appears.
Administrator

associated with the Excel fields to remove macros

from the field when a user performs a save. The The Section Type Configuration dialog
user will be presented with a message stating that appears.
the macros will be removed when the spreadsheet is
3. Right-click Fields, and select New Field.
saved.
The Add Field dialog appears.
Listener IENListener ProgID 4. Type in a name, and select PowerPoint Slide-
show from the dropdown list of field types.
Remove Macros ENStandardCtl9.Remove 5. Click Add.
MacrosFListener
The new field appears in the list of fields.
In order for users to be able to import and export
Managing PowerPoint the MS PowerPoint Slideshows, you must associate
Fields the Active Document Form Tool with the field.

PowerPoint Fields make it possible for users to Once you have added a field to the section type, you
embed and edit MS PowerPoint Slideshows in may add it to the form for the section type. See
E-Notebook sections. An example of a PowerPoint Configuring a Form on page 666 for more
Field is shown below. information.

Managing Context Sensitive

Help Fields
Context Sensitive Help Fields are used in search
forms. They create a shortcut to the E-Notebook
User's Help Guide in the search form. Thus, these
fields make it possible for users to go directly to the
Help guide to find the information regarding the
instructions for using E-Notebook quickly and
easily.

A Context Sensitive Help Field is visible in

search forms next to the text query field as shown:
If the Active Doc Form Tool is associated with the
section, a user may import or export the document.

To add a PowerPoint Field section type: To add a PowerPoint Field section type:

710 Managing Fields CambridgeSoft

Managing Data Fields
 1. In the Collection Tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Type in a name, and select Context Sensitive
Help from the dropdown list of field types.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Managing Captured Image
Fields
Captured Image Fields allow users to view and edit
PDF images and documents, using the same tools
as Adobe Acrobat software, thus helps manage
PDF files in E-Notebook.
If you associate the Active Document Form Tool
with a Captured image field, users can import or
export the PDF documents. Associating the Image
Importer Form Tool allows users to import images
of various types as well.
NOTE: Export to PDF is only available in Enterprise
versions of E-Notebook.
Chem & BioOffice 2006 /E-Notebook
To add a Captured Image field:
1. In the Collection Tree, right-click the section
type to which you wish to add the Captured
Image field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Type in a name, and select PDF Viewer from the
dropdown list of field types.
5. Click Add.
The new field appears in the list of fields.
In order for users to be able to import and export
the PDF documents and to import images, you
must associate the Active Document Form Tool
and Import Image Form Tool respectively with the
field.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Managing Fields 711
Managing Data Fields
 Managing Property Lists
Property Lists are used in forms to record various
types of data properties. Property lists allow the
following data types:
Administrator

Data type User perspective

Date A user may click the date box, and type in a date and
time.

Text A user may enter text.

Number A user may enter a number. A property may also be

configured to have units associated with it.

Enumerated Value A user may choose a value from the drop-down list.
The values may be from either a preconfigured list
or a list that is pulled from an external database.

Validated Value A user may enter a value, which is validated against

an external database.

You may configure property lists so that they are
read-only, or so that they must contain certain
values before a collection transition is performed.
Another feature of property lists is the ability for
users to add references to them. When a user adds
a reference to a property, he may navigate to the
collection or section he has referenced, simply by
clicking a link in the property cell.
See the following topics for more information
about property lists:
Creating a Property List on page 713.
Managing Database Values in Property Lists
on page 716.
Managing Enumerated Values in Property
Lists on page 714.
Managing Property List Listeners on page
719.
Managing Units in Property Lists and Tables
on page 741.

712 Managing Fields CambridgeSoft

Managing Data Fields
Creating a Property List Adding a Property to the Property List
This topic provides instructions for adding a To add a Property:
Property List to a Section Type and configuring the
Property List. 1. Right-click the Property List field in the
Section Type Configuration dialog.
To add a Property List:
A menu appears.
1. In the Collection tree, right-click the Section
Type to which you wish to add the Property
List.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.

2. Select Field Properties.

The Field Properties dialog appears.

3. Click the Properties tab.
3. Right-click Fields, and select New Field. The Properties tab appears.
The Add Field dialog appears. 4. Right-click the name of the field and select
New Property from the menu that appears.

A new property appears in the tree. It's

attributes appear to the right:

4. Enter a name for the field and select Property

List from the list of Field Types.
5. Click Add.
The new Field appears in the list of Fields.

5. Type in a Name and Nickname for the prop-

erty.
Name appears when a user selects the
property for a search.
Nickname is displayed on the screen, in
the printed copy, and in an exported Word
document.

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Managing Data Fields
 6. Select the Type from the drop-down list. (See Configuring the Appearance of a Property List
Managing Units in Property Lists and Tables
on page 741 for more information). To configure the appearance of a property list:

7. Select the Units from the drop-down list (if

Administrator

1. Click the Appearance tab.

applicable for the Type you have selected)
The Appearance tab appears.
8. Click the checkboxes for the attributes you
wish to apply to the property:

Active users can add new instances of the

Property to the Sections they create.

Read-Only the property is for display

only, and users may not edit it.

Required the user may not delete the

property from the section.

Not Blank the user must enter a value for

the property before he van perform a
particular transition on the Collection. For
example, you may set up an experiment
Collection such that it is necessary to enter
an equipment id before a user can close the
experiment. If the user has not entered a
value for the property, he will be prompted
to enter it when he attempts to perform the
transition. The Not Blank attribute must be
used in conjunction with the Required
Properties Transition Listener.
ENTER to Create New Line if a user is
editing the property and presses ENTER, a
new instance of the property will appear in
the property list.
9. If the property is type text, you may select the
following:
Enumerator values displayed in a drop-
down list for any particular property may be
pulled from an external database, or from a
list of values you enter. See Managing
Database Values in Property Lists on page
716.
2. Select a Font from the drop-down list.
3. Select a font size from the Font Size drop-
down list.
4. Select whether or not the grid lines will be
displayed, by clicking the checkbox.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Managing Enumerated Values in Prop-
erty Lists
You may configure a text property so that it will
contain a list of enumerated values. A user may then
select one of the values from a drop-down list that
appears in the property cell. This list of values may
be either manually entered, as described here, or
pulled from an external database, as described in
the Managing Database Values in Property Lists
topic.

714 Managing Fields CambridgeSoft

Managing Data Fields
Associating a list of manually entered values 7. Click the Add Value button.
with a property
A blank item appears in the list.
1. In the Collection Tree, right-click the section
8. Enter a value.
type containing property you wish to
configure.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click the property list field in the list of
fields, and select Field Properties from the
menu that appears.

9. Click Add Value to add another value, or OK to

close the dialog.
The values you entered will appear in a drop-
down list in the property cell.

Editing an Enumerated Values List

The Field Properties dialog appears.
1. In the Collection Tree, right-click the section
4. Click the property for which you would like to type to you wish to configure.
add the list of enumerated values.
2. Select Section Type Configuration from the
The attributes of the property appear to the menu that appears.
right.
The Section Type Configuration dialog
5. Click the drop-down arrow for the Enumer- appears.
ator, and select Enumeration List.
3. Right-click the property list field in the list of
fields, and select Field Properties from the menu
that appears.
4. The Field Properties dialog appears. Click the
6. Click the Properties button. property whose values you wish to edit.

NOTE: The button will only be enabled for a property of The attributes of the property appear to the
data type text. right. Enumeration List is displayed as the type
of Enumerator.
The Enumerated List Properties dialog 5. Click the Properties button under the Enumer-
appears. ator.

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Managing Data Fields
 The Enumerated List Properties dialog
appears:
Administrator
6. Click any value to edit it, or click Remove Value
to delete it. To move a value up or down in the
list, click the Move Value Up or Move Value
Down button, respectively.
7. Click OK to close the dialog.
Modifying Properties without Obscuring
Data
Note that if you change the name of a property, the
name will change in all collections that include the
property, even collections that are in a locked, read-
only state. This means that you could potentially
obscure data by changing property names. So, the
following procedure is recommended for changing
the name of a property:
1. In the collection tree, select the section type
containing the property you wish to modify.
The section type is displayed.
2. Right-click the field containing the property,
and select Field Properties from the menu that
appears.
The properties of the field are displayed.
3. Click the property you wish to change.
The attributes of the property are displayed in
the right frame.
716 Managing Fields
4. Deselect the Active checkbox. This will prevent
users from adding new instances of the prop-
erty to new or existing sections.
5. Add a new property (right-clicking Properties
and selecting New Property from the menu that
appears) and give it the new name.
6. Close the Section Type Configuration dialog.
If a section of this type appears by default in one of
the collection types, you will have to remove the old
property from the collection type.
1. Click the collection type in the tree to select it.
2. In the section containing the property, right-
click the property and select Remove Property.
3. Right-click within the field and select Add Prop-
erty, then select the new property you created in
step 5, above.
Note that once you have made this change, it will
still be possible for users to view the old property in
the collections that contain it, and to conduct
searches that contain the old property as well.
Managing Database Values in Property
Lists
This topic provides instructions for configuring
database lookups in property lists. Database
lookups are used to pull in and display values from
a database. You may also validate a value that a user
enters into a property list against an external
database; see Managing the Validate Value
Property List Listener on page 722 for more
information.
1. In the Collection tree, right-click the section
type to you wish to configure.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
CambridgeSoft
Managing Data Fields
 3. Right-click the property list field in the list of
Fields, and select Field Properties from the
menu that appears.
The Field Properties dialog appears.
4. Click the property for whose value(s) you wish
to pull from an against an external database.
5. Click the drop-down arrow for Enumerator, and
select Database Lookup.
6. Click the Properties button.
The Database Lookup Properties dialog
appears.
7. Enter the properties. See step 2 in Creating a
Database Table Field on page 705 for details.
8. Click OK.
Several examples are given below. Note that the
syntax of the query may vary depending upon the
type of database you are querying.
Chem & BioOffice 2006 /E-Notebook
Example 1 Database Lookup Configuration
In this example, all of the values for suppliername
are pulled in from the external database table
Suppliers. The values will appear in a drop-down list
in the property cell.
suppliername value(s) to be displayed in
E-Notebook property.
Suppliers name of external database table
Example 2 Database Lookup Configuration
In this example, the value suppliername is pulled
from the external database table Suppliers. The
suppliername displayed in the database table field
corresponds to the value that a user has entered into
a property list. A user enters SupplierID into the
Supplier ID property, which exists in a Property
List named ID Number.
suppliername value to be displayed in
E-Notebook property.
Suppliers name of external database table.
SupplierID the supplier ID field in the
external database table.
Managing Fields 717
Managing Data Fields
 ID Number name of the E-Notebook
property list containing the Supplier ID
property.
Supplier ID name of the E-Notebook
Administrator
property into which a user enters the value
for SupplierID.
Managing Enumerated
Values in Property Lists
You may configure a text property so that it will
contain a list of enumerated values. A user may then
select one of the values from a dropdown list that
appears in the property cell. This list of values may
be either manually entered, as described here, or
pulled from an external database, as described in
the Managing Database Values in Property Lists
topic.
Associating a list of manually entered values with a
property:
1. In the Collection Tree, right-click the section
type containing property you wish to
configure.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click the property list field in the list of
fields, and select Field Properties from the
menu that appears.
The Field Properties dialog appears.
718 Managing Fields
4. Click the property for which you would like to
add the list of enumerated values.
The attributes of the property appear to the
right.
5. Click the dropdown arrow for the Enumerator,
and select Enumeration List.
6. Click the Properties button.
NOTE: the button will only be enabled for a property
of datatype text.
The Enumerated List Properties dialog
appears.
7. Click the Add Value button.
A blank item appears in the list.
8. Enter a value.
9. Click Add Value to add another value, or OK to
close the dialog.
The values you entered will appear in a
dropdown list in the property cell.
Editing an Enumerated Values List:
1. In the Collection Tree, right-click the section
type to you wish to configure.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click the property list field in the list of
fields, and select Field Properties from the menu
that appears.
The Field Properties dialog appears.
4. Click the property whose values you wish to
edit.
CambridgeSoft
Managing Data Fields
 The attributes of the property appear to the
right. Enumeration List is displayed as the type
of Enumerator.
5. Click the Properties button under the Enumer-
ator.
The Enumerated List Properties dialog
appears:
6. Click any value to edit it, or click Remove Value
to delete it. To move a value up or down in the
list, click the Move Value Up or Move Value
Down button, respectively.
7. Click OK to close the dialog.
Managing Property List
Listeners
A Property List Listener modifies the behavior of
an E-Notebook property list. E-Notebook
provides a number of standard property list
listeners:
You may also develop your own Property List
Listeners to further customize the behavior of
property lists in E-Notebook.
Chem & BioOffice 2006 /E-Notebook
To add a property list listener:
1. From the Section Type Configuration
dialog, right-click the property list field to
which you wish to add the listener.
2. Select New Field Listener from the menu that
appears.
A dialog appears, prompting you to enter the
ProgID for the listener.
3. Enter the ProgID and click the OK button.
The listener appears in the left frame and you
are prompted to rename it.
4. Enter a name for the listener.
To view and edit the properties of the property list
listener:
1. Click the listener.
The ProgID and properties button appear to
the right.
2. Click the Custom Properties button.
If the listener has properties associate with it,
they are displayed, and may be edited.
Managing Fields 719
Managing Data Fields
 Managing the Formula Listener
The formula listener makes it possible to perform
calculations in a cell using other numerical data in
the section and various functions. The listener
Administrator
allows you to specify the target property, the
formula, and an optional format.
It is also possible to calculate a value in a property
list; see Managing the Formula Property List
Listener for more information.
Listener IENTableListener
ProgID
Formula ENStandardCtl9.Formu-
laListener
To add a formula for a property:
1. Click the Custom Properties button for the
field listener.
The Formula Listener Properties dialog
appears. The dropdown list at the top of the
dialog contains a list of all of the properties in
the table.
2. Select the target property that is to be calcu-
lated from the dropdown list.
The selected property is displayed.
3. Type the formula into the formula box.
4. To reference values in other tables or property
lists within the same section, begin and end the
reference with square brackets ([and]), and use
colons to denote specific properties. For
720 Managing Fields
example, [Reaction Conditions: Reaction
Molarity] refers to the Reaction Molarity prop-
erty in the Reaction Conditions property list.
Standard symbols may be used:
+, -, /, *, =, >, >=, <, <>, <=, &,!,!=,%, +/-
Boolean operators may be used:
NOT, AND, OR, XOR
You may use functions:
IF(test, trueValue, [elseTest, elseTrueValue],
falseValue): returns one of two values,
depending upon whether the test returns
True or False.
OnError: returns the first argument if it can
be calculated without error. If an error
would occur in the calculation of the first
argument, the second argument is returned
(in this example, a blank cell would be
returned).
SaltWeight(salt code): returns the molecular
weight property of the salt with this salt
code. The Salt Codes are found in a user's
User Configuration folder.
SUM(tableproperty): returns the sum of the
table cells for the property you specify.
SELECT (value, tablefield, condition): allows
you to select a value in a table based on a
condition, e.g. SELECT ([Moles]
* [Equivalents], [Reactants], [Limiting?] =
"Yes") returns the value of [Moles] *
[Equivalents] from the Reactants table for
the limiting reactant.
5. Use the format field if you wish to format the
numeric value.
Operands in a formula are evaluated in the
following order:
Parentheses
NOT
*, /,%, &
+, -, +/-
CambridgeSoft
Managing Data Fields
 =, <, <=, >, >=, <>,!=
AND
OR, XOR
Commas are used to separate arguments within
functions.
Whenever the contents of the section are
changed, the formula will be checked, and the
target cell will be recalculated if necessary.
Managing the Block Reference In State
Property List Listener
The Block Reference In State property list listener
may be used to block users from adding a reference
to a specific type of collection that is in a particular
state. If the listener is configured to block the
reference, the user will be unable to add the
reference to the property list. For example, you may
wish to prevent users from adding references to
pages/experiments that are in an archived state.
Property List IENPropertyListListe
Listener ner ProgID
Block Reference In ENStandardCtl9.Block-
State RefInStatePListener
This property list listener has custom properties
associated with it. You must select the collection
type and state corresponding to the references that
will be blocked. In the example below, a user will be
prevented from adding a reference to an Page
collection that is in the Closed state.
Chem & BioOffice 2006 /E-Notebook
Note that you may associate multiple instances of
this listener with a property list, if you would like to
prevent users from adding references to several
different collection types and/or several different
states of a collection type.
Managing the Person Property List
Listener
The Person Property List Listener populates the
value of a property with the logged-on user's name
whenever the value of another property is changed.
Listener Listener ProgID
Person Property ENStandardCtl9.Person-
PropertyPListener
The listener has custom properties associated with
it:
Fill in the following information.
Source Property the property that, when
changed, will populate the target property with
the logged-on user's name.
Target Field the field containing the prop-
erty that will display the user name or user ID.
Target Property the property that will
display the user name or user ID.
Target SQL the SQL statement that selects
the username or user ID.
In the example shown above, a change to the source
property Checksum will populate the Editor
property with the name of the logged-on user.
Managing Fields 721
Managing Data Fields
 Managing the Chemical Properties from the Property drop-down list. Then, enter the
Property List Listener database connection information and the SQL
string to be used for validating the value.
The Chemical Properties Property List Listener
populates the Molecular Weight and Molecular
Administrator

Formula properties automatically as the drawing in

a chemical structure field is changed.

Listener Listener ProgID

Chemical ENStandardCtl9.ChemProper-
Properties tiesCSListener

The following is required in the section type in

order to use this listeners. Managing Spectrum Fields
A chemical structure field. Spectrum Fields allow users to view and analyze
A property list with the following properties: spectrum images, using the same tools as Galactic
Molecular Weight and Molecular Formula. GRAMS32 software.
The listener has no custom properties associated If you associate the Spectrum Form Tool with a
with it. spectrum field, users can import spectrum images
of various types. The form tool allows users to copy
Managing the Validate Value Property and export spectrum images as well.
List Listener
The Validate Value Property List Listener allows
you to validate a value in a property list against an
external database, to ensure the value entered into
E-Notebook is valid. If it is not a valid value, the
user will be presented with an error message to that
effect.

Property IENPropertyListListener
List ProgID
Listener

To add a spectrum field:

Validate ENStandardCtl9.ValidateVal-
Value uePListener 1. In the Collection Tree, right-click the section
type to which you wish to add the spectrum
Clicking the Properties button after adding the field.
listener to a property list displays the following 2. Select Section Type Configuration from the
dialog. Here, you select the property to be validated menu that appears.

722 Managing Fields CambridgeSoft

Managing Data Fields
 The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Type in a name, and select Spectrum from the
drop-down list of field types.
5. Click Add.
The new field appears in the list of fields.
6. In order for users to be able to import and
export the spectrum images, you must asso-
ciate the Spectrum Form Tool with the field.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Managing Stored Document
Fields
With Stored Documents Fields, users can associate
document files with sections in E-Notebook. For
example, a document file may be an MS Excel
spreadsheet or a PDF. Although the file cannot be
viewed from within E-Notebook, a user can be
export it to a selected location, then open it and
view or edit it from there.
An example of a Stored Document Field is shown
below.
Chem & BioOffice 2006 /E-Notebook
To add a stored document field:
1. In the Collection tree, right-click the Section
Type to which you wish to add the stored
document field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Type in a name and select Stored Document
from the drop-down list of field types.
5. Click Add.
The new field appears in the list of fields.
6. In order for users to be able to import and
export the stored documents, you must asso-
ciate the Active Document Form Tool with the
field.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Managing Subsection Fields
With a subsection field, users may add sections that
appear as subtabs. This is one way to keep related
sections together in E-Notebook. An example of a
Managing Fields 723
Managing Data Fields
 subsection field is shown below. In this example,
the subsection field contains two spectrum
sections, which appear as subtabs.
Administrator
To add a subsection field:
1. In the Collection Tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the field and select Subsec-
tion from the list of field types.
5. Click Add.
The new field appears in the list of fields.
6. If you would like users to be able to add new
subsections, you must add the New Subsection
Form Tool to the field. Right click the field and
select Field Properties from the menu that
appears.
724 Managing Fields
The Field Properties dialog appears.
7. Right-click Form Tools and select New Form
Tool.
A new form tool appears.
8. Enter the ProgID ENStandardCtl9.NewSec-
tionFormTool in the right frame.
9. Import icons for the form tool (clicking the
Import button and selecting an icon file).
10. Click the Custom Properties button.
A dialog appears, listing all of the section types
in E-Notebook.
11. Select the section types you would like the user
to be able to add as subsections and click the
Add button.
The section types appear in the right frame.
12. Click the Close button to close the dialog.
CambridgeSoft
Managing Data Fields
13. Rename the form tool, by right-clicking it and
selecting Rename Form Tool. This name will
appear on the button the user will click to add
new subsections.
Managing Subsection Field Listeners
Subsection field listeners are used to modify the
behavior of E-Notebook subsections. E-Notebook
provides a standard subsection listener:
Button View Subsection Field Listener forces
subsections into button view.
To add a subsection field listener,
1. In the Collection Tree, right-click the section
type containing the subsection field, and select
Section Type Configuration from the menu that
appears.
The Section Type Configuration dialog
appears.
2. Right-click the subsection field in the list of
Fields, and select Field Properties from the
menu that appears.
The Field Properties dialog appears.
3. Click the Listeners tab.
The listeners tab appears.
4. Right-click Listeners at the top of the left frame
and select New Field Listener.
The New Field Listener dialog appears:
5. Enter the ProgID for the Field listener and click
OK
The New Field Listener dialog closes.
6. If the listener has custom properties, click the
Properties button to configure them.
7. Close the properties dialog.
Chem & BioOffice 2006 /E-Notebook
Managing the Button View Subsection
Listener
The Button View Subsection Listener forces
subsections into button view, as shown below. A
user may then scroll through the subsections using
the arrow buttons, or right-click a subsection name
and select Go To in order to browse to a specific
subsection.
Subsectio IENSubsectionListener
n Listener ProgID
Button ENStandardCtl9.Button-
View ViewSSListener
The Button View Subsection Listener has no
custom properties.
Managing the Hide Tools Subsection
Listener
The Hide Tools Subsection Listener hides the form
tool area of a subsection for more efficient screen
usage.
Subsectio IENSubsectionListener
n Listener ProgID
Hide Tools ENStandardCtl9.HideToolsSS-
Listener
The listener has no custom properties.
Managing Table Fields
Tables enable users to organize data in an easily
interpreted, tabular format. Tables may contain
several basic types of data text data, numerical
data, dates, or structures. You may set up tables in
different sections in E-Notebook to contain
Managing Fields 725
Managing Data Fields
 different types of information. You may also Tables allow the following types of data:
associate table listeners with tables to modify their
behavior.
Administrator

Datatype User perspective

Date A user may click the date box, and type in a date and time.

Text A user may enter text.

Number A user may enter a number. A property may also be config-

ured to have units associated with it.

Structure A user may enter a chemical structure drawing.

Enumerated Value A user may choose a value from a drop-down list. The list
may either be a preconfigured list, or pulled from an external
database.

Validated Value A user may enter a value, which is validated against an

external database.

You may also configure table properties so that they
are read-only, or so that they must contain values
before a collection transition is performed.
Another feature of tables is the ability for users to
add references to them. When a user adds a
reference to a table, he may navigate to the
collection or section he has referenced, simply by
clicking a link in the table cell.
See the following topics for more information
about table fields:
Creating a Table Field
This topic provides instructions for adding a table
to a section type and configuring the table.
To add a table:
1. In the Collection Tree, right-click the section
type to which you wish to add the table.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.

726 Managing Fields CambridgeSoft

Managing Data Fields
 3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the field and select Table from
the list of field types.
5. Click Add.
The new field appears in the list of fields.
Adding a Property to the Table:
NOTE: Note: The Properties you add to a Table will
initially appear as its columns. Once you have added the table
to a form, however, you may pivot the table so that the
properties appear as rows.
1. Right-click the table field in the Section Type
Configuration dialog.
A menu appears.
Chem & BioOffice 2006 /E-Notebook
2. Select Field Properties.
The Field Properties dialog appears.
3. Right-click the name of the field and select
New Property from the menu that appears.
A new property appears in the tree. It's
attributes appear to the right:
4. Type in a Name and Nickname for the prop-
erty. See step 4 in Creating a Property List on
page 713 for details.
Configuring the Appearance of a Table
To configure the appearance of a table:
1. Click the Appearance tab.
The Appearance tab appears.
2. Select a Font from the drop-down list.
3. Select a font size from the Font Size drop-
down list.
4. Select whether or not the grid lines will be
displayed, by clicking the checkbox.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Managing Fields 727
Managing Data Fields
 Managing Database Values in Tables
This topic provides instructions for configuring
database lookups in tables. Database lookups are
Administrator
used to pull in and display values from a database.
You may also validate a value that a user enters into
a table against an external database; see Managing
the Validate Value Table Listener on page 732 for
more information.
1. In the Collection tree, right-click the Section
Type to you wish to configure.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click the Table Field in the list of Fields,
and select Field Properties from the menu that
appears.
The Field Properties dialog appears.
4. Click the Property for whose value(s) you wish
to pull from an against an external database.
5. Click the drop-down arrow for Enumerator,
and select Database Lookup.
728 Managing Fields
6. Click the Properties button.
The Database Lookup Properties dialog
appears.
7. Enter the properties. See step 2 in Creating a
Database Table Field on page 705 for details.
8. Click OK.
Several examples are given below. Note that the
syntax of the query may vary depending upon the
type of database you are querying.
Example 1 Database Lookup Configuration
In this example, all of the values for suppliername
are pulled in from the external database table
Suppliers. The values will appear in a drop-down list
in the property cell.
suppliername value to be displayed in the
table
Suppliers name of external database table
Example 2 Database Lookup Configuration
In this example, the value suppliername is pulled
from the external database table Suppliers. The
suppliername displayed in the table field
corresponds to the value that a user has entered into
CambridgeSoft
Managing Data Fields
a property list that exists elsewhere in the
E-Notebook section. A user enters SupplierID into
the Supplier ID property, which exists in a Property
List named ID Number.
suppliername value to be displayed in the
table.
Suppliers name of external database table.
SupplierID the supplier ID field in the
external database table.
ID Number name of the E-Notebook prop-
erty list containing the Supplier ID property.
Supplier ID name of the E-Notebook prop-
erty into which a user enters the value for
SupplierID.
Managing Enumerated Values in Tables
You may configure a table property so that it will
contain a list of enumerated values. A user may then
select one of the values from the list. This list of
values may be either manually entered, as described
here, or pulled from an external database, as
described in the Managing Database Values in
Tables topic.
Associating a list of manually entered values
with a property
1. In the Collection Tree, right-click the section
type containing table you wish to configure.
2. Select Section Type Configuration from the
menu that appears.
Chem & BioOffice 2006 /E-Notebook
The Section Type Configuration dialog
appears.
3. Right-click the table field in the list of fields,
and select Field Properties from the menu that
appears.
The Field Properties dialog appears.
4. Click the property for which you would like to
add the list of enumerated values.
The attributes of the property appear to the
right.
5. Click the drop-down arrow for the Enumer-
ator, and select Enumeration List.
6. Click the Properties button. Note: the button
will only be enabled for a property of data type
text.
The Enumerated List Properties dialog
appears.
7. Click the Add Value button.
A blank item appears in the list.
8. Enter a value.
9. Click Add Value to add another value, or OK to
close the dialog.
The values you entered will appear in a drop-
down list in the table.
Managing Fields 729
Managing Data Fields
 Editing an Enumerated Values List
1. In the Collection Tree, right-click the section
type to you wish to configure.
Administrator
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click the table field in the list of fields,
and select Field Properties from the menu that
appears.
The Field Properties dialog appears.
4. Click the property whose values you wish to
edit.
The attributes of the property appear to the
right. Enumeration List is displayed as the type
of Enumerator.
5. Click the Properties button under the Enumer-
ator.
The Enumerated List Properties dialog
appears:
6. Click any of the values to edit it, or click
Remove Value to delete it. To move a value up
or down in the list, click the Move Value Up or
Move Value Down button, respectively.
7. Click OK to close the dialog.
Managing Table Listeners
Table listeners are used to modify the behavior of
E-Notebook tables. E-Notebook provides several,
standard table listeners.
See Managing Field Listeners for instructions on
associating a field listener with a field.
Managing the Reactants Table Listener
The reactants table listener calculates and displays
properties of reactants in a stoichiometry grid. The
table can be combined with a products field (a table
field with the products table listener) to create a
stoichiometry grid. The combination of the
730 Managing Fields
stoichiometry grid with a chemical structure field,
and the addition of the Reaction Form Tool creates
a Reaction Section.
Reaction Sections allow users to draw a reaction in
the chemical structure field, then analyze the
reaction, automatically populating the
stoichiometry grid with information about the
reactants and products. In addition, the Next Step
function creates a new page or experiment
containing the products of the chemical reaction.
Table Listener IENTableListener
ProgID
Reactants ENStandardCtl9.Reac-
tantsListener
Managing the Products Table Listener
The products table listener calculates and displays
properties of products in a stoichiometry grid. The
table can be combined with a reactants field (a table
field with the reactants table listener) to create a
stoichiometry grid. The combination of the
stoichiometry grid with a chemical structure field,
and the addition of the Reaction Form Tool creates
a Reaction Section.
Reaction Sections allow users to draw a reaction in
the chemical structure field, then analyze the
reaction, automatically populating the
stoichiometry grid with information about the
reactants and products. In addition, the Next Step
function creates a new page containing the
products of the chemical reaction.
Table IENTableListener ProgID
Listener
Products ENStandardCtl9.ProductsListener
CambridgeSoft
Managing Data Fields
Managing the Products Fixed Limiting Table Managing the Reactants Fixed Limiting Table
Listener Listener
This listener is similar to the Products Table
Listener. The difference is that the limiting This listener is similar to the Reactants Table
equivalents cannot vary if the Products Fixed Listener. The difference is that the limiting
Limiting listener is used. . equivalents cannot vary if the Reactants Fixed
Limiting listener is used.
Table IENTableListener ProgID
Listener Table Listener IENTableListener
ProgID
Products ENStandardCtl9.FixedLimit-
Fixed ingEqProducts Reactants Fixed ENReaction9.FixedLimit-
Limiting Limiting ingEqReactants

Managing the Add Reactant Table Listener

Managing the Block Reference In State Table
The Add Reactant Table Listener makes it possible Listener
for a user to populate the stoichiometry grid with
the properties of a reactant he selects from the The Block Reference In State Table Listener may be
Collection Tree. The user does this by right-clicking used to block users from adding a reference to a
within the table and selecting Add Reactant from specific type of collection that is in a particular state.
the menu that appears. If the listener is configured to block the reference,
the user will be unable to add the reference to the
Table Listener IENTableListener table. For example, you may wish to prevent users
ProgID
from adding table references to pages/experiments
that are in an archived state.
Add Reactant ENReaction9.AddReactant-
TListener
Table IENTableListener ProgID
Listener

Block ENStandardCtl9.BlockRefIn-
Reference StateTListener
In State

This table listener has custom properties associated

with it. You must select the collection type and state
corresponding to the references that will be
blocked. In the example below, a user will be
prevented from adding a reference to an Ancillary
File Version collection that is in the Draft state.

Chem & BioOffice 2006 /E-Notebook Managing Fields 731

Managing Data Fields
 Note that you may associate multiple instances of
this listener with a table, if you would like to prevent
users from adding references to several different
collection types and/or several different states of a
Administrator
field. In addition, you must associate the Analyze
Reaction Chemical Structure Listener with the
reaction field.

collection type. Active IENActiveDocListener

Managing the Validate Value Table Listener Document ProgID
Listener
The Validate Value Table Listener allows you to
validate a values of a property in a table against an
Analyze ENStandardCtl9.AnalyzeRx-
external database, to ensure the values entered into
Reaction nTListener
E-Notebook are valid. If a user enters a value that
is not valid, he will be presented with an error
message to that effect. This listener has no custom properties associated
with it.
Table IENPropertyListListener Managing the Unique Property Table Listener
Listener ProgID
The Unique Property Table Listener prevents
adding more than one property of the same type to
Validate ENStandardCtl9.ValidateVal- a table.
Value ueTListener

Table IENPropertyListListener
Clicking the Properties button after adding the
Listener ProgID
listener to a table displays the following dialog.
Here, you select the property to be validated from
the Property drop-down list. Then, enter the Unique ENStandardCtl9.UniqueProp-
database connection information and the SQL Property ertyTListener
string to be used for validating the value.
Managing the Analyze Reaction Table Listener Managing URL Display
The Analyze Reaction Table Listener automatically Fields
updates the reactants and products tables in a
URL Displays make it possible for users to store
stoichiometry grid when a user edits a reaction
URL's within E-Notebook and to display their
drawing. This listener must be associated with both
corresponding content. You may use a URL
the Reactants table field and the Products table
Display Field for either an internal intranet site or
an external webpage.

732 Managing Fields CambridgeSoft

Managing Data Fields
To create a URL Display field:
1. In the Collection tree, right-click the Section
Type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the Field and select URL
Display from the list of Field Types.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
After you have added the URL Display Field to a
form, you may enter a URL and display its
corresponding page. Each time a user creates
a section of this type, the URL and its content will
appear.
To do this:
1. Enter the URL address as shown above. In this
example, http://www.cambridgesoft.com was
entered.
2. Click the Go button to the right of the address.
Chem & BioOffice 2006 /E-Notebook
The page corresponding to the URL appears.
You may navigate from within the displayed page, if
desired. Note, however, that the URL does not
change to reflect your navigation. If you wish to
change the URL that is saved with the section type,
you must type in another address.
Managing Search Fields
Several field types are designed for use exclusively
within search forms, to search for data in
E-Notebook. They are:
Chemical Query Fields
Collection Query Fields
Collection Type Query Fields
Query Text Fields
State Query Fields
Property Query Fields
Table Query Fields
Unannotated Version Query Fields
Search Location Fields
Join Type Fields
See Managing Data Fields for information about
the other E-Notebook Fields.
Chemical Query Fields
Chemical Query Fields are used in search forms, for
finding chemical structures in E-Notebook tables
and chemical structure fields.
The search is a substructure search. See the User
Guide if you would like more information on
structure searching.
Managing Fields 733
Managing Search Fields
 To create a Chemical Query Field:
1. In the Collection tree, right-click the section
type to which you wish to add the field.
Administrator
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the field and select Chemical
Query from the list of field types.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Collection Query Fields
Collection Query Fields are used in search forms,
for finding collections that match the metadata
criteria that a user specifies:
734 Managing Fields
Users must select each of the criteria they wish to
specify for the search.
To create a Collection Query Field:
1. In the Collection tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the field and select Collection
Query from the list of field types.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
CambridgeSoft
Managing Search Fields
Collection Type Query Fields
Collection Type Query Fields are used in search
forms, for specifying the collection type over which
a search is run. For example, a user may specify a
Page, or an Experiment, so that any other type of
collection will not be included in the search results.
Users must select this item in the search form in
order to specify it for the search.
To create a Collection Type Query Field:
1. In the Collection tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the field and select Collection
Type Query from the list of field types.
5. Click Add.
Chem & BioOffice 2006 /E-Notebook
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Join Type Fields
Join Type fields are used in search forms. They
make it possible for a users conduct a search that is
a union of two searches, an intersection of two
searches, or a subtraction of one set of search
results from another. A join field is shown below:
To create a join type field:
1. In the Collection tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the field and select Join Type
from the list of field types.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Managing Fields 735
Managing Search Fields
 Property Query Fields
Property Query Fields are used in search
forms. They make it possible for a users to search
Administrator
for specific properties in E-Notebook property
lists. (Note that Table Query Fields are used to
search for properties in E-Notebook tables).
To create a Property Query Field:
1. In the Collection tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
4. Enter a name for the field and select Property
Query from the list of field types.
5. Click Add.
736 Managing Fields
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Query Text Fields
Query Text Fields are used in search forms. The
following fields data in E-Notebook is searched
when a user runs a search that contains query text:
MS Word Fields
Styled Text Fields
Property Lists
Tables
Text in chemical structure fields
MS Excel Fields
Certain types of stored document files MS
Word, MS Excel, MS PowerPoint
To create a Query Text Field:
1. In the Collection tree, right-click the Section
Type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
CambridgeSoft
Managing Search Fields
 4. Enter a name for the field and select Query
Text from the list of field types.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
State Query Fields
State Query Fields are used in search forms. They
make it possible for a user to specify the state of the
collections over which a search is conducted. For
example, a user may only want to search for
Collections that were in the Closed state as of a
particular date.
To create a State Query Field:
1. In the Collection Tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
Chem & BioOffice 2006 /E-Notebook
4. Enter a name for the field and select State
Query from the list of field types.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Table Query Fields
Table Query Fields are used in search forms. They
make it possible for a users to search for specific
properties in E-Notebook tables. (Note that
Property Query Fields are used to search for
properties in E-Notebook property lists).
To create a Table Query Field:
1. In the Collection tree, right-click the Section
Type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
Managing Fields 737
Managing Search Fields
 The Add Field dialog appears. The Add Field dialog appears.
Administrator

4. Enter a name for the field and select Table 4. Enter a name for the field and
Query from the list of field types. select Unannotated Version Query from the list
of field types.

5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Unannotated Version Query
Fields
Unannotated Version Query Fields are used in
search forms. They make it possible for a users to
search for collections in which changes that
required annotation have been made, but for which
no annotation has been provided.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.
Search Location Fields
Search Location Fields are used in search
forms. They make it possible for a users to search
for collections and sections that exist in a particular
branch of the Collection Tree.

To create an unannotated version query field:

1. In the Collection Tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.

738 Managing Fields CambridgeSoft

Managing Search Fields
To create a search location field:
1. In the Collection tree, right-click the section
type to which you wish to add the field.
2. Select Section Type Configuration from the
menu that appears.
The Section Type Configuration dialog
appears.
3. Right-click Fields, and select New Field.
The Add Field dialog appears.
Chemical Structure and Table field types, but you
can also develop custom field types to manage
specialized kinds of data or perform complex tasks.
For information about each of the standard types of
fields and their properties, see Managing Fields.
To access the Add-In Configuration and view or
edit the E-Notebook field types,
1. Right-click any blank area of the Collection
Tree.
A menu appears.

4. Enter a name for the field and select Search

Location from the list of field types.

2. Select Add-In Configuration .

The System Configuration dialog appears.
5. Click Add.
The new field appears in the list of fields.
Once you have added a field to the section type, you
may add it to the form for the section type. See
Configuring a Form on page 666 for more
information.

Managing the Add-In

Configuration
The Add-In Configuration dialog contains
information about the field types that are used as
the basis for fields in E-Notebook. E-Notebook This dialog displays the following information
provides a number of standard field types, such as about each of the Field Types:

Chem & BioOffice 2006 /E-Notebook Managing Fields 739

Managing the Add-In Configuration
 Field Type the name of the field type
IENFormTool ProgID the programmatic
identifier that the Windows registry uses to
uniquely identify the object that implements
Administrator
the corresponding interface. The format is
OleServerName.ObjectName.
IENFormToolCtl ProgID the program-
matic identifier that the Windows registry uses
to uniquely identify the object that implements
the corresponding interface. The format is
OleServerName.ObjectName.
License Key
Active an indication of whether new fields of
this type may be added to section types
Changing a Field Type
To change the information for a particular field
type:
1. Click the field type in that you wish to edit in
the list.
The field type is highlighted.
2. Edit any of the information for the field type,
changing its name, ProgID's, license key, or
active status.
3. Click the Change button.
Your changes are saved.
Adding a new Field Type
To add a new field type to E-Notebook:
1. From the Add-In Configuration dialog, click
the New Field Type button.
2. Fill in the following information:
Field Type the name of the Field Type
IENFormTool ProgID the
programmatic identifier that the Windows
registry uses to uniquely identify the object
740 Managing Fields
that implements the corresponding
interface. The format is:
OleServerName.ObjectName.
IENFormToolCtl ProgID the
programmatic identifier that the Windows
registry uses to uniquely identify the object
that implements the corresponding
interface. The format is
OleServerName.ObjectName.
License Key if necessary.
Active an indication of whether new fields
of this type may be used in section types. If
the checkbox is selected, the field type is
active.
Deleting a Field Type
You may only delete field types that are not in use
within E-Notebook section types.
To delete a field type:
1. From the Add-In Configuration dialog, click
the field type in that you wish to delete.
The field type is highlighted.
2. Click the Delete button.
A message appears, asking you to confirm that
you wish to delete the field Type.
3. Click Yes.
If the field type is not used in an E-Notebook
section type, it is deleted. Otherwise, an error
message appears, notifying you that the field
type is in use and cannot be deleted.
Time Settings
Whenever a date or time is displayed in
E-Notebook, it is displayed with a time zone bias
from UTC (Coordinated Universal Time). The
format of the time zone bias is +HHMM. The plus
sign indicates time zones that are east of UTC to the
international date line by a specified number of
hours and minutes (Paris to Auckland and beyond);
CambridgeSoft
Time Settings
a minus sign indicates time zones that are west of
UTC to the international date line (Azores to
Midway Island, and beyond).
Dates appear in the following locations:
1. The history display
2. The Collection Properties dialog box
3. The Version Properties dialog box
4. The Session Manager dialog box
5. The properties field type control
6. The tables field type control
7. The query table field type control
8. The collection query field type control
9. The state query field type control
10. The table of contents
In the history display, the Collection Properties
dialog box, the Version Properties dialog box and
the Session Manager dialog box, dates are
displayed using the time zone of the client machine
that generated the date. For example, the time of a
version is displayed in the time zone of the user
who saved the version; the time of an annotation is
displayed in the time zone of the user who created
the annotation.
In the properties and tables field type controls,
when a user is about to edit a date, the date to be
edited is changed to the corresponding time stamp
of the editing user's time zone. For example, User A
in New Jersey enters a date of June 1, 2004 12:00:00
PM in a date property in a property list. After
editing, the date appears as 06-01-2004 12:00:00
PM -0500. User B in New Jersey views the
property list with the saved date and the date
appears the same. If User B decides to edit the date,
then, when the edit controls appear, the edit
controls are initialized with the date 06-01-2004
09:00:00 AM. If the user makes no changes, then
the value does not change. If the user changes the
Chem & BioOffice 2006 /E-Notebook
time to 09:00:01 AM, then the date appears in the
property list as 06-01-2004 09:00:01 AM -0800.
When user C in London views the date, it will
appear as 01-06-2004 09:00:01 AM -0800 because
user Cs date settings on their client machine specify
that days appear before months in short dates.
In the query table field type control, the collection
query field type control and the state query field
type control, only the date is specified, along with a
time zone. When searching, the dates are converted
to UTC using the time zone associated with the
date. The time zone appears in a popup menu next
to the date. In the event of editing a section
containing one of these field types, if the stored
time zone is different from the time zone of the
client machine, the popup menu will contain the
time zone of the client machine as well, so that the
user can change the query to match the time zone
of the client machine.
Queries by date compare the 24 hour period that
conforms to the date specified by time zone
associated with the query date. For example, if a
user in California searches for date properties with
a value of 06-01-2004 -0800 then any date
property with a value between 06-01-2004 08:00:00
AM +0000 and 06-02-2004 07:59:59 AM +0000
(inclusive) matches that date, wherever it was
entered in the world.
In the Table of Contents, only dates appear, with no
time zone reference. The date corresponds to the
date in the time zone of the generator of the date.
Managing Units in Prop-
erty Lists and Tables
You may associate the following types of
measurements with a property in a property list or
table. The units may then be specified or displayed
in the several units shown. Note that in all cases, the
Managing Fields 741
Managing Units in Property Lists and Tables
 standard units are the SI units for the given type,
which may not be the units commonly entered or Type of Standard Permitted
displayed. Measurement Units Units
Administrator

Type of Standard Permitted molarity mol/m3 mol/l

Measurement Units Units (quantity per molar
volume of solu- mmolar
tion) molar
density kg/m3 g/ml
g/ml
mg/ml moles mol mmol
g/l (quantity of mol
mg/l substance) mol
g/l
kg/l normality mol/m3 N
kg/m3 (ion equivalents mN
per volume of N
length m m solution)

nm pressure Pa atm
m Pa
mm kPa
cm torr
bar
mass kg g mbar
g
mg temperature K C
kg K
F
molality mol/kg mol/kg
(quantity per mass mol/g time s s
of solvent or mmol/kg ms
substrate) mmol/g s
mol/kg min
mol/g hr

molar mass kg/mol g/mol velocity m/s m/s

kg/mol km/hr
dalton mi/hr
D
kD

742 Managing Fields CambridgeSoft

Managing Units in Property Lists and Tables

Type of Standard Permitted
Measurement Units Units
volume m3 ml
l Leading and trailing spaces are removed.
l A trailing period, if present, is removed.
m3
Specification of Units
To specify the units for a property in a property list
or table:
1. In the Section Type Configuration dialog,
right-click the field containing the property
whose units you wish to set.
2. Select Field Properties from the menu that
appears.
The Properties dialog appears.
3. Click the property in the tree to select it.
The attributes of the property are displayed.
The Units list will be disabled if the Type is
text, number, date, or structure. Otherwise, its
contents will change to reflect the permitted
units for the unit type you have selected. The
default selection in the units list will be the first
units in the list, which will be ordered as in the
table above.
4. Select the default Units from the Units drop-
down list.
These are the units that will be displayed by
default when a user enters only a numerical
value into the cell.
Chem & BioOffice 2006 /E-Notebook
Entry of data
When a user enters a value for a property list entry
or table cell which has been defined as a type that
has units, the text is interpreted as follows:
If a hyphen, dash, or minus sign is present and
not the first character of the string, the string is
deemed to represent a range, and divided into
the part before and the part after the first such
character. Spaces surrounding the character are
discarded. Each string is further interpreted
according to the subsequent rules.
The string is tested iteratively, beginning with
the entire string, and truncating one character
off the end during each iteration, until a string
is found which is determined to be numeric, as
defined by the Visual Basic IsNumeric function.
If no such leading numeric substring is found,
the string is deemed uninterpretable.
The remaining part of the string after removing
the leading numeric substring and any
contained spaces is compared against the list of
units permitted for this type. If this string is not
empty, and a match is not found, the string is
deemed uninterpretable.
If the string was found to consist of a range,
and a valid units designation was found only
for the second element of the range, that units
designation is used for both elements.
If no units designation is present, then the
default units designation is applied.
Note that all measurements described in this topic
are stored in an E-Notebook property lists or
tables. This topic does not apply to quantities in
text fields.
Managing Fields 743
Managing Units in Property Lists and Tables
Administrator

744 Managing Fields CambridgeSoft

Managing Units in Property Lists and Tables
Chapter 39: Managing Collection
Types
Information in E-Notebook is organized into
collections, which are the items that appear in the
collection tree. When a user creates a collection, the
properties and content of the collection are
determined by the collection type, which you
configure as an administrator.
You may configure a collection type such that any
of the following are associated with it:
Section Types collection types may be
configured so that they contain section types, which
are the E-Notebook data forms. A page or
experiment is an example of a collection type that
contains section types. Alternatively, a collection
typefor example, a foldermay not have section
types associated with it, but may simply contain
other collection types.
Contained Collection Types A contained
collection is a collection that may exist within
a particular collection in the collection tree. For
example, a user group may contain users; user is a
contained collection type within the user group
collection type. Or, notebooks may contain
experiments; experiment is a contained collection
type within the notebook collection type.
Contained Reference Types A contained
reference is a shortcut that allows E-Notebook
users to view a collection from elsewhere in the
collection tree. Any changes made to the original
are reflected in the reference.
States a state is a condition that defines certain
properties of a collection, such as whether the
collection may be edited. Multiple states may be
used to define the life cycle of a collection. You may
configure change control options based on state.
Chem & BioOffice 2006 /E-Notebook
Search Engines A search engine allows users to
search for information in E-Notebook. For
example, the collection search engine makes it
possible to search for collections that match certain
metadata criteria, such as creation date and owner.
Collection Listeners collection listeners modify
behaviors of collections, such as the move or create
behaviors. An example is the User Collection
Listener, which displays a dialog for entry of
UserID, user name, etc., when a new user is created.
Form Tools form tools perform a certain
function when a user selects themfor example,
creating a new collection or a new section.
See the following topics for more information:
Creating a New Collection Type on page
746.
Adding a Section Type to a Collection Type
on page 747.
Managing Contained Collection Types on
page 749.
Managing Contained Reference Types on
page 750.
Managing Collection Listeners on page 753.
Managing Collection Type Form Tools on
page 762.
Managing States and Transitions on page
768.
Configuring Change Control Options on
page 776.
Managing Templates on page 761.
Managing Export Templates of Collection
Types on page 779.
Managing Collection Types 745
 Creating a New Collec- The entire Collection Tree appears, showing
the Configuration Folder.
tion Type
Collections organize related information in
Administrator

E-Notebook, and each collection appears as an

item in the Collection Tree. When you create a new
collection type, you create a new means of
organizing information in E-Notebook. For
example, you could create a collection type of
Project or Experiment. E-Notebook Users would
then be able to use these Projects or Experiments
to organize their information in E-Notebook.

When you create a new collection type, you define

the rules that determine which sections users can
add to collections of this type. Also, you set up the 3. If you wish, you may right-click the Configura-
rules that govern how the collection type is related tion Folder and select Browse Here, so that the
to other collection types in the Collection Tree: Configuration Folder will appear at the top of
where can a new collection of this type be created, the Collection Tree.
and what types of collections can be created within
it? You can set up the rules that are modeled after
your workflow.

To create a new collection type:

1. Right-click a blank area of the Collection Tree.

A menu appears.
2. Select Browse All.

4. Right-click the Collection Types folder and

select New, then Collection Type.
A new Collection Type appears within the
Collection Types folder, and you are prompted
to rename it.
5. Enter a name for the Collection Type.
6. Right-click the new Collection Type and select
Collection Type Configuration .

746 Managing Collection Types CambridgeSoft

Creating a New Collection Type
 The Collection Type Configuration dialog
appears.
7. Specify the following information:
Plural Name the name applied to
multiple collections of this type.
Icon Name the icon to be associated with
the collection type in the Collection Tree.
8. If you would like the collection type to be used
as an organizational tool for administrators,
you may select any of the following options.
Normally these options are not selected for
new collection types. In the default E-Note-
book setup, only Folders, such as the Collec-
tion Types folder, may contain collection types
and section types.
Can Contain Collection Types a check
mark indicating whether administrators may
add collection types to this collection type.
Can Contain Section Types a checkbox
indicating whether administrators may add
section types to this collection type.
Can Contain Collection Type References
a checkbox indicating whether new
administrators may add references
(shortcuts) to collection types to this
collection type.
Can Contain Section Types a checkbox
indicating whether administrators may add
references (shortcuts) to section types to
this collection type.
Chem & BioOffice 2006 /E-Notebook
Once you have created the collection type, you will
want to configure it. See the related topics for
instructions.
Adding a Section Type to
a Collection Type
By adding sections types to a collection type, you
determine which sections an E-Notebook user can
add to that collection type in E-Notebook. For
example, and Experiment/Page may have several
section types associated with it, including reaction
sections or MS Word sections. When a user creates
an Experiment/ Page, he may add any of these
sections to the Experiment/Page.
You may configure a collection type such that a
particular section appears by default, or, you may
configure it so that the user can add the section if
desired.
To add a section type to a collection type:
1. Right-click the collection type to which you
wish to add the section type, and select
Collection Type Configuration from the menu
that appears.
The Collection Type Configuration dialog
appears.
2. Expand Form Tools, and right-click the New
Section Form Tool.
NOTE: It may be necessary for you to add this form
tool to the collection type. See Managing the New
Section Form Tool on page 661 for more information).
3. In the right frame, click the Custom Properties
button.
A dialog appears, listing all of the section types
in the left panel.
4. Click the section type(s) you wish to add. You
may use Ctrl+click to select multiple section
types, or Shift+click to select a range.
Managing Collection Types 747
Adding a Section Type to a Collection Type
 5. Click the Add>> button.
The section type(s) are moved into the right
panel.
6. Click the Close button.
Administrator
The Section Types dialog closes. The section
type(s) are added to the collection type. When
a user creates the collection in E-Notebook, he
will be able to add these sections to it.
Having a Section Appear by
Default
If you would like a section to appear automatically
when a user creates the collection:
1. Click the New Default Section button in
the right frame.
A menu appears, listing all of the E-Notebook
section types.
748 Managing Collection Types
Removing a Section Type from a Collection Type
2. Select a section type from the list.
The section appears.
3. If you wish, you can add data to the section, or
change the appearance of the section. The
alterations you make will appear only when an
E-Notebook user creates this particular type of
collection.
Removing a Section Type
from a Collection Type
If you no longer wish to include a particular section
type in a collection type, you can remove the section
type.
To do this:
1. Right-click the collection type from which you
wish to remove the section type, and select
Collection Type Configuration from the menu
that appears.
The Collection Type Configuration dialog
appears.
2. Expand Form Tools, and right-click the New
Section Form Tool.
3. In the right frame, click the Custom Properties
button.
A dialog appears, listing of the section types in
the right panel.
CambridgeSoft
 4. Click the section type(s) you wish to remove.
You may use CONTROL+click to select
multiple section types, or SHIFT+click to
select a range.
5. Click the Remove>> button.
The section types are moved to the left pane.
6. Click the Close button.
The dialog closes, and the section type can no
longer be added to the collection type.
NOTE: If you have added the section to the collection type,
so that the section will appear automatically in
E-Notebook when a user creates the collection, you must
delete the existing section from the collection type.
Managing Contained
Collection Types
Contained collection types are collections that may
exist within a particular collection in the Collection
Tree. For example, a user group may contain users;
user is a contained collection type within the user
group collection type. Or, notebooks may contain
experiments; experiment is a contained collection
type within the notebook collection type.
This topic covers adding and removing contained
collection types, and changing the relationship
between a contained collection type and the parent
collection type.
Chem & BioOffice 2006 /E-Notebook
Adding a Contained Collec-
tion Type
To add a contained collection type to a collection
type.
1. In the Collection Tree, right-click the collection
type that is to be the parent collection and
select Collection Type Configuration.
In this example, user group is the parent
collection type, and we are adding the ability to
create foldersthe contained collection
typewithin user groups.
The Collection Type Configuration dialog
appears.
2. Right-click Contained Collection and Page
Types.
A menu appears with the option New
Contained Collection or Page Type.
3. Select New Contained Collection or Page Type.
A dialog box appears, listing the collection
types in E-Notebook (and their corresponding
templates).
4. Click the collection type you wish to add, and
click the Add button.
5. The new contained collection type appears in
the left pane. In the right pane, the features of
the contained collection type within the parent
(or container) collection are displayed.
For example, if the contained Collection is the
child within the parent collection:
New children can be added to parents.
Managing Collection Types 749
Managing Contained Collection Types
 Copies of existing children can be added to
parents.
Children can be deleted from parents.
Administrator
Children can be moved into parents.
Children can be removed from parents and
moved into different collections.
6. Click the checkboxes to select the features you
wish to apply to the contained collection type.
Changing the Relationship
between a Contained Collec-
tion Type and the Parent
Collection Type
To change the relationship between a contained col-
lection type and its parent collection type:
1. In the collection tree, right-click the parent
collection type and select Collection Type
Configuration.
The Collection Type Configuration dialog
appears.
2. Click the plus sign to expand the contained
collection types.
3. Click the contained collection type for which
you wish to change the relationship.
The relationship features appear to the right.
4. Select or deselect the features as desired.
5. Click the Close button in the upper right
corner to close the Collection Type Configu-
ration dialog.
750 Managing Collection Types
Removing a Contained
Collection Type from a
Collection Type
If you wish to remove a contained collection type:
1. In the Collection Tree, right-click the the
parent collection type and select Collection Type
Configuration.
The Collection Type Configuration dialog
appears.
2. Click the plus sign to expand the contained
collection types.
3. Right-click contained collection type you wish
to remove, and select Delete Relationship from
the menu that appears.
A message appears, asking you to confirm that
you wish to delete the relationship.
4. Click Yes.
The contained collection type is deleted. Note
that this change will not affect the relationships
that users have already created. It will only
apply going forward.
Managing Contained
Reference Types
You can set up a collection type to permit users to
add references to other collection types. A
contained reference type differs from a contained
collection type, because a reference is a shortcut
CambridgeSoft
Managing Contained Reference Types
that allows an E-Notebook user to view an original
from elsewhere in the Collection Tree. Any changes
made to the original are reflected in the reference.
This topic covers adding and removing contained
reference types, and changing the relationship
between a contained reference type and the parent
collection type.
Adding a Contained Refer-
ence Type
To add a contained reference type to a collection
type:
1. In the Collection Tree, right-click the collection
type that is to be the parent collection type and
select Collection Type Configuration.
In this example, user group is the parent
collection type, and we are adding the ability to
create references to foldersthe contained
reference typewithin user groups.
Chem & BioOffice 2006 /E-Notebook
The Collection Type Configuration dialog
appears.
2. To expand the collection type to which you
wish to add a contained reference type, either
double-click it or click the plus sign next to it.
3. Right-click Contained Reference Types.
A menu appears with the option New
Contained Reference Type.
4. Select New Contained Reference Type.
A dialog box appears, listing the collection
types in E-Notebook (and their corresponding
Templates).
5. Click the collection type you wish to add as a
contained reference type, and click the Add
button.
6. The new contained reference type appears in
the left pane. In the right pane, the features of
the contained reference type within the parent
collection are displayed. For example, if the
contained reference is the child within the
parent collection:
New references to children can be added to
parents.
Copies of existing references to children can
be added to parents.
References to children can be deleted from
parents.
References to children can be moved into
parents.
References to children can be removed from
parents and moved into different
collections.
Managing Collection Types 751
Managing Contained Reference Types
 7. Click the checkboxes to select the features you
wish to apply to the contained reference type.
Changing the Relationship
Administrator
between a Contained Refer-
ence Type and the Parent
Collection Type
To change the relationship between a contained ref-
erence type and its parent collection type:
1. In the Collection Tree, right-click the parent
collection type and select Collection Type
Configuration.
The Collection Type Configuration dialog
appears.
2. Click the plus sign to expand the contained
reference types.
3. Click the contained reference type for which
you wish to change the relationship.
The relationship features appear to the right.
4. Select or deselect the features as desired.
5. Click the Close button in the upper right
corner to close the Collection Type Configu-
ration dialog.
Removing a Contained
Reference Type from a
Collection Type
If you wish to remove a contained reference type:
1. In the Collection Tree, right-click the the
parent collection type and select Collection Type
Configuration.
The Collection Type Configuration dialog
appears.
2. Click the plus sign to expand the contained
reference types.
752 Managing Collection Types
Configuring Relationships to Unspecified Types of Collections
3. Right-click the contained reference type you
wish to remove, and select Delete Relationship
from the menu that appears.
A message appears, asking you to confirm that
you wish to delete the relationship.
4. Click Yes.
The contained reference type is deleted. Note
that this change will not affect the relationships
that users have already created. It will only
apply going forward
Configuring Relation-
ships to Unspecified
Types of Collections
E-Notebook has an Unspecified Types of
Collections feature that you can use to configure
the relationship between a container collection type
and any collection type for which no relationship is
explicitly defined. For example, if you add
Unspecified Types of Collections as a contained
collection type within a Folder collection type, the
relationship you define will apply to all of the
E-Notebook collection types, excluding collection
types for which an individual relationship is set up.
In the example below, users will be able to add or
delete any type of collection from a Folder. The
features of Reactant collections within Folders may
be different, however, because this relationship is
defined separately:
CambridgeSoft
Unspecified Types of Collections and
Unspecified Types of Template appear in the list
of collection types when you add a new contained
collection type or contained reference type.
Managing Collection
Listeners
Collection listeners modify the behaviors of
collectionssuch as the creating, hiding, renaming,
duplicating, and moving behaviors. E-Notebook
provides several, standard collection listeners that
you may associate with collection types. See the
following topics for more information:
Adding a Collection Listener to a Collection
Type on page 753.
Viewing and Editing the Properties of a
Collection Listener on page 754.
Removing a Collection Listener from a
Collection Type on page 754.
Managing the Standard Collection Listeners
on page 755.
You may also develop your own, customized
collection listeners to perform additional functions.
Chem & BioOffice 2006 /E-Notebook
Adding a Collection Listener
to a Collection Type
You can associate a collection listener with a
collection type if you would like a particular
function to occur when a user takes an action on a
collection. For example, if you create a new user and
the user collection listener is associated with the
user collection type, a dialog will appear prompting
you to enter a LoginID and other pertinent
information.
See Managing the Standard Collection Listeners
on page 755 for information about the various
collection listeners that E-Notebook provides.
To add a collection listener to a collection type:
1. Right-click the collection type in the Collection
Tree, and select Collection Type Configuration
from the menu that appears.
2. Right-Click Collection Listeners and select
New Collection Listener from the menu that
appears.
A new collection listener appears and you are
prompted to rename it.
3. Type in a name for the collection listener.
4. Enter the IENCollectionListener ProgID for
the Listener you wish to add. (This is the
programmatic identifier that the Windows
registry uses to uniquely identify the object that
implements the corresponding interface. The
format is OleServerName.ObjectName).
The collection listener is associated with the
collection type.
5. To close the Collection Type Configuration
dialog, click the close button in the upper
right corner.
The dialog closes.
Managing Collection Types 753
Managing Collection Listeners
 Viewing and Editing the 2. If necessary, click the plus sign next to Collec-
tion Listeners to view the collection listeners
Properties of a Collection that are associated with this collection type.
Listener Click the collection listener whose properties
Administrator

you wish to view or edit.

You can view and edit the custom properties that
you may be associated with a collection listener. To 3. Click the Custom Properties button.
do this:
1. Right-click the collection type that contains the
listener in the Collection Tree, and select
Collection Type Configuration from the menu
that appears.

The Collection Listener Properties dialog

appears. This example shows the dialog for the
Auto Number Listener, which is one of the
standard E-Notebook collection listeners.
(Note that if the collection listener has no
custom properties associated with it, a message
to that effect will appear when you click the
Custom Properties button).
4. Edit the properties, if you wish.

5. Click OK to close the dialog.

6. To close the Collection Type Configuration

dialog, click the close button in the upper right
corner.

The Collection Type Configuration dialog The dialog closes and your changes are saved.
appears.
Removing a Collection
Listener from a Collection
Type
If you no longer want a particular collection listener
to be associated with a collection type, you can
remove it from the collection type.

754 Managing Collection Types CambridgeSoft

Managing Collection Listeners
To do this:
1. Right-click the collection type that contains the
listener in the Collection Tree, and select
Collection Type Configuration from the menu
that appears.
The Collection Type Configuration dialog
appears.
2. If necessary, click the plus sign next to Collec-
tion Listeners to view the collection listeners
that are associated with this collection type.
3. Right-click the collection listener you wish to
remove from the collection type.
A menu appears.
Chem & BioOffice 2006 /E-Notebook
4. Select Delete Collection Listener.
A message appears, asking you to confirm that
you wish to delete the collection listener.
5. Click Yes.
The collection listener is removed from the
collection type.
6. To close the Collection Type Configuration
dialog, click the close button in the upper right
corner.
The dialog closes.
Managing the Standard
Collection Listeners
E-Notebook provides several, standard collection
listeners that you may associate with collection
types. Collection listeners are used to modify the
behaviors of collectionssuch as the creating,
hiding, renaming, duplicating and moving
behaviors.
Managing the Auto Number Collection
Listener
The Auto Number Listener is used to automatically
name newly created collections by appending a
serial number to the name of the collection that
contains the newly created collection.
For example, if a Notebook collection contains
experiments and the notebook is named NB-001,
the Auto Number Collection Listener can be
associated with the Experiment collection type to
automatically number experiments within the
collection (for example, NB-001-001).
Listener Listener ProgID
Auto Number ENStandard9.AutoNum-
berListener
Managing Collection Types 755
Managing Collection Listeners
 The Auto Number Listener has three custom
properties: minimum, increment, and maximum.
The minimum is used to specify the serial number
of the first newly created collection. The increment
Administrator
is used to specify the increment between newly
created collections. The maximum is used to limit
the number of collections that can be contained.
When renaming a collection whose name was
generated with the Auto Number Collection
Listener, the collection will check to ensure that the
name fits within the parameters described by the
Auto Number Listener properties. The name must
begin with the name of the parent collection
followed by a dash and a serial number.
Managing the Audit Collection Listener
The Audit Collection Listener is used to prevent
users from deleting a collection if the collection has
been modified since it was created. If this listener is
associated with a collection type, then the delete
command will be disabled if the collection has been
modified.
Listener Listener ProgID
Audit Collection ENStandard9.AuditCollec-
tionListener
This collection listener has no custom properties
associated with it.
756 Managing Collection Types
Managing the Change Display Collec-
tion Listener
The Change Display Collection Listener is used to
enable Visual Display of Changes when a user
creates a particular type of collection. (See
Managing Visual Display of Changes on page
776).
Listener Listener ProgID
Change Display ENStandard9.ChangeDisplay-
Listener
The Change Display Collection Listener is used to
enable Visual Display of Changes from collection
creation onward. Note that there is also a transition
listener that enables Visual Display of Changes
when a particular transition is performed on a
collection. See Managing the Change Display
Transition Listener on page 772 for more
information.
Managing the Clear Value Collection
Listener
The Clear Value Collection Listener is associated
with a collection type containing sections with
tables/property fields. This listener can be used to
clear specified properties in tables or property list
fields when a collection is duplicated.
For example, you may wish to clear the table section
of a collection when a user duplicates that section.
Listener Listener ProgID
Clear Value ENStandard9.ClearValue-
CListener
With the Custom Properties of the listener, you
specify the section type, the field, and the property
whose values are to be cleared. The top dropdown
CambridgeSoft
Managing Collection Listeners
list displays the Target Section Type in the
collection type. The middle dropdown list displays
the Target Fields in the selected section type. The
bottom dropdown list displays all of the Target
properties in the field you have selected.
Managing the Delete Spawn
Enterprise
Collection Listener
The Delete Spawn collection listener is used in
conjunction with the batch explorer. (The batch
explorer is a form tool that makes it possible for
users to view the successors and predecessors of
reactions in a tree-like layout). When the Delete
Spawn Listener is associated with a collection type,
any batch explorer links to a collection of that type
will be deleted when the user deletes the collection.
Listener Listener ProgID
Delete Spawn ENStandard9.DelSpawn-
LinkLstnr
This collection listener has no custom properties
associated with it.
Managing the Parent Prefix Collection
Listener
The Parent Prefix listener is used to ensure that
when a user renames a collection, any contained
collection that has a name generated by the Auto
Number Listener is renamed with the new prefix.
For example, consider a Notebook collection that
contains Experiments. The Auto Number listener is
associated with the Experiment collection type and
the Parent Prefix listener is associated with the
Notebook collection Type. If a notebook name is
Chem & BioOffice 2006 /E-Notebook
changed from NB to Notebook, then the
Parent Prefix listener renames the contained
experiments so that they begin with Notebook.
Listener Listener ProgID
Parent ENStandard9.ParentPrefixListener
Prefix
This collection listener has no custom properties
associated with it.
Managing the Database Procedure
Collection Listener
The Database Procedure Collection Listener is used
to execute a database procedure during an
operation on a collection.
For example, you may wish to clear the table section
of a collection when a user duplicates that section.
Listener Listener ProgID
Database ENStandard9.DBProcCollection-
Procedure Listener
With the Custom Properties of the listener, you
specify the name of the procedure and when it
should be called: for example, after create, before,
create, etc.
Managing the Fixed Name Collection
Listener
The Fixed Name Listener is used to prevent the
user from renaming collections. If the Fixed Name
Listener is associated with a collection type, then
Managing Collection Types 757
Managing Collection Listeners
 the Rename command in the collection menu is
made inactive when collections of that type are
selected.
Administrator
Listener Listener ProgID
Fixed Name ENStandard9.FixedNameListener
The Fixed Name Collection Listener has no custom
properties associated with it.
Managing the Offline Collec-
Enterprise
tion Listener
The Offline Collection Listener is associated with
Offline Collection type. This listener automatically
creates a reference to a newly created collection in
the offline folder.
Listener Listener ProgID
Offline ENStandard9.UniqueChild-
OfTypeCListener
This collection listener has custom properties
associated with it to configure. The dropdown list
displays all of the collection types in the Container
Collection type and you can select the container
collection type to which you wish to add the Offline
Collection.
Managing the Owner Full Control
Collection Listener
The Owner Full Control collection listener
provides the user with Full Control permission for
this type of collection when he/she is the owner.
For example, if this listener is associated with the
758 Managing Collection Types
notebook collection type, then the user who creates
a notebook will automatically be able to assign and
remove access permissions for the notebook.
Listener Listener ProgID
Owner Full Control ENStandard9.OwnerFull-
ControlCListener
This Collection Listener has no custom properties
associated with it.
Managing the No Create
Enterprise
Offline Collection Listener
The No Create Offline Collection Listener prevents
the creation of this type of collection when the user
is working offline..
Listener Listener ProgID
No Create Offline ENStandard9.NoCre-
ateOfflineCListener
This collection listener has no custom properties
associated with it
Managing the Parent Prefix Collection
Listener
The Parent Prefix listener is used to ensure that
when a user renames a collection, any contained
collection that has a name generated by the Auto
Number Listener is renamed with the new prefix.
For example, consider a Notebook collection that
contains Experiments. The Auto Number listener is
associated with the Experiment collection type and
the Parent Prefix listener is associated with the
Notebook collection Type. If a notebook name is
CambridgeSoft
Managing Collection Listeners
changed from NB to Notebook, then the
Parent Prefix listener renames the contained
experiments so that they begin with Notebook.
Listener Listener ProgID
Parent Prefix ENStandard9.ParentPre-
fixListener
This collection listener has no custom properties
associated with it.
Managing the Prevent Reference Copy
Collection Listener
The Prevent Reference Copy collection listener
prevents users from copying collections that
contain references to specific types of collections
that are in specific states. For example, if this
listener is associated with an experiment/page
collection type, it may be configured to prevent
users from copying pages/experiments that contain
references to folders that are in a Closed state.
Listener Listener ProgID
Prevent Reference ENStandard9.NoCopyRef-
Copy StateCListener
Select the custom properties as shown below:
Chem & BioOffice 2006 /E-Notebook
Target Collection Type the collection type
that is referenced.
Target State the state of the target collection
that would prevent a user from copying a
collection that has this listener associated with
it.
Managing the Prevent Delete when
Referenced Collection Listener
The Prevent Delete when Referenced Collection
Listener prevents users from deleting a collection if
the collection is referenced from another collection
in E-Notebook. The reference may occur in a
property list, a table, or an active document field.
You associate the listener with the collection type
that should not be deleted when it is referenced. For
example, if you want to prevent users from deleting
an Experiment/Page collection when that
Experiment Page is referenced, you would associate
the listener with the Experiment/Page collection
type.
Listener Listener ProgID
Prevent Delete ENStandard9.NoDeleteRef-
when Referenced CListener
The Prevent Delete when Referenced Collection
Listener has no custom properties associated with
it.
Managing the Refresh Database Table
Privilege Change Collection Listener
The Refresh Database Table Privilege Change
listener is used to refresh the contents of a database
table when the privileges associated with a
Managing Collection Types 759
Managing Collection Listeners
 collection change. The listener has properties that
describe the field that is refreshed when a privilege
is added or removed from a collection.
Administrator
Listener Listener ProgID
Refresh Database ENStandard9.Refresh-
Table Privilege DBTablePCListener
Change
With the Custom Properties of the listener, you
specify the target section type and target field. The
Target Section Type popup list contains a list of all
of the section types the currently logged in user can
read. The Target collection type should be set to the
section type that contains the field to be refreshed.
The Target Field popup list contains a list of all of
the database table fields in the Target section type.
The Target field should be set to the field which
displays the data that is changed when the privileges
change.
Managing the Section List Collection
Listener
When the Section List Collection Listener is
associated with a collection type, a list of the
sections in each collection of that type is cached on
the E-Notebook client. This makes it possible for
E-Notebook add-ins and field controls to use the
list. For example, in the default configuration, the
Section List Collection Listener is associated with
the Acronym collection type. A list of the sections
in an Acronym collection is cached on the client,
and the reaction toolbar accesses this list and
displays it in the Quick Add dropdown.
Listener Listener ProgID
Section List ENStandard9.SectionList-
CListener
760 Managing Collection Types
This collection listener has no custom properties
associated with it.
Managing the Security Collection
Listener
The Security Collection Listener allows you to
assign security privileges to a collection when it is
created. For example, you may define a collection
type that allows users to record their ideas and
concepts. For IP reasons, you may want this type of
collection to be visible only to the owner and, for
example, a legal group in the company. This listener
allows you to limit access to certain groups and
individuals automatically, when the collection is
created.
The owner of the collection is given Full Control
privilege by default.
Listener Listener ProgID
Security ENStandard9.SecurityCLis-
tener
With the Custom Properties of the listener, you
specify individual users and groups who will be able
to access collections of this type.
Managing the Sequence Collection
Listener
The Sequence Collection Listener names a new
collection based on a global sequence that you
specify.
Listener Listener ProgID
Sequence ENStandard9.Sequence-
NumberCListener
CambridgeSoft
Managing Collection Listeners
With the Custom Properties of the listener, you
specify the prefix, format, suffix, and database
sequence names.
Managing the Unduplicatable Collec-
tion Listener
If the Unduplicatable Collection Listener is
associated with a collection type, contents of that
type will not be copied when a user copies the
selected collection. For example, there may be a
Page/Experiment collection. If the Unduplicatable
Collection Listener is associated with the
Page/Experiment collection type, these
experiments will not be copied when a user copies
the Experiment collection.
Listener Listener ProgID
Unduplicatable ENStandard9.Unduplicat-
Collection ableCListener
This collection listener has no custom properties
associated with it.
Managing the Unique Child Collection
Listener
The Unique Child Collection Listener ensures the
uniqueness of a collection of this type within its
container collection. For example, if you associate
the listener with the User Configuration collection
type, then specify User as the container collection,
it will only be possible to create a single User
Configuration within each user collection.
Listener Listener ProgID
Unique Child ENStandard9.UniqueChild-
OfTypeCListener
With the Custom Properties of the listener, you
specify the container collection.
Chem & BioOffice 2006 /E-Notebook
EnterpriseManaging the User Collec-
tion Listener
The User Collection Listener is designed for those
systems that use the Standard Oracle Authenticator
to authenticate users with E-Notebook.
The User Collection Listener is associated with the
User collection type to automatically set up users
correctly for authentication. When a new user is
created, the User Collection Listener displays the
User Properties dialog:
Once the user is specified, a new user collection is
created with the same name as the account. The
name of the user collection can be modified to any
valid version of the name.
Listener Listener ProgID
User ENStandard9.UserListener
Note that the User collection listener can only be
added to the User collection type, as E-Notebook
does not support multiple user collection types.
The User Collection Listener has no custom
properties associated with it.
Managing Templates
Templates make it possible for E-Notebook users
to avoid reentering information unnecessarily. For
example, a user may create a template for a
particular experiment/page. It may contain data
Managing Collection Types 761
Managing Templates
 and notes that he often uses, or typical values for
various properties. The user can use the template as
the basis for new experiments/page collections.
Each time a collection type is created in
Administrator
E-Notebook, a template of that type is created
automatically. As an administrator, you configure
the rules that determine which types of templates
an E-Notebook user can create, and which
collection types can contain or reference the
templates. You set up these rules the same way you
would set them up for any, other collection type: by
adding templates to collection types as contained
collection or reference types.
The template collection type should be added as a
contained collection type to a collection type that is
not the container into which users will drag the
templates to create new collections. For example, if
Notebooks contain Experiments, the Experiment
Template collection type should be added as a
contained collection type within, for example, a
Folder or a User. If Experiment Template is a
contained collection type within Notebook, then a
user will simply create a new template when he
drags a template into a Notebook.
See the following topics for information about
adding templates to your E-Notebook
configuration:
Managing Contained Collection Types on
page 749.
Managing Contained Reference Types on
page 750.
Managing Collection Type
Form Tools
There are several form tools that may only be
associated with collection types, for example, the
New Section Form Tool. These form tools are
762 Managing Collection Types
described here. E-Notebook also provides a
number of standard form tools that you may only
associate with section types. See Managing the
Standard Form Tools for more information.
Managing the Duplicate Collection
Form Tool
The Duplicate Collection Form Tool allows users
to create a copy of the selected collection. For
example, if a user clicks the Duplicate Collection
Form Tool on a Page/Experiment collection, the
Page/Experiment collection will be copied. The
new copy will appear within the same container
collection in the Collection Tree.
Form Tool Form Tool Control
ProgID
Duplicate Collec- ENStandardCtl9.DuplicateC-
tion FormTool
Managing the Structure Form Tool
The Structure Form Tool is used to perform the
Analyze Structure command. The Analyze
Structure command populates a property list with
the chemical formula and molecular weight of the
associated chemical structure.
In order to use the Structure Form Tool in an
E-Notebook form, one of each of the following
types of fields must be present in the form:
Chemical Structure Field
Property List - containing
a Molecular Weight property and
CambridgeSoft
Managing Templates
 a Molecular Formula property. Managing the New Section Form Tool
.i.Managing the New Section Form Tool;
Form Tool Form Tool Control
ProgID The New Section Form Tool allows users to add
new sections to a collection, for example, to a page
Structure ENStandardCtl9.Structure- or an experiment. When the user clicks the form
FormToolCtl tool he will be presented with a list of the types of
sections he may add.
When you add a Structure Form Tool to a Form,
you must configure the following custom Form Tool Form Tool Control
properties. ProgID

Managing the Next Step Form Tool New Section ENStandardCtl9.NewSection-

The Next Step Form Tool is used to create a new
page or experiment containing the products of the
associated chemical reaction.
In order to use the Next Step Form Tool in an
E-Notebook form, one of each of the following
types of fields must be present in the form:
Chemical Structure Field
Table Field with Reactants Listener
Table Field with Products Listener
FormTool
Managing the New Child Collection
Form Tool
The New Section Form Tool allows users to add
new contained collections to the selected collection.
For example, a user could click this form tool on a
notebook in order to create a new page/experiment
within the notebook.

Form Tool Form Tool Control Form Tool Form Tool Control
ProgID ProgID

Next Step ENStandardCtl9.Reaction- New Section ENStandardCtl9.NewChild-

FormTool CFormTool

When you add a Reaction Form Tool to a form, you

must configure the following custom properties.
Managing the New Sibling
Enterprise

The E-Notebook User Guide provides more Collection Form Tool

information about the tool and the calculations in
the stoichiometry grid. The Stoichiometry grid is The New Sibling Collection Form Tool allows users
the combination of the Reactants and Products to create a new collection of the same type. For
Fields. example, if a user clicks the New Sibling Form Tool

Chem & BioOffice 2006 /E-Notebook Managing Collection Types 763

Managing Templates
 on a notebook, a new notebook will be created. The 2. Select Browse All.
new sibling will appear within the same container
collection in the Collection Tree.
Administrator

Form Tool Form Tool Control

ProgID

New Sibling ENStandardCtl9.NewSib-

Collection lingCFormTool

The entire Collection tree appears, showing the

Managing Search Types Configuration Folder.
3. If you wish, you may right-click the Configura-
Search types allow users to search for information tion Folder and select Browse Here, so that the
in E-Notebook. Users can run searches, then save Configuration Folder will appear at the top of
their queries and results in the Collection Tree. the Collection tree.
In E-Notebook, search types are simply collection
types that have search engines and search forms
associated with them. E-Notebook provides
several, standard search engines. You may also
develop your own, custom search engines. For
example, you could use the tool to perform various
types of calculations and put the results into a
manageable format within an E-Notebook
collection.

You can configure your own search forms to

contain the fields you require.

Creating a Search Type

You can define your own search types for finding
and managing E-Notebook information that is
important to your users. In E-Notebook, search
types are simply collection types that have search
engines and search forms associated with them. 4. Right-click the Search Types folder (or another
folder) and select New, then Collection Type.
To create a search type, A new collection type appears in the Collection
Tree, and you are prompted to rename it.
1. Right-click a blank area of the Collection Tree.
5. Enter a name for the collection type (i.e., the
A menu appears. search type).

764 Managing Collection Types CambridgeSoft

Managing Search Types
 6. Right-click the search type, and select Collec-
tion Type Configuration from the menu that
appears.
The Collection Type Configuration dialog
appears.
7. Specify the following information:
Plural Name enter the name applied to
multiple collections of this type.
Icon Name select Search as the icon to be
associated with the search type in the
Collection tree.
8. Right-click Search Engines, and select New
Search Engine from the menu that appears.
A new search engine appears and you are
prompted to rename it. Its attributes appear to
the right. The name that you enter for the
Chem & BioOffice 2006 /E-Notebook
search engine is the name that will appear in the
Search For: drop-down list when an
E-Notebook user is in Search mode.
9. Enter the following information. (See
Managing the Standard Search Engines on
page 765 for more information about the stan-
dard, E-Notebook Search Engines).
IENSearchEngineProgID
IENResultsCtlProgID
IENResultsCtl License Key
Once you have created the search type, you
configure it as you would any other collection
type. The section type you associate with it
should be a search form. See Creating a
Search Form on page 766.
Managing the Standard
Search Engines
E-Notebook provides a several standard search
engines:
Managing Collection Types 765
Managing Search Types
 Collection Search Engine Chemical Structure Search Engine
The Collection Search Engine is used to perform The Chemical Structure Search Engine is used to
searches for collections and match criteria specified perform searches for chemical structures. The
Administrator

in the following fields: results are organized by substructure. For each

chemical structure that matches a specified query, a
Collection Query field
set of references is created that contain that
Collection Type Query field chemical structure.
State Query Field
See Managing Chemical Query Fields.
Search Location
Search ProgID Search Engine
Search Search Engine Search Engine Engine Control ProgID
Engine ProgID Control ProgID
Chem- ENChemSearch9.C ENChemSearch9
Collection ENSearchEngine9 ENSearchEngine9 ical hemSearchEngine .Chem-
.CollectionSearch- .CollectionRe- Structure SearchResults Ctl
Engine sultsResultsCtl

Creating a Search Form

Section Search Engine
A search form is simply a section type that contains
The Section Search Engine is used to perform search fields. The search fields make it possible for
searches for sections and match criteria specified in users to search for the following information within
the a variety of field types:
E-Notebook. For information about each of the
Property Query search fields and its usage, please see Managing
Search Fields.
Table Query
Query Text
When you configure a search form, the information
that a user can search for is determined by 1) the
Chemical Query search fields in the form and 2) the search engine
associated with the search type.
In addition, any of the field types listed for the
Collection Search Engine, above, may be used.
To create a new search form,

Search Search Engine Search Engine

Engine ProgID Control ProgID
1. In the Collection Tree, right-click the folder or
Section ENSearchEngine9 ENSearchEngine9 collection into which you are adding the search
.SectionSearch- .CollectionRe- form.
Engine sultsResultsCtl
The collection menu appears.

766 Managing Collection Types CambridgeSoft

Managing Search Types
 2. Select New, then Section Type. 1. Right-click the search type in the Collection
Tree, and select Collection Type Configuration
from the menu that appears.

A new section type appears in the Collection

Tree; its blank form appears to the right. You
are prompted to enter a name for the section
type.
3. Type in a name for the section type.
4. Right-click the new section type in the Collec-
tion Tree and select Section Type Configuration
from the menu that appears.
The Section Type Configuration dialog
appears. This is the dialog through which you The Collection Type Configuration dialog
add and configure the components that make appears.
up the Form
Fields 2. Double-click Search Engines to expand the
category.
Form Tools
Section Listeners 3. Click the search engine.

When you add Fields to the Section Type, you must Its ProgID's appear to the right.
add search fields.
For information about how to configure the section
type, see Managing Section Types and Forms.

Viewing and Editing the

Properties of a Search
Engine
4. Click the Custom Properties button.
In some cases, a search engine may have custom
properties associated with it. You can view and/or If the search engine has custom properties
edit the properties that are associated with a search associated with it, the Properties dialog is
engine. displayed. You may edit the properties at this point.

Chem & BioOffice 2006 /E-Notebook Managing Collection Types 767

Managing Search Types
 If the search engine has no custom properties, a
dialog box appears, stating that the search engine
has no properties associated with it.
Administrator
To add states to a collection type:
1. Right-click the collection type in the Collection
Tree, and select Collection Type Configuration
from the menu that appears.

NOTE: None of the standard, E-Notebook search engines

have custom properties associated with them.

Managing States and

Transitions
You can associate states with a collection type to
define properties of a collection at certain phases or
points in its life cycle. Transitions are the actions a
user takes to move collections from one state to
another. For example, a page/experiment may have
several stateseach of which has different
annotation rules associated with it.

Transition listeners perform certain functions as

the collection moves from one state to another. For
example, a user may be prompted to enter values The Collection Type Configuration dialog
for certain fields, or a visual display of the changes appears.
a user makes to a collection may be enabled. Right-click States and select New State from the
menu that appears:
See the following topics for more information:

Adding States to a Collection Type

Configuring a Transition between States

Managing Transition Listeners

Managing the Standard Transition Listeners

A new state appears and you are prompted to
Adding States to a Collection rename it.
Type 2. Enter a name for the State. Also, specify the
annotation rules that will apply to the State.
The states of a collection type define properties, There are four annotation rules from which
such as change control options, that vary you may choose. The rules appear in the drop-
throughout its life cycle. down lists.

768 Managing Collection Types CambridgeSoft

Managing States and Transitions
 The options are: To configure a transition between states:

Writable with Optional Annotation the 1. Right-click the collection type in the Collection
user may supply annotation for changes if he Tree, and select Collection Type Configuration
wishes. He will not be prompted to supply it. from the menu that appears.

Read-Only the collection cannot be The Collection Type Configuration dialog

edited in this state.
Writable with Prompted Optional
Annotation the user is prompted to
supply annotation for changes, but is not
required to supply it.
Writable with Required Annotation the
user must supply annotation for changes.
The user will be prompted to enter
annotation whenever a version of the
collection is saved.
To add another state to the Collection Type, repeat
steps 2 and 3.
appears.
2. Click the plus sign next to States to expand the
category and see the states that are associated
with the collection type.
3. Click the plus sign next to the state that is to be
the initial state in the transition. In this
example, we are setting up a transition from the
Open state to the Closed state.
The Transition Types category appears.
4. Right-click Transition Types and select New
Transition Type from the menu that appears.

Once you have defined the states, you must

configure the transitions from one state to another.
To set up a transition between states, see
Configuring a Transition between States.

Configuring a Transition
between States A dialog appears, listing the possible target
States for the Transition,
A transition is the action a user takes to move a
collection from one state to another. For example,
a Close transition may allow a user to move a
collection from an Open state in which edits are
permitted to a Closed state in which the collection
is read-only.

You may also associated transition listeners with a

transition, so that the effect of the transition is
modified, usually by performing an operation that is
associated with the transition. 5. Click a target state and click the Add button.

Chem & BioOffice 2006 /E-Notebook Managing Collection Types 769

Managing States and Transitions
 The target state appears within the list of
Transition Types. To the right, a checkbox
appears, with which you may specify whether
the owner of the collection can perform the
Administrator
Transition. By default, the owner of the
collection can perform the transition, but in
some cases, you may set up a transition that can
only be performed by administrators or certain
users.
6. Select whether the owner may perform the
transition.
To associate a transition Listener with the
transition, see Managing Transition Listeners.
Managing Transition
Listeners
Transition listeners are used to perform a certain
function with the transition of a collection from
one state to another. For example, a transition may
be from an open state that permits edits to a closed,
read-only state. One of the standard transition
listeners checks that required properties have been
entered before the transition can be completed.
E-Notebook provides several, standard transition
listeners that you may associate with transitions.
You may also develop your own, customized
transition listeners to perform additional functions.
See the following topics for more information:
Associating a Transition Listener with a Transi-
tion
Viewing and Editing the Properties of a Tran-
sition Listener
770 Managing Collection Types
Removing a Transition Listener from a Transi-
tion
Managing the Standard Transition Listeners
Associating a Transition Listener with a
Transition
Transition Listeners modify the effects of
transitions, usually by performing an operation that
is associated with the transition.
To associate a transition listener with a transition:
1. Right-click the collection type in the Collection
tree, and select Collection Type Configuration
from the menu that appears.
The Collection Type Configuration dialog
appears.
2. Click the plus sign next to states to expand the
category and see the states that are associated
with the collection type.
3. Click the plus sign next to the state that is the
initial state in the transition. In this example,
the transition is from the Open state to the
Closed state.
The Transition Types category appears.
4. Click the plus sign next to Transition Types to
expand it and see the transitions.
5. Right-click the transition with which you wish
to associate the transition listener
A menu appears:
6. Select New Transition Listener .
CambridgeSoft
Managing States and Transitions
 A new transition listener appears, and you are
prompted to rename it.
7. Enter a name for the Transition Listener, and
fill in its IENTransitionListener ProgID.
The transition listener is associated with the
transition. The function it performs will occur each
time a a user conducts this type of transition on this
type of collection.
See Managing the Standard Transition Listeners for
descriptions of the standard, transition listeners
that E-Notebook provides.
Viewing and Editing the Properties of a
Transition Listener
A transition listener may have custom properties
associated with it.
To view and/or edit the custom properties:
1. Right-click the relevant collection type in the
Collection tree, and select Collection Type
Configuration from the menu that appears.
The Collection Type Configuration dialog
appears.
2. Click the plus sign next to states to expand the
category and see the states that are associated
with the collection type.
3. Click the plus sign next to the state that is the
initial state in the transition. In this example,
the transition is from Open State to the Closed
State.
The Transition Types category appears.
4. Click the plus sign next to Transition Types to
expand it and see the transitions.
Chem & BioOffice 2006 /E-Notebook
5. Click the transition listener whose properties
you wish to view or change.
6. Click the Custom Properties button.
If the transition listener has custom properties
associated with it, a Properties dialog appears, and
you may view and/or edit the properties. If the
transition listener has no custom properties
associated with it, a message appears to that effect.
Note that none of the standard transition listeners
have custom properties associated with them.
Removing a Transition Listener from a
Transition
In some cases, you may no longer want to have a
particular transition listener associated with the
transition for a collection type.
To remove a transition listener from a transition:
1. Right-click the relevant collection type in the
Collection Tree, and select Collection Type
Configuration from the menu that appears.
The Collection Type Configuration dialog
appears.
2. Click the plus sign next to states to expand the
category and see the states that are associated
with the collection type.
3. Click the plus sign next to the state that is the
initial state in the transition. In this example,
the transition is from Open state to the Closed
state.
The Transition Types category appears.
4. Click the plus sign next to Transition Types to
expand it and see the transitions.
Managing Collection Types 771
Managing States and Transitions
 5. Right-click the transition listener you wish to If you would like to make the annotation required,
remove. you can configure the custom properties.

A menu appears:
Administrator

Click the Annotation Required checkbox to select

it. Then, click OK to close the dialog.

Managing the Change Display Transi-

6. Select Delete Transition Listener.
A message appears, asking you to confirm that
you wish to delete the Transition Listener.
7. Click Yes.
The transition listener is removed from the
transition.
Managing the Standard
Transition Listeners
Transition listeners are used to perform a certain
function that is associated with a transition from
one state of a collection to another. E-Notebook
provides several, standard transition listeners that
you may associate with transitions.
tion Listener
The Change Display Transition Listener is used to
enable Visual Display of Changes when a user
performs a particular transition. (See Managing
Visual Display of Changes).
Listener Listener ProgID
Change Display ENStandard9.ChangeDis-
playTListener
The Change Display Transition Listener has no
custom properties associated with it.
Note that there is also a collection listener that can
be used to enable Visual Display of Changes as
soon as a collection is created. See Managing the
Change Display Collection Listener for more
information

Managing the Annotate Transition

Listener

When a user performs the transition, the Annotate

listener prompts the user for an annotation that is
associated with the transition.

Listener Listener ProgID

Comment ENStandard9.AnnotateTListener

772 Managing Collection Types CambridgeSoft

Managing States and Transitions
Managing Change Security Transition
Listener
The Change Security Transition Listener enables
Inherits Security for a collection during a transition.
This may be used, for example, to limit access to an
experiment before it is in a Closed state.
Listener Listener ProgID
Change Security ENStandard9.ChangeSecu-
Transition TransLstnr
With the custom properties of the transition
listener, you have the option to specify whether, if a
particular property in the collection is filled in, the
Inherits Security option should remain off even
after the transition is completed. Specifically, you
can specify:
Whether the property is in the collection or an
associated indexing collection.
Section type containing the property
Property list containing the Property
Whether inherits security should be set or not
if the property is filled in.
Managing Confirm Transition Listener
The Confirm Transition Listener prompts a user to
confirm a specific transition prior to the transition
occurring and displays a message to the user
whenever he goes for any transition, asking him to
confirm that he is sure he wants to proceed with a
transition. If the user clicks Yes, then the transition
proceeds. If the user clicks No, then the transition
is canceled.
Listener Listener ProgID
Confirm Transi- ENStandard9.ConfirmTLis-
tion tener
Chem & BioOffice 2006 /E-Notebook
The Confirm Transition Listener has no custom
properties associated with it.
Managing the Export Transition Listener
The Export Transition Listener supports the
printing workflow. It makes it possible to export the
contents of a collection as part of a transition.
Listener Listener ProgID
Export Transi- ENStandard9.ExportTLis-
tion tener
The rendering sections and their corresponding
templates must be set as properties of this listener.
Managing the Final Print Transition
Listener
The final print transition listener can be added to a
transition to force the printout of the entire
collection before the transition continues. The
name of the export template used for the final print
is <Region> Final Print where <Region> is
replaced by the name of the region of the currently
logged-on user.
When this transition listener is associated with a
transition type, transitions will be interrupted with
a message box as follows:
Click OK to print the final print of <Collec-
tion> using the printer <PrinterName>.
where <Collection> is replaced with a description
of a collection, such as experiment CS-00005 and
<PrinterName> is replaced with the name of the
default printer.
If the user clicks OK, then the transition proceeds
by printing all of the pages of the collection to the
default printer. If the user clicks Cancel, then the
transition is canceled.
Managing Collection Types 773
Managing States and Transitions
 After the printout is completed, another message
box appears as follows:
Did the final print of <Collection> succeed?
Administrator
Yes Continue with this transition
No Print again
Cancel Abort this transition
where <Collection> is replaced with a description
of a collection.
If the user clicks Yes, then the transition proceeds.
If the user clicks No, then the pages are printed
again and the message box re-appears. If the user
clicks Cancel, then the transition is canceled.
If the user wants to change the default printer, they
should choose print setup prior to performing the
transition.
Listener Listener ProgID
Final Print ENStandard9.FinalPrintTListener
The Final Print Transition Listener has no custom
properties associated with it.
Managing the Locked Container Transi-
tion Listener
The Locked Container listener checks to ensure
that the container of the collection is in a state
which permits full control over the contents of the
container.
For example, consider an Experiment collection
contained within a Notebook collection. Closed is a
read-only (locked) state; the Reopen transition
moves a collection from the Closed, read-only state
to a state in which edits are permitted. If the Locked
Container Listener is associated with the Reopen
transition of the Experiment collection type, then
774 Managing Collection Types
users will be prevented from reopening an
Experiment within a Notebook that is in the Closed
(locked) state.
Listener Listener ProgID
Locked Contents ENStandard9.LockedContain-
erListener
The Locked Container Transition Listener has no
custom properties associated with it.
Managing the Print Transition Listener
The Print Transition Listener supports the printing
workflow. It makes it possible to print the contents
of a collection as part of a transition.
Listener Listener ProgID
Print Transi- ENStandard9.PrintTListener
tion
The rendering sections and their corresponding
templates must be set as properties of this listener.
Managing the Required Non-Blank
Properties Transition Listener
The Required Non-blank Properties Transition
Listener prevents a transition from occurring if
specific properties are not filled in.
Listener Listener ProgID
Required Non- ENStandard9.RequiredNon-
blank Proper- BlankTListener
ties Transition
CambridgeSoft
Managing States and Transitions
Managing the Required Rows Transition
Listener
The Required Rows Transition Listener prevents a
transition from occurring if specific rows are
missing from a table.
Listener Listener ProgID
Required Rows ENStandard9.RequiredRow-
Transition sTListener
Managing the Required Properties Tran-
sition Listener
The Required Properties listener checks to ensure
that the contents of the property list and table
section cells within the specified collection
conform to the Required and Not Blank options
associated with the properties of the property list
and table fields. If a property in a property list or a
table property does not conform with the
corresponding Required or Not Blank option, then
the transition will not be completed.
Listener Listener ProgID
Required ENStandard9.RequiredProper-
Properties tiesListener
The Required Properties Transition Listener has no
custom properties associated with it.
Chem & BioOffice 2006 /E-Notebook
Managing the Sign Version
Enterprise
Transition Listener
The Sign Version Transition Listener invokes E-
Signatures with a particular transition.
Listener Listener ProgID
Sign Version ENStandard9.SignVersionTL
Transition
The Configuration of this listener includes:
Whether or not a countersignature is required
The transition that should occur upon
successful completion of the signature process
(e.g., to Closed)
The transition that should occur upon failure
of the signature process (e.g., to Open)
Managing the Unlocked Contents Tran-
sition Listener
The Unlocked Contents listener checks to ensure
that the collections contained within a collection are
all locked before the container collection can
transition into a locked state (meaning that the
change and annotation rules for the state are Read-
Only).
For example, consider an Experiment collection
contained within a Notebook collection. Closed is a
read-only state, and the Close transition moves a
collection from an unlocked, editable state to the
Closed, read-only state. If the Unlocked Contents
Listener is associated with the Close transition of
Managing Collection Types 775
Managing States and Transitions
 the Notebook collection type, then users will be
prevented from closing a Notebook if it contains
experiments that are not Closed.
Administrator
In addition, you may configure E-Notebook such
that users must annotate the changes they make to
collections. You may also enable Visual Display of
Changes at some point in the life cycle of a

collection.
Listener Listener ProgID
See the following topics:
Unlocked ENStandard9.UnlockedCon-
Contents tentsListener Managing Visual Display of Changes

Configuring Annotation Options

The Unlocked Contents Transition Listener has no
Configuring Autosave
custom properties associated with it.

Managing Visual Display of

Managing the View Signed
Enterprise
Changes
Versions Transition Listener
Depending the collection type and its state, it is
The View Signed Versions Transition Listener possible for users to view a Visual Display of
allows a user to view all of the electronically-signed Changes that have been made to data in the
renditions of a collection. This listener is used with collection. If Visual Display of Changes is enabled,
the E-Signatures feature. the changes that have been made to a collection can
be viewed in E-Notebook, and the changes will be
Listener Listener ProgID
shown in the printed collection.

Visual Display of Changes may be enabled from the

View Signed ENStandard9.DisplaySignedVer-
Versions Tran- sionTL
sition
This listener has no custom properties.
Configuring Change
Control Options
E-Notebook provides auditing and change control
features. For every change that a user makes, an
audit trail records the logged in identity of the user,
the date, and the time. This is done automatically
when users add, delete, or update data. The audit
trail information is stored in the E-Notebook
database.
very beginning of the collection life cycle, when the
collection is first created. Alternatively, you may
enable Visual Display of Changes when a user
performs a particular collection transition; a
common example is the transition from a closed,
read-only state to a reopened state in which edits are
permitted.
The version of the collection that existed when the
Visual Display of Changes began is called the
Baseline Version of the collection. (Note: a version
is created each time the collection is saved). Users
will see this version highlighted in the History Pane.
If Visual Display of Changes is enabled, there are
visual indicators next to the data that was changed
after the Baseline Version was saved. See the User
Guide for further description of the ways changes
are presented to the user.

776 Managing Collection Types CambridgeSoft

Configuring Change Control Options
When Visual Display of Changes is enabled for a
collection, the printed output will include 1) the
baseline version that existed at the time that Visual
Display of Changes began and 2) all subsequent
changes.
Note that once Visual Display of Changes is
enabled for a collection, it remains enabled for the
life of the collection.
Enabling Visual Display of Changes
from Collection Creation Onward
To begin the Visual Display of Changes at collec-
tion creation,
1. Right-click the Collection Type in the
Collection tree, and select Collection Type
Configuration from the menu that appears.
2. Right-Click Collection Listeners and select
New Collection Listener from the menu that
appears.
A new collection listener appears and you are
prompted to rename it.
3. Type in a name for the collection listener.
4. Enter the ENStandard8.ChangeDisplayListener
as the IENCollectionListener ProgID for the
listener you wish to add.
The collection listener is associated with the
collection type.
Chem & BioOffice 2006 /E-Notebook
5. To close the Collection Type Configuration
dialog, click the close button in the upper right
corner.
The dialog closes. New collections of this type
will have Visual Display of Changes enabled
for their entire life cycles.
Enabling Visual Display of Changes
with a Transition
To enable Visual Display of Changes when a user
performs a particular collection transition:
1. Right-click the collection type in the Collection
tree, and select Collection Type Configuration
from the menu that appears.
The Collection Type Configuration dialog
appears.
2. Click the plus sign next to States to expand the
category and see the states that are associated
with the collection type.
3. Click the plus sign next to the state that is the
initial state in the transition. For example, the
transition is from Closed state to the Reopened
state.
The Transition Types category appears.
4. Click the plus sign next to Transition Types to
expand it and see the transitions.
5. Right-click the transition with which you would
like the Visual Display of Changes to begin.
A menu appears:
Managing Collection Types 777
Configuring Change Control Options
 6. Select New Transition Listener.
A new Transition Listener appears, and you are
prompted to rename it.
Administrator
7. Enter a name for the transition listener, and
enter ENStandard8.ChangeDisplayTListener
as its IENTransitionListener ProgID.
Visual Display of Changes will be enabled when a
user performs this transition on a collection of this
type.
Note that even when Visual Display of Changes is
not enabled, the audit trail still captures the history,
and the history pane displays a list of the saved
versions and transitions for a collection.
Configuring Annotation Options
You may configure E-Notebook such that users can
annotate the changes they make to collections.
E-Notebook provides four options for annotation.
You configure these options on a per collection
type, per state basis. This allows you to configure
different annotation rules for the different phases
of a collection life cycle.
To configure the annotation rules for a state:
1. Right-click the collection type in the Collection
tree, and select Collection Type Configuration
from the menu that appears.
The Collection Type Configuration dialog
appears.
2. Click the plus sign next to states to expand the
category and see the states that are associated
with the collection type.
778 Managing Collection Types
3. Click the state for which you are configuring
the annotation options.
You may select an annotation rule for 1)
Existing Sections and 2) New Sections.
There are four annotation rules from which
you may choose. The rules appear in the drop-
down lists.
The options are:
Writable with Optional Annotation the
user may supply annotation for changes if he
wishes. He will not be prompted to supply it.
Read-Only the collection cannot be
edited in this state.
Writable with Prompted Optional
Annotation when the collection is saved,
the user is prompted to supply annotation
for changes, but is not required to supply it.
Writable with Required Annotation
when the collection is saved, the user must
supply annotation for changes. The user will
be prompted to enter annotation whenever
a version of the collection is saved.
4. Select the annotation rules you wish to apply to
the state.
When a collection of this type is in this state,
the annotation option you have selected will
apply.
If you would like users to provide annotation when
they perform a particular transition, you can
associate the Annotate Listener with the transition.
CambridgeSoft
Configuring Change Control Options
Configuring Autosave The autosave interval appears in the
Collection Properties dialog.
The Autosave feature allows changes to be saved
automatically to the database after a specified time
interval following a change made to the contents of
a section. The autosave interval for a particular
collection can either by specified by a user that has
full control over the collection or can be inherited
from the parent collection.

To specify the autosave interval for a collection

1. In the collection tree, right-click the collection

and choose the Collection Properties from the
menu that appears.

The autosave interval appears, in units of

minutes. If no autosave interval has been
specified for the collection or its containing
collection, then the autosave interval is None
(as shown above) and no autosave will occur
for the collection.

2. Click the Edit Autosave Interval button.

The Edit Autosave Interval dialog box
appears. A dialog box appears in which the user
can specify the autosave interval for the
collection. The top portion of the dialog box
displays the autosave interval for the parent
collection.
If the autosave interval you have specified is
greater than the autosave interval of the
container of the collection, then the autosave
interval of the container will override the
autosave interval specified for the collection.
Managing Export
Templates of Collection
Types
Collection type export templates allow users to
print E-Notebook sections in a collection, or to
export sections to Microsoft Word. You create
export templates in MS Word sections, using tags to
refer to E-Notebook fields.

3. Enter the autosave interval for the collection An export template must be set up for each, new
and click OK . collection type you create.

Chem & BioOffice 2006 /E-Notebook Managing Collection Types 779

Managing Export Templates of Collection Types
 To view the export template of a collection type: 2. Select Show, then Export Templates.

1. Right-click the collection type in the Collection The right frame is blank if there is no export
Tree. template associated with the collection type. If
you wish to edit an existing export template,
Administrator

A menu appears.
see Editing the Export Template for a
2. Select Show, then Export Templates. Collection Type below.
3. Right-click the section icon in the right frame.
The section menu appears.

If the collection type has an export template,

the template appears in the right frame. If not,
the right frame is blank, and you must create a
new template.
See the following topic:
Creating and Editing the Export Template for
a Collection Type 4. Select Section Types.
The Section Types dialog box appears.
Creating and Editing the
Export Templates for a
Collection Type
The export template for a collection type allows
users to print the E-Notebook sections in a
particular collection, and to export sections to
Microsoft Word. The headers and footers from the
collection type export template are used in the
printout.

Creating the Export Templates for a

Collection Type 5. Select Export Template and click the Add button.

To create an export template: 6. Click the Close button.

The Section Types dialog closes.
1. Right-click the collection type in the Collection
Tree. 7. Right-click the section menu icon again.
A menu appears. The section menu appears.

780 Managing Collection Types CambridgeSoft

Managing Export Templates of Collection Types
 8. Select New then Export Template. Editing the Header and Footer Informa-
tion

The header and footer is printed on every page

when a user prints the collection or a portion of the
collection. The header and footer of a collection
type export template can contain standard
replacement tags with the following data:
An MS Word section appears in the right
frame.
Tag Replacement
9. Right-click the section menu icon and select
Rename.
<collectionStatus> The state of the collection.
10. Type in the name of one of the regions. (The (Note that if you are using
region names are found in the Region tab of the Final Print Transition
the Collection Properties dialog for a user Listener, the state will print
collection), for example, United States. as the initial state of the tran-
11. Create an additional export template for each sition, and not as the target
of the other regions to which your system users state. In this specific case, if
are assigned. Name each template after the you would like the name of
regione.g., Europe and Asia/Pacific. the target state to print,
12. Add the text <Contents> into each of the simply type the text name of
templates. An example is shown below: the state into the header or
footer.)

<dateCreated> The timestamp of creation

of the collection

<dateModified> The timestamp of last modi-

fication

<datetoday> The timestamp of the

creation of the export docu-
ment or printout

<collectionOwner> The name of the owner of

the collection

<collectionName> The name of the collection

<collectionType> The type of the collection

Chem & BioOffice 2006 /E-Notebook Managing Collection Types 781

Managing Export Templates of Collection Types
 To edit this data, 2. Double-click the header or footer.

1. While viewing the export template in 3. Edit as desired.

E-Notebook, click the print layout view button
in the lower left corner of the MS Word field.
Administrator

It is the third button in the row.

The export template appears in print layout
view, and the header is visible

782 Managing Collection Types CambridgeSoft

Managing Export Templates of Collection Types
Chapter 40: User Administration
You can create new users and associate logon IDs, 3. Select User.
passwords, and security properties with
them. Security properties determine who
has access to a user and the collections that fall
under the user in the collection tree.
To streamline user administration, you can create
user groups, then create users who inherit the
access privileges that you have assigned to the user
groups.
Users and user groups are types of collections and
they appear in the Collection Tree. You can manage A User is created within the collection you
users and user groupscopying them, referencing selected. You are prompted to enter a Login ID
them, moving them, etc.as you would other and select whether the User is a system
collections. administrator. (Note: with some systems, you
See the following topics for more information may be prompted to enter a password for the
about users and groups: user as well).

Creating a User
Setting the Region for a User
Creating a User Group
Changing a User's Properties

Creating a User
You create a User just as you would create any other
collection. Users are often created within User
Groups. See Creating a User Group for more
information.
1. Right-click the collection (which may be a User
Group) to which you wish to add the User.
A menu appears.
2. Select.
A list of the types of collections you may add
appears.
Once you have created the User, you must assign a
geographical region. See Setting the Region for a
User.
The User automatically inherits the security
privileges of the User Group (or other container
collection) to which he was added. You may disable
inherited security and set the access permissions for
the User independently. In addition, you may add
additional security permissions to the User
Collection.
See Managing Collection Security for more
information.

Chem & BioOffice 2006 /E-Notebook User Administration 783

Creating a User
 Creating a User Group
You create a User Group just as you would create
another collection. You can then add Users to the
Administrator
group, and the Users automatically inherit the
security profile of the group. It is possible to add
additional permissions to a User's individual
security profile as well.
To create a User Group:
1. Right-click the collection to which you wish to
add the User Group. This is often the root
collection of E-Notebook.
A menu appears.
2. Select New.
A list of the collections you may add appears.
3. Select User Group:
A User Group is created and you are prompted
to give it a name.
Depending upon your configuration, you may add
Users to the group by either 1) adding references to
the Users, or 2) adding User collections to the User
Group directly.
784 User Administration
You may then assign security permissions to the
User Group, so that all members of the group have
access to the collections you specify. See Managing
Collection Security for more information.
Changing a User's Prop-
erties
If you are a system administrator, you can change a
users security and logon properties.
To change the logon ID and/or administrator sta-
tus of a user:
1. Right-click the user in the Collection Tree.
A menu appears.
2. Select User Info.
The User Properties dialog box appears.
3. You may edit the logon ID and password, and
select whether or not the user has administra-
tive privileges.
NOTE: The Administrator checkbox is only visible if
you are a full system administrator, and the password
field may not be present with your specific configuration
of E-Notebook.
Changing the Security Prop-
erties of a User Collection
You may change the security properties for a User
Collection as well, to determine who may view or
edit the collections that the user creates. You
CambridgeSoft
Creating a User Group
change the security properties for a user just as you
would change the security properties of any other
collection. See Managing Collection Security.

Chem & BioOffice 2006 /E-Notebook User Administration 785

Changing a User's Properties
Administrator

786 User Administration CambridgeSoft

Changing a User's Properties
Chapter 41: Managing E-Notebook
Security
Security in E-Notebook is set up on a collection
basis. Security properties may be set up for any
collection in the Collection Treewhether it be a
User, a Notebook, a Folder, etc. The security
properties of a collection determine who has read,
write, or full control access to that collection. These
access privileges may be assigned to individual users
or to user groups.
By default, each collection inherits the security
properties of its parent in the Collection Tree. The
inherited security option may be disabled, however,
so that the security properties of a collection can be
configured independently of its parent.
In addition to security at the collection level, you
may also set up security for collection transitions,
specifying which users may or may not perform
certain transitions on collections.
In order for you to see who is logged into
E-Notebook, there is a Session Management tool.
This tool also provides the ability to end the
E-Notebook session for a particular user.
Chem & BioOffice 2006 /E-Notebook
See the following topics for more information:
Managing Collection Security
Managing the Security Properties of a Collec-
tion Type
Managing the Security Properties of a Section
Type
Using the Session Manager
Managing Collection
Security
As an Administrator, you may change the access
privileges that E-Notebook Users have to specific
collections.
The default security for a new collection is Inherits
Security, meaning that a collection has the same
security profile as its parent collection in the
collection tree. You may disable inherited security if
you would like the security profile of a collection to
be independent of the security profile of its parent.
Managing E-Notebook Security 787
Managing Collection Security
 To disable inherited security: Collection Security
1. Right-click the collection for which you wish to
To configure or change the security properties of a
disable inherited security.
collection:
Administrator

A menu appears.
1. Right-click the collection whose security
properties you wish to change.
A menu appears.
2. Select Collection Properties.

The Collection Properties dialog box

appears.

2. If Inherits Security is checked, select it to clear

the checkmark.
Inherits Security is disabled.

NOTE: If you disable Inherits Security, the

permissions that the collection had inherited will become
assigned permissions. You must remove these
permissions explicitly if you do not wish these users or
groups to have access to the collection.
3. Click the Collection Security tab.

788 Managing E-Notebook Security CambridgeSoft

Managing Collection Security
 The Security tab appears. The Groups and
Users who have permission to access this item
appear in one of the two lists: Inherited
Permissions, Assigned Permissions.
Chem & BioOffice 2006 /E-Notebook
Inherited Permissions are permissions
inherited from the parent collection in the
collection tree. (These permissions can only be
changed by disabling inherited security, as
discussed above, or by changing the security
profile of the parent collection). Only the
Assigned Permissions can be changed from
this dialog.
Managing E-Notebook Security 789
Managing Collection Security
 4. Take the appropriate action:
Desired Result Action to take

Add a User or Group 1. Click Add...

Administrator

to the list of Assigned

Permissions. The Choose User or
Group dialog
appears.

2. Select the appropriate

user or group from the
tree. (You may either 1)
right-click within a
blank portion of the
tree and select Browse
All to see all of the
Users, or 2) click the
Search button and
perform a search for a
User or group of
Users).

3. Click Add.

4. Select the appropriate

access from the
listbox:

Read permits a user

to view the
Collection, but not
edit it.

Read and Write

permits a user to view
and edit the
Collection.

Full Control
permits a user to view
the Collection, edit it,
and assign or remove
security permissions
for it.

790 Managing E-Notebook Security CambridgeSoft

Managing Collection Security
 2. Select Collection Properties.
Desired Result Action to take The Collection Properties dialog box
appears.
Remove a User or 1. Highlight the user or
3. Click the Transition Security tab.
Group from the list group in the list.
The Security tab appears. The groups and users
2. Click Remove. who have permission to apply a transition to
this item appear in one of the two lists:
Change the type of 1. Highlight the user or Inherited Permissions, Assigned Permissions.
access for a user or group in the list of
group currently in the Assigned Permissions.
list.
2. Select the appropriate
access from the listbox:

Read

Read and Write

Full Control

NOTE: Note that a user

with Full Control permission
over his home collection (his
user collection) is also able to
end his own sessions by using
the Session Manager.

Transition Security Inherited Permissions are permissions inherited

Transition Security is the security applied to the
collection transitions. For example, some users may
be allowed to close a collection while others can
also reopen the collection.
To change the Transition Security Properties of a
collection:
from the parent collection in the Collection Tree.
(These permissions can only be changed by
disabling inherited security, as discussed above, or
by changing the security profile of the parent
collection). Only the Assigned Permissions can be
changed from this dialog.

1. Right-click the collection whose Security

Properties you wish to change.

A menu appears.

Chem & BioOffice 2006 /E-Notebook Managing E-Notebook Security 791

Managing Collection Security
 4. Take the appropriate action: Managing the Security
Desired Result Action to take
Properties of a Collection
Type
Administrator

Add a User or 1. Click Add...

Group to the list
The Choose User or
of Assigned
Group dialog appears.
Permissions.
2. Select the appropriate user
or group from the tree.
(You may either 1) right-
click within a blank portion
of the tree and select
Browse All to see all of the
Users, or 2) click the
Search button and perform
a search for a User or group
of Users).
3. Click Add.
The Choose Transition
Types dialog appears.
4. Select the appropriate
transition type(s).
The access privileges that you set up for a collection
type determine which users may create new
collections of this type in the Collection Tree, and
which users may modify the configuration of the
collection type.
As with other collections, the default security for a
collection type is Inherits Security, meaning that a
collection type has the same security profile as its
parent collection in the Collection Tree. You may
disable inherited security if you would like the
security profile of a collection type to be
independent of the security profile of its parent.
To disable inherited security:
1. Right-click the collection type for which you
wish to disable inherited security.
The Collection menu appears.

5. Click Add.

The User or Group

appears in the Assigned
Permissions list, along
with the transition type(s)
you selected.

Remove a User or Click Remove.

Group from the
list.

792 Managing E-Notebook Security CambridgeSoft

Managing the Security Properties of a Collection Type
 2. If Inherits Security is checked, select it to clear 3. Click the Collection Security tab.
the checkmark. The Security tab appears. The groups and users
Inherits Security is disabled. who have permission to access this item appear
in one of the two lists: Inherited Permissions,
NOTE: If you disable Inherits Security, the Assigned Permissions.
permissions that the collection had inherited will become
assigned permissions. You must remove these
permissions explicitly if you do not wish these users or
groups to have access to the collection.

Collection Type Security

To set up or change the security properties of a col-
lection type:

1. Right-click the collection type whose security

properties you wish to change.
A menu appears.
2. Select Collection Properties.

The Collection Properties dialog box

appears.

Inherited Permissions are permissions

inherited from the parent collection in the
collection tree. (These permissions can only be
changed by disabling inherited security, as
discussed above, or by changing the security
profile of the parent collection). Only the
Assigned Permissions can be changed from
this dialog.

Chem & BioOffice 2006 /E-Notebook Managing E-Notebook Security 793

Managing the Security Properties of a Collection Type
 4. Take the appropriate action
Administrator

794 Managing E-Notebook Security CambridgeSoft

Managing the Security Properties of a Collection Type
Desired Action to take
Result
Add a User 1. Click Add...
or Group to
the list of The Choose User or
Assigned Group dialog appears.
Permissions
2. Select the appropriate user
or group from the tree. (You
may either 1) right-click
within a blank portion of
the tree and select Browse
All to see all of the users, or
2) click the Search button
and perform a search for a
user or group of users).
3. Click Add.
4. Select the appropriate
access from the listbox:
Read permits a user to
create new collections of
this type in the Collection
Tree. (Note: If a user also
has read access to the
parent collection of this
collection type, he will be
able to view the collection
type in the collection tree).
Read and Write permits
a user make changes to the
configuration and content
of the collection type itself.
These users may also
create new collections of
this type in the collection
tree.
Full Control permits a
user to view the collection
type, modify it, and assign
or remove security
permissions
Chem & BioOffice 2006 for it.
/E-Notebook
Managing the Security Properties of a Collection Type
Desired Action to take
Result
Remove a 1. Highlight the user or group
User or in the list.
Group from
the list 2. Click Remove.
Change the 1. Highlight the user or group
type of in the list of Assigned
access for a Permissions.
user or
group 2. Select the appropriate
currently in access from the listbox:
the list Read permits a user to
create new collections of
this type in the Collection
Tree. (Note: If a user also
has read access to the
parent collection of this
collection type, he will be
able to view the collection
type in the Collection
Tree).
Read and Write permits
a user make changes to the
to the configuration and
content of the collection
type itself. These users may
also create new collections
of this type in the
Collection Tree.
Full Control permits a
user to view the collection
type, modify it, and assign
or remove security
permissions for it.
Managing E-Notebook Security 795
 Managing the Security To disable inherited security:

Properties of a Section 1. Right-click the section type for which you wish
to disable inherited security.
Type
Administrator

A menu appears.
The access privileges that you set up for a section
type determine which users may create view or
configure modify the section type.
This topic applies only to the security of the section
type itself. If a user has access to a particular
collection type that contains the section type, it is
not necessary for the user to have access to the
section type in order to view/create sections within
a collection. That is, the privileges you set up for a
collection type apply to all of its sections.
As with other collections, the default security for a
section type is Inherits Security, meaning that a
section type has the same security profile as its
parent collection in the Collection Tree. You may
disable inherited security if you would like the
security profile of a section type to be independent
of the security profile of its parent.

2. If Inherits Security is checked, select it to clear

the checkmark.
Inherits Security is disabled.

NOTE: If you disable Inherits Security, the

permissions that the collection had inherited will become
assigned permissions. You must remove these
permissions explicitly if you do not wish these users or
groups to have access to the collection.

Section Type Security

To set up or change the security properties of a
section type:
1. In the Collection Tree, right-click the section
type whose properties you wish to change.
A menu appears.
2. Select Collection Properties.

796 Managing E-Notebook Security CambridgeSoft

Managing the Security Properties of a Section Type
 The Collection Properties dialog box The Security tab appears. The groups and users
appears. who have permission to access this item appear
in one of the two lists: Inherited Permissions,
Assigned Permissions.

3. Click the Collection Security tab.

Inherited Permissions are permissions

inherited from the parent collection in the
Collection Tree. (These permissions can only
be changed by disabling inherited security, as
discussed above, or by changing the security
profile of the parent collection). Only the
Assigned Permissions can be changed from
this dialog.

Chem & BioOffice 2006 /E-Notebook Managing E-Notebook Security 797

Managing the Security Properties of a Section Type
 4. Take the appropriate action:
Desired Action to take
Result
Administrator
Add a User 1. Click Add...
or Group to
The Choose User or
the list of
Assigned Group dialog appears.
Permissions
2. Select the appropriate user
or group from the tree. (You
may either 1) right-click
within a blank portion of
the tree and select Browse
All to see all of the users, or
2) click the Search button
and perform a search for a
user or group of users).
3. Click Add.
4. Select the appropriate
access from the listbox:
Read permits a user to
view the section type in the
Collection Tree. (Note that
the user must also have
Read access to the parent
collection of a section type
in order to view it in the
tree).
Read and Write permits
a user make changes to the
to the configuration of the
section type.
Full Control permits a
user to view the section
type, modify it, and assign
or remove security
permissions for it.
798 Managing E-Notebook Security
Desired Action to take
Result
Remove a 1. Highlight the user or group
User or in the list.
Group from
2. Click Remove.
the list
Change the 1. Highlight the user or group
type of in the list of Assigned
access for a Permissions.
user or
group 2. Select the appropriate
access from the listbox:
currently in
the list Read permits a user to
view the section type in the
Collection Tree. (Note that
the user must also have
Read access to the parent
collection of a section type
in order to view it in the
tree).
Read and Write permits
a user make changes to the
to the configuration of the
section type.
Full Control permits a
user to view the section
type, modify it, and assign
or remove security
permissions for it.
Using the Session
Manager
The Session Manager makes it possible for you to
see who is logged in to E-Notebook at any given
time. This tool also provides the ability to end the
E-Notebook session for a particular user. You may
CambridgeSoft
Using the Session Manager
want to end a user's session if the user has locked a The Session Manager appears.
collection for editing and another user must access
the collection.
To access the Session Manager:
1. Right-click within a blank portion of the
Collection Tree.
A menu appears:

This dialog shows the Users, Session numbers, and

Start Times for each current session.

Ending a Session
If you wish to end a particular user's session, you
may do so. To end a session:
1. Click the session in the list.
The session is highlighted.
2. Select Session Manager....
2. Click End Session.
A message appears, asking you to confirm that
you wish to end the session.
3. Click Yes.
The session is ended. The user must log on to
E-Notebook again.

NOTE: A user with Full Control permission over his

home collection (his user collection) may use the Session
Manager to end his own sessions.

Chem & BioOffice 2006 /E-Notebook Managing E-Notebook Security 799

Using the Session Manager
Administrator

800 Managing E-Notebook Security CambridgeSoft

Using the Session Manager
Chapter 42: Summary of the Standard
Add-Ins
This topic summarizes the functions of all the
standard E-Notebook add-inslisteners, field
types, and form toolsthat you may use to
configure E-Notebook.
Collection Listeners
Collection listeners are used to modify the
behaviors of collectionssuch as the creating,
hiding, renaming, duplicating and moving
behaviors.
Auto Number Collection Listener allows the
administrator to specify a customized
numbering scheme for a Collection Type.
Audit Collection Listener prevents the user
from deleting a collection if the collection has
been modified since it was created.
Change Display Collection Listener enables
Visual Display of Changes when a user creates
a particular type of collection.
Clear Value Collection Listener clears speci-
fied properties in tables or property list fields
when a collection is duplicated.
Enterprise Delete Spawn Collection
Listener deletes any batch explorer links to a
collection when the collection is deleted.
Database Procedure Collection Listener
executes a database procedure during an oper-
ation on a collection.
Fixed Name Collection Listener prevents the
user from renaming collections.
Chem & BioOffice 2006 /E-Notebook
Enterprise Offline Collection Listener
automatically creates a reference to a newly
created collection in the offline folder.
Owner Full Control Collection Listener
provides the user with Full Control permission
for this type of collection when he/she is the
owner.
Enterprise No Create Offline Collection
Listener prevents the creation of this type of
collection when the user is working offline.
Parent Prefix Collection Listener ensures that
when the collection is renamed, any contained
collection that has a name generated by the
Auto Number listener has the correct prefix if
the name of the parent collection changes.
Prevent Delete when Referenced Collection
Listener prevents users from deleting this
type of collection when it is referenced from
another collection.
Prevent Reference Copy Collection Listener
prevents users from copying collections that
contain references to specific types of collec-
tions that are in specific states.
Refresh Database Table Privilege Change
Collection Listener used to refresh the
contents of a database table when the privileges
associated with a collection change.
Section List Collection Listener caches a list
of sections in a collection on the E-Notebook
client.
Summary of the Standard Add-Ins 801
Collection Listeners
 Security Collection Listener allows you to
assign security privileges to a collection when it
is created.
Sequence Collection Listener names a new
Administrator
collection based on a global sequence that you
specify.
Unduplicatable Collection Listener blocks
the duplication of a specific type of collection.
Unique Child Collection Listener ensures the
uniqueness of a collection of this type within its
container collection.
User Collection Listener when a User is
created, this listener displays a dialog box for
key information that must be entered, such as
logon ID.
Transition Listeners
Transition listeners are used to perform a certain
function that is associated with a transition from
one state of a collection to another.
Annotate Transition Listener prompts the
user for an annotation that is associated with
the transition.
Change Display Transition Listener enables
Visual Display of Changes when the transition
is performed.
Change Security Transition Listener enables
Inherits Security for a collection during a tran-
sition.
Confirm Transition Transition Listener a
user to confirm a specific transition prior to the
transition occurring.
Export Transition Listener exports the
contents of a collection as part of a transition.
Locked Container Transition Listener checks
to ensure that the container of the collection is
in a state which permits full control over the
contents of the container.
Print Transition Listener prints the contents
of a collection as part of a transition.
802 Summary of the Standard Add-Ins
Required Non-blank Properties Transition
Listener prevents a transition from occurring
if specific properties are not filled in.
Required Rows Transition Listener prevents
a transition from occurring if specific rows are
missing from a table.
Required Properties Transition Listener
checks to ensure that the contents of the prop-
erty list and tables meet the configured
Required or Not Blank option. If they do not,
then the transition will not be completed
Unlocked Contents Transition Listener
checks to ensure that the collections contained
within a collection are all locked before the
container collection can transition into a locked
state.
Section Listeners
E-Notebook provides a number of standard
Section Listeners, which may be used to modify the
behavior of sections:
Audit Section Listener prevents a user from
deleting the section only if it has been modified
since it was created.
Clear Value Section Listener clears specified
values when a user duplicates a section.
Fixed Section Name Listener prevents the
user from renaming the section.
New Name Section Listener prompts a user
to enter a name for a section when it is created.
Required Section Listener prevents the user
from deleting the section at any time.
Unduplicatable Section Listener prevents
certain sections from being copied when a user
copies the collection that contains them.
Form Tools
E-Notebook provides a number of standard form
tools, which may be associated with section types to
perform certain functions:
CambridgeSoft
Transition Listeners
Section Type Form Tools
Active Document (Import/Export) Form
Tool allows the import and export of MS
Word documents and stored document Fields.
Enterprise Batch Explorer Form Tool
allows a user to view a tree diagram of the
predecessors and successors of a batch or
compound.
Character Map Form Tool allows a user to
enter Unicode characters into a text field, prop-
erty list, or table.
Import Image Form Tool allows a user
import a standard image file as a PDF.
Insert/Export Form Tool to insert and
export MS Word documents.
Insert Reference Form Tool allows a user
to reference to a specific collection type in a
target property of a property list.
Load Query Form Tool allows the user to
copy the contents of the currently selected
query into the query panel, to conduct a search.
Mail Section Form Tool allows a user to send
a section to the inbox of another collection,
such as an experiment or a user collection.
New Subsection Form Tool creates a new
subsection when clicked.
Next Step Form Tool creates a new collec-
tion with a reaction section containing the
products of the selected reaction.
Spectrum Form Tool enables the import of
various spectra files, and allows users to copy,
paste, import, and export those files.
Word Link Form Tool allows a user to create
a link from an MS Word document to a section
or collection in E-Notebook.
Collection Type Form Tools
Duplicate Collection Form Tool allows a user
to create a copy of the collection.
Chem & BioOffice 2006 /E-Notebook
New Child Collection Form Tool creates a
new collection within the selected collection.
For example, the tool may be used to created a
new page within a notebook.
New Section Form Tool allows a user to
associate a new section with a collection.
Enterprise New Sibling Collection Form
Tool allows a user to create a new collection
of the same type.
Search Engines
Three, standard search engines may be used:
Collection Search Engine used to search for
collections, based on their metadata.
Section Search Engine used to perform
searches for sections and match criteria speci-
fied in the a variety of field types.
Chemical Structure Search Engine used to
perform searches for chemical structures. The
results are organized by substructure.
Field Types
The following field types are designed for use in
data forms, for data entry, analysis, and display:
Active Document Fields (MS Word fields)
AutoText Fields
Chemical Structure Fields
Context Sensitive Help Fields
Captured Image Fields
Database Table Fields
Database Value Fields
Excel Fields
PowerPoint Fields
Property List Fields
Spectrum Fields
Stored Document Fields
Subsection Fields
Summary of the Standard Add-Ins 803
Search Engines
 Table Fields
URL Display Fields
Several fields types are designed for use exclusively
within search forms, to search for data in
Administrator
E-Notebook. They are:
Chemical Query Fields used for finding
chemical structures in E-Notebook tables and
chemical structure fields.
Collection Query Fields used for
finding collections that match the metadata
criteria that a user specifies.
Collection Type Query Fields used for speci-
fying the collection type over which a search is
run.
Query Text Fields used for finding text that
occurs in several types of E-Notebook fields.
State Query Fields used to specify the state of
the collections over which a search is
conducted.
Property Query Fields used for finding
specific properties in E-Notebook property
lists.
Table Query Fields used for finding specific
properties in E-Notebook tables.
Unannotated Version Query Fields used for
finding collections in which changes that
required annotation have been made, but for
which no annotation has been provided
Search Location Fields used to specify the
branch of the collection tree over which the
search is to be run.
Field Listeners
Field listeners may be associated with fields to
modify their behavior.
Generic Field Listeners can be applied to any
field type:
Block User Edit Field Listener makes a
particular field read-only to users.
804 Summary of the Standard Add-Ins
Block Edit Cell Field Listener makes a partic-
ular field read-only to users and administrators.
Copy Default Field Listener removes the
content of a field when a user copies the collec-
tion that contains the field.
Active Document Field Listeners:
Analyze Reaction Chemical Structure
Listener automatically updates reactants
and products tables in a stoichiometry grid
when a user modifies the reaction drawing.
Prevent External Link Active Document
Listener may be associated with an Active
Document field to prevent users from
linking to external URLs.
Chemical Structure Field Listeners:
Analyze Reaction Chemical Structure
Listener updates a stoichiometry grid
when a user edits a reaction
Chemical Property Chemical Structure
Listener Calculates chemical structure
properties of molecular weight and
molecular formula, and inserts them into a
property list when the contents of the
chemical structure change.
MS Excel Field Listeners:
Break External Links Listener notifies the
user the external link in MS Excel files
stored in E-Notebook will be broken.
Hide Add-Ins Listener allows the user to
disable add-ins associated with MS Excel in
E-Notebook.
Remove Macros Listener allows the user
to disable add-ins associated with MS Excel
in E-Notebook.
Property List Listeners
Block Reference In State Property List
Listener prevents a user from adding a
reference to a particular type of collection
that is in a particular state
CambridgeSoft
Field Listeners
 Person Property List Listener populates
the value of a property with the logged-on
user's name whenever the value of another
property is changed.
Chemical Properties Property List Listener
populates the Molecular Weight and
Molecular Formula properties automatically
as the drawing in a chemical structure field is
changed
Validate Value Property List Listener
validates a value in an E-Notebook property
list against an external database.
Formula listener allows you to associate a
formula with a cell in a property list, and
display the returned value in the cell.
Table Listeners:
Analyze Reaction Table Listener
automatically updates reactants and
products tables in a stoichiometry grid when
a user modifies a reaction drawing.
Block Reference table listener prevents a
user from adding a reference to a specific
type of collection that is in a particular state.
Formula listener allows you to associate a
formula with a table cell, and display the
returned value in the cell.
Products table listener is associated with
the products table field in the stoichiometry
grid of a reaction section.
Products Fixed Limiting table listener
same as the Products listener, but the
limiting equivalents cannot vary.
Reactants table listener is associated with
the reactants table field in the stoichiometry
grid of a reaction section.
Reactants Fixed Limiting table listener
same as the Reactants listener, but the
limiting equivalents cannot vary.
Chem & BioOffice 2006 /E-Notebook
Validate Value Table Listener validates a
value in an E-Notebook table against an
external database.
Unique Property Table Listener prevents
adding more than one property of the same
type to a table.
Subsection Listeners:
Button View Subsection Field Listener
forces subsections into button view (as
opposed to the standard tab view).
Hide Tools Subsection Listener hides the
form tool area of a subsection for more
efficient screen usage.
Commands
Commands can be associated with a collection
types and sections types to render content in:
exporting to MS Word, PDF, or printing.
Collection Commands
Export to MS Word Collection Command
this command allows you to render the
contents of a collection to an MS Word
document type.
Enterprise Export to PDF Collection
Command allows to render and save the
contents of a collection to a PDF document.
Print Collection Command prints the
contents of a collection using an MS Word
document.
Section Commands
Export to MS Word Section Command
this command allows you to render the
contents of a section to an MS Word
document type.
Print Section Command prints the
contents of a section using an MS Word
document.
Summary of the Standard Add-Ins 805
Commands
 Rendering Add-ins
Rendering add-ins may be used to modify the
behavior of rendering printing and exporting to
Administrator
Word.
Fixed Text After Word Renderer This
renderer renders some fixed text at the end of
a collection when rendering the collection.
Full History Word Renderer This renderer
renders the entire history of a collection when
rendering the collection.
Tracked History Word Renderer This
renderer renders the history of a collection
since change display was turned on for the
collection.
806 Summary of the Standard Add-Ins
Fixed Table Field Renderer renders the
contents of a table according to the tags in a
Word table.
NonBlank Property Field Renderer renders
the name and value of a property if the prop-
erty is not blank.
One Property Value Field Renderer renders
the value of a single property according to the
tags in a Word table.
One Table Value Field Renderer renders the
value of a single table cell according to the tags
in a Word table.
Property Value Field Renderer renders the
values of all the properties in a property list
without their corresponding names.
CambridgeSoft
Rendering Add-ins
Chapter 43: Using the Batch Import
Facility
The batch import facility in E-Notebook provides
for a means to import a partial or complete
configuration in a single menu command. This
process is controlled by an import script called the
Batch File, which is an xml file adhering to the
schema described in this document. The Batch File
typically refers to additional files, either
E-Notebook content files created with the Export
command (called Content Files) or subsidiary batch
files. This process is initiated by selecting a
collection in the E-Notebook collection tree (which
will be referred to as the Parent Collection) and
choosing the Import command.
<batch>
The root element must be a <batch>. There are no
attributes defined for the batch element. A batch
may contain zero or more of any of the following
elements, interspersed in any order, except as
dictated by the dependencies between the imported
collection and section types.
log
alert
refresh
import
<import>
The import element causes a single file to be
imported. This file may contain any content,
including section types, collection types, collections,
or sections. There are no attributes defined for the
Chem & BioOffice 2006 /E-Notebook
import element. Each import element may contain
a target element, if none is specified, the target is the
parent collection. Each import element must
contain a source element.
<target>
The target element describes where in the
E-Notebook collection hierarchy the imported
content is to be placed. This element must contain
one of the following elements, depending on what
sort of content is being imported:
collectionType
childReference
<collectionType>
A collectionType element indicates that the
relationships for a previously imported collection
type are to be imported. The name attribute
specifies the name of the collection type for which
relationships are to be imported, and the
collectionType element must include a collection
element which specifies by position the first (and
only) collection which defines that collection type.
For example:
<import>
<target><collectionType name="Binder">
<collection position="1"/></collectionType>
</target>
<source>Collection Types/Binder.xml
</source>
</import>
Chapter 43: Using the Batch Import Facility 807
<batch>
 <childReference>
A <childReference> indicates a reference to a
collection contained within the Parent Collection.
Administrator
This element must contain a name or position
attribute, but is invariably used with a name. For
example, this may be used to create a grandchild of
the Parent Collection, as follows:
<import>
<source>Section Types.xml</source>
</import>
<import>
<target><childReference name="Section Types"/>
</target>
<source>General Information.xml</source>
</import>
Assuming Section Types.xml describes a
collection named Section Types and that
General Information.xml describes a section
type, this <import> will create a Section Types
collection, and within that, a General Information
section type.
The E-Notebook collection hierarchy distinguishes
between the nodes, called collections, and the
links between the nodes, called references. Every
reference has one container collection and one
target collection, and a collection may be referred to
as the target of any number of references. Thus, the
<childReference> describes a reference, but if a
<target> specifies a reference, it is assumed that the
target is the reference's target collection. A
<childReference> may contain a <targetCollection>
element explicitly to indicate that the target is the
collection, not the reference, but this is optional
unless one wishes to further specify a collection
contained within this collection. For example, to
specify deeper levels in the collection hierarchy, one
might use:
<import>
<target>
808 Chapter 43: Using the Batch Import Facility
<childReference name="Some Folder">
<targetCollection>
<childReference name="Another Folder"/>
</targetCollection>
</childReference>
</target>
<source>Deeper Folder.xml</source>
</import>
<source>
The source element contains text which specifies
the path of the file to be imported. This is
interpreted relative to the batch file.
<log>
The log element contains text which is written to
the client log file, if logging is enabled. If logging is
not enabled, this element is ignored. Example:
<log>General Information section type created
</log>
<alert>
The alert element causes a message to be displayed.
This element must contain the text to be displayed,
and may have a title attribute which specifies the
title of the message box, and may have a buttons
attribute which may be 0 or 1. If the buttons
attribute is 0 or not specified, the message box will
have an OK button only. If the buttons attribute is
1, the message box will have OK and Cancel, and if
Cancel is pressed, the import process will stop.
<refresh>
The refresh element causes the client to refresh the
display of section and collection type information
to show the effect of any imported objects. One
commonly uses a refresh element at the end of the
import script.
CambridgeSoft
<childReference>
Appendix O: Technical Support
Overview
CambridgeSoft Corporation (CS) provides
technical support to all registered users of this
software through the internet, and through our
Technical Support department.
Our Technical Support webpages contain answers
to frequently asked questions (FAQs) and general
information about our software. You can access our
Technical Support page using the following
address: http://www.cambridgesoft.com/services/
If you dont find the answers you need on our
website, please do the following before contacting
Technical Support.
1. Check the ReadMe file for known limitations
or conflicts.
2. Check the system requirements for the soft-
ware at the beginning of this Users Guide.
3. Read the Troubleshooting section of this
appendix and follow the possible resolution
tactics outlined there.
4. If all your attempts to resolve a problem fail, fill
out a copy of the CS Software Problem Report
Form at the back of this Users Guide. This
form is also available on-line at:
http://www.cambridgesoft.com/services/mail
Try to reproduce the problem before
contacting us. If you can reproduce the
problem, please record the exact steps that
you took to do so.
Record the exact wording of any error
messages that appear.
Record anything that you have tried to
correct the problem.
Chem & BioOffice 2006 /Appendix
You can deliver your CS Software Problem Report
Form to Technical Support by the following
methods:
Internet:
http://www.cambridgesoft.com/services/mail
Email: support@camsoft.com
Fax: 617 588-9360
Mail: CambridgeSoft Corporation
ATTN: Technical Support
100 CambridgePark Drive
Cambridge, MA 02140 USA
Serial Numbers
When contacting Technical Support, you must
always provide your serial number. This serial
number was on the outside of the original
application box, and is the number that you entered
when you launched your CambridgeSoft
application for the first time. If you have thrown
away your box and lost your installation
instructions, you can find the serial number in the
following way:
Choose About CS <application name> from the
Help menu. The serial number appears at the
bottom left of the About box.
For more information on obtaining serial numbers
and registration codes see:
http://www.cambridgesoft.com/services/codes.cfm
Troubleshooting
This section describes steps you can take that affect
the overall performance of CambridgeSoft
Desktop Applications, as well as steps to follow if
your computer crashes when using a CS software
product.
Technical Support 809
Serial Numbers
 Performance
Below are some ways you can optimize the
performance of CambridgeSoft Desktop
Applications:
Administrator
In the Performance tab in the System control
panel, allocate more processor time to the
application.
Install more physical RAM. The more you
have, the less ChemOffice Desktop Applica-
tions will have to access your hard disk to use
Virtual Memory.
Increase the Virtual Memory (VM). Virtual
memory extends RAM by allowing space on
your hard disk to be used as RAM. However,
the time for swapping between the application
and the hard disk is slower than swapping with
physical RAM.
Change the VM as follows:
System control panel, Performance tab.
System Crashes
CambridgeSoft Desktop Applications should never
crash, but below are the steps you should go
through to try to resolve issues that cause computer
crashes while using a CS software product.
1. Restart Windows and try to reproduce the
problem. If the problem recurs, continue with
the following steps.
2. The most common conflicts concern Video
Drivers, Printer Drivers, screen savers, and
virus protection. If you do need to contact us,
be sure to determine what type and version of
drivers you are using.
810 Technical Support
Video Driver related problems: If you are
having problems with the display of any
CambridgeSoft Desktop Application, try
switching to the VGA video driver in the
display Control Panel (or System Setup, then
retest the problems. If using a different driver
helps, your original driver may need to be
updatedcontact the maker of the driver and
obtain the most up-to-date driver. If you still
have trouble contact us with the relevant
details about the original driver and the
resulting problem.
Printer Driver related problems: Try using
a different printer driver. If using a different
driver helps, your original driver may need to
be updatedcontact the maker of the driver
and obtain the most up-to-date driver. If you
still have trouble contact us with the relevant
details about the original driver and the
resulting problem.
3. Try reinstalling the software. Before you rein-
stall, uninstall the software and disable all back-
ground applications, including screen savers
and virus protection. See the complete unin-
stall instructions on the CambridgeSoft Tech-
nical Support web page.
4. If the problem still occurs, use our contact
form at: http://www.cambridge-
soft.com/services/mail and provide the details
of the problem to Technical Support.
CambridgeSoft
Troubleshooting
Appendix P: Accessing the Cambridge-
Soft Web Site
Online Menu
Overview
The ChemOffice Online menu gives you quick
access to the CambridgeSoft web site from within
ChemOffice. With the Online menu, you can:
Register your software.
Search for compounds by name or ACX
number and insert the structure in a worksheet
Use ACX numbers, or names or structures in
the worksheet, to search for chemical informa-
tion
Browse the CambridgeSoft website for tech-
nical support, documentation, software
updates, and more
To use the Online menu, you must have internet
access.
Registering Online
Chem & BioOffice 2006 applications utilize a new
security scheme. In order to activate any
ChemOffice application, you must register with the
Chem & BioOffice 2006 /Appendix
CambridgeSoft website to receive a registration
code. Upon filling out a registration form, the
registration code is sent to you by email. This
registration scheme does not apply to site licenses.
If your serial number is invalid for any reason, or if
you do not have an internet connection, you will
have to contact CambridgeSoft Support to receive
a registration code.
You may use your ChemOffice application a limited
number of times while waiting for the registration
process to be completed. Once the application
times out, you must register to activate the software.
In addition to registering your software, you can
request literature, or register for limited free access
to ChemFinder.com, ChemACX.com,
ChemClub.com, and the email edition of
ChemNews from the Register Online link of the
Online menu. This link connects you to the
Cambridgesoft Professional Services page. From
this page you can link to a registration form.
To register online:
1. From the Online menu, choose Register
Online.
The Cambridgesoft Professional Services page
opens in your browser.
Register tab
2. Select the Register tab.
Accessing the CambridgeSoft Web Site 811
Registering Online
 Accessing the Online
ChemDraw Users Guide
Administrator
The Online menu link Browse CS ChemDraw
Documentation opens the Cambridgesoft Desktop
Manuals page, where you can access current and
previous versions of the Appendix Users Guide.
To access the CambridgeSoft Manuals page:
1. From the Online menu, choose Browse
CS ChemDraw Documentation.
The Desktop Manuals page appears. PDF
versions of the CambridgeSoft manuals can be
accessed from this page.
NOTE: If you do not have a CambridgeSoft User
account, you will be directed to a sign-up page first.
2. Click version of the manual to view.
812 Accessing the CambridgeSoft Web Site
Accessing Cambridge-
Soft Technical Support
The Online menu link Browse CS Appendix
Technical Support also opens the Cambridgesoft
Professional Services page. There are a number of
links on this page for Troubleshooting, Downloads,
Q&A (the ChemOffice FAQ), Contact, and so
forth.
Finding Information on
ChemFinder.com
The Find Information on ChemFinder.com menu item
links your browser to the ChemFinder database
record of the compound you have selected.
ChemFinder is the public-access database on the
ChemFinder.com website. It contains physical,
regulatory, and reference data for organic and
inorganic compounds.
To access ChemFinder.com:
1. In Appendix, select a structure you want to
look up.
2. From the Online menu, choose Find Informa-
tion on ChemFinder.com.
The ChemFinder.com page opens in your
browser with information on the selected
structure.
In ChemFinder.com you can search for chemical
information by name (including trade names), CAS
number, molecular formula, or molecular weight.
CambridgeSoft
Accessing the Online ChemDraw Users Guide
Follow the links to do substructure queries.The
following illustration shows part of the page for
Benzene.
Finding Chemical
Suppliers on ACX.com
The Find Suppliers on ChemStore.Com menu item
links your browser to the chemacx.com database
record of suppliers of the compound you have
selected.
ChemACX (Available Chemicals Exchange) is a
Webserver application that accesses a database of
commercially available chemicals. The database
contains catalogs from research and industrial
chemical vendors.
ChemACX allows the user to search for particular
chemicals and view a list of vendors providing those
chemicals.
Chem & BioOffice 2006 /Appendix
To use Find Suppliers on ChemStore.Com menu
access:
1. In Appendix, select a structure you want to
look up.
2. From the Online menu, choose Find Suppliers
on ChemStore.com.
The ChemACX.Com page opens in your
browser with information on the selected
structure.
For example the ChemACX.com page for Benzene
is shown below.
For more information on using the ChemACX
website, see the ChemOffice Enterprise
Workgroup & Databases Manual.
Finding ACX Structures
and Numbers
Appendix searches ACX and returns information
about related structures and numbers. You can
place the returned information in your document.
ACX Structures
There are two ways to find ACX structures: by ACX
number or by name.
Accessing the CambridgeSoft Web Site 813
Finding Chemical Suppliers on ACX.com
 To find a structure that corresponds to an ACX ACX Numbers
number:
To Find an ACX number for a structure:
1. From the Online menu, choose Find Structure
1. In a Appendix document, select the structure
Administrator

from ACX Number.

The Find Structure from ACX number
dialog box appears.
for which you want to find an ACX number.
2. From the Online menu, choose Find ACX
Numbers from Structure.
The ACX number appears in the Find ACX
Numbers from Structure dialog box.

2. Type the ACX registry number.

3. Click OK.
The Structure appears in your document.
To find a structure from a name
1. From the Online menu, choose Find Structure
from Name at ChemACX.com.
The Find Structure from Name dialog box
appears.
Browsing Chem-
Store.com
Browse ChemStore.com opens the ChemStore
page of the CambridgeSoft web site.
To access Browse ChemStore.com:
From the Online menu, choose Browse Chem-
Store.com.
The ChemStore.Com page opens in your
browser.

2. Type in a name. As with ChemFinder.com, you

can use a chemical name or a trade name.

3. Click OK.

The Structure appears in your document.

814 Accessing the CambridgeSoft Web Site CambridgeSoft

Browsing ChemStore.com
You can search ChemStore.Com for chemicals, lab
supplies, chemistry-related software, and other
items you want to buy. You can access
ChemACX.Com, LabEqwip.Com, and other pages
from ChemStore.Com.
Browsing Cambridge-
Soft.com
Browse CambridgeSoft.com opens the Home page
of the CambridgeSoft web site.
To access the CambridgeSoft Home Page:
From the Online menu, choose Browse
CambridgeSoft.com.
The CambridgeSoft web site in your browser.
Chem & BioOffice 2006 /Appendix
Check the CambridgeSoft web site for new product
information. You can also get to ChemStore.Com,
ChemNews.Com, and other pages through
CambridgeSoft.Com.
Using the ChemOffice
SDK
The ChemOffice Software Developers Kit (SDK)
enables you to customize your applications.
To browse the ChemOffice SDK:
From the Online menu, choose Browse
ChemOffice SDK.
The CS ChemOffice SDK page opens in your
browser.
The ChemOffice SDK page contains
documentation, sample code, and other resources
for the Application Programming Interfaces
(APIs).
Accessing the CambridgeSoft Web Site 815
Browsing CambridgeSoft.com
Administrator

816 Accessing the CambridgeSoft Web Site CambridgeSoft

Using the ChemOffice SDK
Index
Symbols Access database, opening 337
% wildcard character 403 Accessing relational data using subforms 361
(, in query 405 Activating the select tool 58
(-CHR-) bending force parameters 262 ActiveX control 460
* wildcard character 403 Actual field editing 132
-, in query 405 Actual field measurements 49
<, in query 405 ACX information, finding 813
= symbol, in query 403 ADD indicator 378
=, in query 405 ADD indicator, description 305
>, in query 405 ADD indicator, when displayed 307
\, in query 413 Add New Record command 378
Adding
Numerics buttons 343
2D programs, using with Chem3D 97 checkboxes 343
2D to 3D conversion 219 data 378
3D enhancement data box menu 348
depth fading 80 fields 374, 439
hardware 83 formal charges 99
red-blue 80 fragments 106
stereo pairs 83 information to the stoichiometry table 536
3D properties 408 items from the autotext pane 544
3D searching 408 menu to a data box 348
3D structure display 347 new collections 514
3DM file format 147 new reactant collections 519
3RINGANG.TBL, see Angle bending table new reactants 518
4-Membered Ring Torsionals 251 parameters to MOPAC 294
4RINGANG.TBL, see Angle bending table pictures 343
plain text 342
A properties to the field 625
A (any), special atom type 469 reaction templates to the reaction worksheet
About the E-Notebook Guide 508 498
Access records 307, 320, 378
attaching tables from 373 reference within the user collection 514
manipulating .mdbfiles 439 references to the folder 517
multi-user 367 scroll bars 349
read-only 367 serial numbers, tutorial example 55
secured 368 spectra 567
using with ChemFinder 439 structures 378, 533

Chem & BioOffice 2006/Index i

 Adding, continued Aligning
tables 365, 384, 439 objects 354
to groups 138 parallel to an axis 123
Adding a Collection Listener to a Collection Type parallel to plane 123
Administrator

753 to center 124

Adding a Contained Collection Type 749 Aligning and distributing objects 354
Adding a Contained Reference Type 751 Allingers force field 290
Adding a Field to a Section Type 656 Alternate Groups
Adding a Field to an ExistingForm 669 searching with 408
Adding a Form Tool to a Section Type 658 Alternative Groups
Adding a link attachment point symbol 409
from a property list to a collection 564 defining 409
from a property list to a section 565 description 408
from a property list to an external URL 565 Anchored substring text queries 403
from a table to a collection 575 AND operator, hit lists 424
from a table to a section 576 AND operator, queries 403, 405, 412
Adding a new Field Type 740 Angle bending force constant field 259
Adding a Property to the Property List 713 Angle bending table 251, 259
Adding a Property to the Table Angle defining atom 125
727 Angle type field 259
Adding a Section Listener to a Section Type 664 Angles and measurements 211
Adding a Section Type to a Collection Type 747 Animations 139
Adding multiple structures to forms 376 Annotation of changes 603
Adding States to a Collection Type 768 Annotations, showing 430
Adding structures to non-chemical databases 377 Anti-aromaticity 469
Advanced text searching 627 Applying a filter 534
Advanced text searching options Aromaticity 469
ABOUT 628 ASCII file, exporting 401
AND (&) 628 Assigning atom types 217
Backslash 628 Assigning fields to data boxes 318
Curly Brackets {} 627 Associating a list of manually entered values with a
EQUIValence (= ) 629 property 715, 729
Fuzzy (?) 629 Associating a Transition Listener with a Transition
MINUS (-) 630 770
NEAR 630 Atom
NOT (~) 631 label colors, see Customizing fonts
OR (|) 632 labels 81, 99
Soundex (!) 632 lists 426, 618
Stem ($) 633 movement, when setting measurements 108
ALC file format 144, 147 not-lists 618
Alchemy 221 pairs, creating 65
Alchemy file format 147, 221 pairs, setting 108
Alchemy, FORTRAN format 222 properties 617

ii CambridgeSoft
Atom, continued
replacing with a substructure 103
size by control 78
size% control 78
spheres, hiding and showing 77
to-Atom Mapping 622
type characteristics 217
type field 260, 263
type number 263
type number field 252, 255
Atom Lists 469
Atom Not-Lists 470
Atom Properties 469
Atom types
A (any) 469
and bond types 426
assigning automatically 47
creating 218
in cartesian coordinate files 223
link node 427
M (metal) 469
overview 426
pop-up information 129
Q (heteroatom) 469
table 254
X (halogen) 469
Atomic Weight field 264
Atoms 465, 615
aligning to plane 123
changing atom types 105
coloring by element 79
coloring by group 79
coloring individually 81
displaying element symbols 81
displaying serial numbers 81
mapping colors onto surfaces 92
moving 118
moving to an axis 123
positioned by three other atoms 125
removing 98
selecting 113
setting formal charges 109
size 78
Chem & BioOffice 2006/Index
Atom-to-Atom mapping 411
Atom-to-Atom mapping, reaction queries 411
Attaching
files from a file-based database 373
tables from other applications 373
Attaching files from a non file-based database 373
Attachment point rules 211
Attachment Points
defining 409
tool 409
Automatic Labels 342
Autosave, saving changes with 602
Autotext
based on other fields in the section 547
inserting custom 546
inserting links with 545
working with 543
AVI file formats 147
B
Background color 81
Background effects 156
Backing-up databases 377
Ball & stick display 76
Basic text searching 626
Batch import commands
807, 808
Bending constants 262
Bin, definition 388
Binding sites, highlighting 116
BioViz
changing fields 385
curve fitting 389
details window 386
empty points 386
filter sliders 391
histogram plots 386
selecting points 385
setting display range 391
statistical analysis 389
BioViz, tutorial 330
Bitmap file format 146
Bitscreen 477
iii
 BMP file format 146 Boxes
Bond changing styles 346
angles 48 creating 340
angles, setting 108 deleting 353
Administrator

dipole field 258 font 349

length 48 hiding or showing 349
length and bond order, tutorial example 53 moving 352
length, pop-up information 129 properties 345
length, setting 108 resizing 352
length, uniform 430 selecting 352
order matrix 295 style 345
order, changing 105 Break Bond command 106
order, pop-up information 129 Bring to Front command 353
proximate addition command 106 Browsing
stretching force constant field 258 at a higher level 529
stretching parameters 257 databases 369
stretching table 252, 257 from home 529
tools, building with 97 limiting collection 528
tools, tutorial example 51 plates 502
type field 258, 261, 267 the entire collection tree 530
types, overview 426 up to the user group 515
Bond properties 472, 620 Browsing search results 453
in queries 472 Browsing with the record tool 369
ring/chain 472 Btrieve 373
Bond types Building
double either 466 controls, see Model building controls
in queries 465 modes 95
special 472 toolbar 40
Bonds 228, 465, 616 with bond tools 97
creating between nearby atoms 106 with other 2D programs 97
creating uncoordinated 98 with substructures 101
moving 118 with substructures, examples 101, 102, 103
removing 98 with the ChemDraw panel 96
selecting 113 with the text building tool 99
BONDS keyword 295 Building models 44, 95
Boolean operations, in queries 403 from Cartesian or Z-Matrix tables 103
Boolean operations, on hit lists 424 order of attachment 100
Bound-to order 256 rings 100
Bound-to type 256 with bond tools 51
Box Creation commands 480 with ChemDraw 59
Box creation commands, CAL 480 with the text building tool 56
Box Manipulation commands 481 Buttons, creating 343
Box Manipulation commands, CAL 481

iv CambridgeSoft
 C Changing, continued
C3DTABLE 254 Z-matrix 125
CAL Changing a Field Type 740
commands 479?? Changing a section 583
execute with button 343 Changing a User's Properties 784
help 435, 479 Changing Box Orientation 676
overview 435 Changing collection security properties 593
Calculating the dipole moment of meta-nitro- Changing colors 393
toluene 184 Changing the Dimensions of a Box Manually 674
Calculation toolbar 42 Changing the display 393
Cambridge Crystal Data Bank files 226 Changing the Relationship between a Contained
CambridgeSoft.com 815 Collection Type and the Parent Collection Type
Canonicalization 308 750
Cart Coords 1, see Cartesian coordinate file format Changing the Relationship between a Contained
Cart Coords 2, see Cartesian coordinate file format Reference Type and the Parent Collection Type
Cartesian coordinate 49, 144, 148 752
displaying 133 Changing the Security Properties of a User Collec
file format 148, 223 tion 784
FORTRAN file format 226 Changing the Weight of a Box 673
pop-up information 129 Charge field 255
positioning 123 Charge property 178
CC1, see Cartesian coordinate file format Charge, adding formal 99
CC2, see Cartesian coordinate file format Charge-Dipole interaction term 291
CCD, see Cambridge Crystal Data Bank file format Charges 178
CCITT Group 3 and 4 147 Charges and Radicals 466
CDX file format 144 Charges and radicals 617
Centering a selection 124 Charges, adding 102
CFS file format 438 Charges, from an electrostatic potential 178
CFW file format 340, 439 Charges, in queries 466
Chain bonds 472 Charges, pop-up information 129
Changes and audit trail 601 Check valences 431
Changes menu 602 Checkboxes 343
Changing Chem3D
atom to another atom type 105 changes to Allingers force field 290
atom to another element 104 synchronizing with ChemDraw 96
bond order 105 viewing models 383
box style 346 Chem3D 9, comparison with (table) 28
database scheme 384 Chem3D, about 27
elements 99 Chem3D, whats new in 10.0? 28
layout of an existing form 354 ChemClub.com 811
layout of an existing subform 364 ChemDraw
orientation 122 editing structures 382
stereochemistry 110 panel 42

Chem & BioOffice 2006/Index v

 ChemDraw, continued
synchronizing with Chem3D 96
transferring models to 154
ChemDraw ActiveX control 460
Administrator
Close Contacts command 255
Closed shell system 297
Closing and reopening pages and experiments 516
CMYK Contiguous 147

ChemDraw format, viewing in 346 COEA, see ChemOffice Extension Architecture

ChemDraw panel 96 Collection
ChemFinder changing security properties 593
automation language, see CAL deleting a 591
basics 303 duplicating within a container 590
GUI 303 E-Notebook
opening options 431 adding from a property list 564
starting 309 adding from a table 575
toolbars 306 exporting 593
ChemFinder.com 813 exporting to MS Word 597
ChemFinder/Office importing 593
customizing 459 limiting browsing 528
GUI 449 moving bewteen containers 589
Look In tab 450 moving within containers 588
overview 449 organizing 588
preferences 460 printing 597
Search Options tab 457 printing multiple 597
Send To menu 455 reactant
settings 459 adding a new 519
ChemFinder/Office, using CombiChem with 503 adding a new reactant to existing 518
Chemical Structure Search Engine 766 renaming 591
Chemicals, purchasing online 814 saving and hiding 528
ChemNews.Com 815 saving changes 601
ChemOffice Extension Architecture 27 security 594
ChemOffice SDK, accessing 815 transition, performing 597
ChemStore.com 814 tree, browsing the entire 530
Chromatek stereo viewers 80 tree, hiding 528
CI, microstates used 295 user
CIS 295 adding a new collection to 514
Cleaning structures 381 adding a reference within 514
Cleaning up a model 112 viewing properties 592
Clear Molecular Surfaces command 88 Collection Listeners 801
Clearing Fields when Configuring a Form 675 Collection Search Engine 766
Clearing forms 378, 416 Collection Security 788
Clicking the changes icon 602 Collection Type Security 793
Clipboard Color
exporting with 154 applying to individual atoms 81
Clipboard, copying to 154
Clipboard, importing with 97

vi CambridgeSoft
Color, continued Commands, continued
background 81 file 484
by depth 80 find 417
by depth for Chromatek stereo viewers 80 find current molecule 418
by element 79 find list 405
by group 79 find text 375
by partial charge 79 first record 369
displays 79 go to record 369
field 254 import file 35
preferences 430 intersect with current list 424
settings 79 last record 369
Color, setting 351 menu 479
Coloring groups 139 next record 369
Coloring the background window 81 previous record 369
Columns program execution 482
adding in 439 read file 344
changing formats 439 read structure 399
structure 500 redo 384
use (Y/N) 500 replace current list 424
Combi experiments 501 restore list 424
creating 500 save list 424
product sheet 501 save structure 401
reactant sheets 501 script-only 487
CombiChem 461 search over list 330
creating a workbook 497 select fragment 36
engine 461, 495 send to back 353
help 496 undo changes 379
using with ChemFinder/Office 503 variable 485
Combined searches, see Searching, combined Comments panel 44
Commands Commit Changes command 381, 382
add new record 378 Commit changes command 379
box creation 480 Committing changes vs. saving 339
box manipulation 481 Committing new data 379
bring to front 353 Communicating with other applications 437
clear molecular surfaces 88 Communicating with other applications using
close contacts 255 DDE 437
commit changes 379, 381, 382 Communicating with other applications using OLE
compute properties 176 automation 438
current record 305, 307 Communicating with other applications using
data source 335, 373 scripts 437
database 484 Commutative principle 477
delete record 384
enter query 416, 417

Chem & BioOffice 2006/Index vii

 Comparing Conventions, documentation 24
cation stabilities in a homologous series of Copy As Bitmap command 154
molecules 182 Copy As ChemDraw Structure command 154
models by overlay 63 Copy as InChI 308
Administrator

the stability of glycine zwitterion in water and Copy as name 308

gas phase 185 Copy command 154
Complete Structure Similarity, see Tanimoto similar- Copy Measurements to Messages control
ity GAMESS 204
Compression 147 COSMO solvation 180
Compute Properties Counterions 382
Gaussian 200 Covalent radius field 254
MOPAC 176 Create Database button 371
Compute Properties command 176 Create table dialog box 372
Computing partial charges 71 Creating
Computing properties 200 and editing tabs 344
Computing properties for a movie 63 and playing movies 139
Computing steric energy, tutorial example 60 atom pairs 65
CON file format 148 atom types 218
Concurrent access 367 bonds by bond proximate addition 106
Configuring boxes 340
plates 501 boxes with frames 341
Configuring a Form 666 button 343
Configuring a New Form 667 CombiChem workbook 497
Configuring a Transition between States 769 data box menu 348
Configuring a Database Table Field 705 data boxes 314, 341
Configuring Annotation Options 778 databases 337, 371
Configuring Autosave 779 Experiments 500
Configuring Change Control Options 776 fields 374
Configuring Relationships to Unspecified Types of folders 517
Collections 752 forms 340
Configuring the Appearance of a Property List 714 forms automatically 338
Configuring the Appearance of a Table 727 forms with the database tree 344
Conformations, examining 59 forms, manually 340
Conformations, searching 63 forms, overview 335
Conjugated pi-system bonds table 252 forms, tutorial 313
Connection table file format 148, 395 frames 341
Connection tables 148 groups 138
Connolly molecular surface 91 MOPAC input files 189
displaying 91 movies 139
overview 91 multiple tables 365, 384
Constraining movement 118 new autotext definitions 546
Constraints, setting 109 notebooks 515
Context menus, saving and closing 34 pages or experiments 516

viii CambridgeSoft
Creating, continued Current Record command 305, 307
pages or experiments from a template 516 Curve fitting, see BioViz
parameters 253 Customizing
picture boxes 343 ChemFinder 429
portal databases 377 dihedral graphs 63
references within a table cell 575 favorites tree 432
references within the collection tree 589 fonts 349
scripts 435 numbers 350
sections 583 text 349
structures from ARC files 190 toolbars 433
subforms 332, 361, 363 user interface 34
substructures 211 Cutoff distances 263
tables 372 Cutting and pasting a section 584
tabs 344 Cylindrical bonds display 76
text 342
uncoordinated bonds 98 D
Creating a Database Table Field 705 DAT file format 150
Creating a database, tutorial 319 Data
Creating a New Collection Type 746 adding 378
Creating a New Section Type 655 committing 379, 384
Creating a plot 387 deleting 384
Creating a Property List 713 displaying 340
Creating a Search Form 766 editing 380
Creating a Search Type 764 entering 378, 384
Creating a Table Field 726 exporting 400
Creating a User 783 items 310
Creating a User Group 784 labels 46
Creating and editing forms 335 sorting 380
Creating and Editing the Export Templates for a Data Box tool 341
Collection Type 780 Data boxes
Creating and saving forms 316 deleting 316
Creating the Export Template for a Section Type editing 315
678 Data boxes, creating 341
Creating the Export Templates for a Collection Data boxes, hiding or showing 349
Type 780 Data Source
CT file format 144, 148 command 335, 373
CUB file format 149 ODBC 373
Cubic and quartic stretch constants 262 selecting 335, 373
Current list Data Source - Find Chemical Structures window
counter 307 449
description 304 Data Table
size 307 sorting 380
Current Mol, as query command 418 subforms 365

Chem & BioOffice 2006/Index ix

 Data table Defining
displaying 369 atom types 218
moving columns 369 groups 115
resizing columns 370 substructures 211, 212
Administrator

resizing rows 370 Delete a structure 574

Data tables 369 Delete Record command 384
Data, importing 395 Deleting
Database boxes 353
commands 484 contents of fields 384
commands, CAL 484 data 384
creating 337 data boxes 316
Database Lookup Configuration 717, 728 fields 376
Database Model, description 310 groups 138
Database tree, using 344 measurement table data 50
Database, connecting to a form 317 objects 353
Databases records 384
adding structures 377 tables 372
cells 310 Deleting a Box from a Form 670
compressing 439 Deleting a collection 591
creating 371 Deleting a Field Type 740
data items 310 Delimited text files 401
flat-file 371 Delocalized bonds field 256
logon 368 Demo database 322
model 310 Demo toolbar 42
moving 377 Depth fading 80
multiple tables 373 Deselecting atoms and bonds 114
non-chemical 373, 377 Deselecting, changes in rectification 114
opening 335, 367 Deselecting, description 114
read-only 307 Details window, see BioViz
resetting 381 Deviation from plane 132
searching 499 dForce field 261
selecting 335 DFORCE keyword 295
size 306, 307 Dialog boxes
vs. forms 311 Preferences 34
Date fields 375 Dielectric constants 263
Date queries, see Searching, for dates Dihedral angles
Dates, display preferences 405 rotating 120
dBASE 373 Dihedral angles, setting 108
DDE, to communicate with other applications 437 Dihedral Driver 62
Debugging scripts 436 Dihedral type field 265
Default minimizer 173 Dimension, definition 388
Define Group command 115 Dipole moment 178
Dipole moment, example 182

x CambridgeSoft
Disabling security 360 Editing
Display control panel 75 atom labels 99
Display Every Iteration control Cartesian coordinates 49
GAMESS 204 data 380
Display preferences 429 data boxes 315
Display types 75 display type 75
Displaying fields 380
atom labels 81 file format atom types 221
coordinates tables 133 form layout 354
dot surfaces 78 forms 352
hydrogen bonding 117 forms, overview 335
hydrogens and lone pairs 48, 118 internal coordinates 48
labels atom by atom 82 labels 342
models 46 measurements 131
molecular surfaces 85 models 95
polar hydrogens 117 movies 140
solid spheres 77 parameters 290
Distance-defining atom 125 redo 353
Distributing objects 354 selections 114
dLength field 261 structures 381
Docking models 65 structures with ChemDraw 382
Documentation web page 812 tabs 344
Domains 423 undo 353
Dot density 79 Z-matrix 125
Dot surfaces 79 Editing a structure or image 574
Dots surface type 87 Editing an Enumerated Values List 730
Double bond tool, tutorial example 54 Editing the Export Template for a Section Type
Double bonds field 256 678
Double either bond type 466 Editing the Header and Footer Information 781
Drag and drop 399 Editing an Enumerated Values List 715
Drawing a structure or reaction 531 EF keyword 173
Drawing and analyzing reactions 532 Eigenvector following 173
Dummy atoms 98 Eigenvectors 295
Duplicating Electron field 260
records 379 Electronegativity adjustments 261
Duplicating a collection within a container collec- Electrostatic
tion 590 and van der Waals cutoff parameters 263
Duplicating a section between collections 585 and van der Waals cutoff terms 291
Duplicating a section within a collection 585 cutoff distance 263
cutoff term 291
E potential 179
Edit menu 35 potential, derived charges 178
potential, overview 179

Chem & BioOffice 2006/Index xi

 Element editor 434 EPS file format 146
Element ranges in queries 405 Eraser tool 98
Element symbols, see Atom labels Escape characters 627
Elements ESR spectra simulation 180
Administrator

color 79, 434 Estimating parameters 253

physical data 434 Even-electron systems 297
selecting 434 Exact phrase matching 627
Elements table 252, 254 Exact searching see also Normal searching, Similar-
EMF file format 146 ity searching 406
Empty points, see BioViz Exact text match queries 403
Enabling Visual Display of Changes from Collec- Examining
tion Creation Onward 777 bond length and bond order, tutorial example
Enabling Visual Display of Changes with a Transi- 53
tion 777 conformations 59
Enantiomers, creating using reflection 111 Excel
Encapsulated postscript file 146 communicating with, using CAL 435
Ending a Session 799 communicating with, using DDE 437
Ending a session 653 data limit 501
Energy components, MOPAC 295 security setting when importing 358
Energy correction table 251, 261 Excited state, RHF 298, 299
Enhanced metafile format 146 Excited state, UHF 298, 299
E-Notebook 505 Expanding the drawing window 531
getting started 508 Exporting
introducing 505 ASCII files 401
refreshing 654 current hit list 424
User's Guide 513 data files 400
ENPART keyword 295 delimited text files 401
Enter label dialog box 343 graphic formats 154
Enter Query command 416, 417 InChI 154
Enter Script command dialog box 435 models using different file formats 144
Entering security settings 359
and submitting a query 416 SMILES 154
data 384 subform fields 402
data into a database 378 tables 439
queries 307, 413, 416 with the clipboard 154
reaction queries 418 Word files 401
structural queries 417 Exporting a collection 593
structures 378 Exporting a collection or section to MS Word 597
Entering a template 461 Exporting sections to MS Word 585
Enumeration 462 Exporting to another application 455
Environment Variables 487 Extended Hckel method 85
Environment Variables, CAL 487 Extended Hckel surfaces, tutorial example 68
EPS field 264

xii CambridgeSoft
Extended Hckel, molecular surface types available File formats, continued
86 .EMF (Enhanced Metafile) 146
External tables 44 .EPS (Encapsulated postscript) 146
External tables, overview 251 .GJC (Gaussian Input) 144
Extraneous fragments, permitting in full structure .INT (Internal coordinates) 144
searches 415 .MCM (MacroModel) 144
.MOL (MDL) 144
F .MOP 144
FAQ, online, accessing 812 .MSM (MSI ChemNote) 144
FAQ, technical support 809 .PDB (Protein Data Bank) 144
Fast overlay, tutorial 63 .RDL (ROSDAL) 144
FCH file format 149 .SM2 (SYBYL) 144
Field Listeners 804 .SMD (Standard Molecular Data, STN Ex-
Field Types 803 press) 144
Fields .SML (SYBYL) 144
adding 439 3DM 147
changing formats 439 ALC (Alchemy) 147
date 375 Alchemy 147
deleting 376 AVI (Movie) 147
deleting contents 384 Bitmap 146
editing 380 Cambridge Crystal Data Bank 226
formula 371 Cartesian coordinates file 223
integer 374 CON (connection table) 148
memo 375 CT (connection table) 148
Mol_ID 371 CUB (Gaussian Cube) 149
molecular weight 371 DAT (MacroModel) 150
picture 374 editing atom types 221
real 374 examples 221
sorting 380 FCH (Gaussian Checkpoint) 149
structure 371 Gaussian Input 149
text 374 GIF (Graphics Interchange Format) 147
Fields, assigning to data boxes 318 GJC (Gaussian Input) 149
File commands 484 GJF (Gaussian Input) 149
File Commands, CAL 484 GPT (MOPAC graph) 153
File formats 242 INT (Internal coordinates) 149, 227
.alc (Alchemy) 144, 221 JDF (Job description file) 153
.BMP (Bitmap) 146 JDT (Job Description Stationery) 153
.CC1 (Cartesian coordinates) 144 MacroModel 229
.cc1 (Cartesian coordinates) 148 MCM (MacroModel) 150
.CC2 (Cartesian coordinates) 144 MOL (MDL MolFile) 150, 231, 468
.cc2 (Cartesian coordinates) 148 MOPAC (MOP,MPC) 150, 237
.CDX 144 MSI MolFile 233
.CT (connection table) 144 MSM (MSI ChemNote) 150

Chem & BioOffice 2006/Index xiii

 File formats, continued Formats for chemistry modeling applications 147
PDB (Protein Data Bank) 153 Formatting graphic files 145
PNG 147 Forms
Postscript 146 adding multiple structures 376
Administrator

Protein Data Bank file 239 clearing 416

QuickTime 147 creating automatically 338
RDL (ROSDAL) 153, 242 creating manually 340
SMD (Standard Molecular Data, STN Express) editing 352
153 layout, changing 354
SML (SYBYL) 153 moving 377
SYBYL MOL2 247 saving 339
SYBYL MOLFile 245 setting security 356
TIFF 146 style 338
ZMT (MOPAC) 150 vs. databases 311
File formats, supported 395 Forms, creating and saving 316
File menu 35 Formula field 371
File-based databases, attaching tables 373 Formula input rules 475
Files Formula queries, see Searching, for formulas
dsd 454, 455 Formula searching, see Searching, for formulas
log 398 Formula, searching by 453
sdf 454 Formulas
selecting with Look In tab 450 input rules 475
selecting with Open File menu 450 sorting 380
Filtering 390 FORTRAN Formats 222, 226, 229, 230, 233, 237,
Filtering acronyms with the reaction toolbar 534 238, 240, 247
Find and replace 308 FoxPro 373
Find command 417 Fragments
Find Current Molecule command 418 creating 106
Find List command 405 in full structure searches 415
Find Text command 375 rotating 120
First Record command 369 searching 407
Fit to box 430 selecting 115
Fixed labels 341, 348 Fragments, rotating 64
Flat-file databases 371 Fragments, separating 63
Fonts, customizing 349 Frame tool 341
Force constant field 267 Framed box tool 341
Form Framed boxes 341
permissions, change from earlier versions of Framed boxes, creating 342
ChemFinder 358 Framed boxes, description 305
tool 340 Frames 341
toolbar 305, 340 Frames, creating 341
Form Tools 802 Framing pictures 430
Formal charge, definition 71 Free sites, in queries 471

xiv CambridgeSoft
Freehand rotation 120 editing 88
Fujitsu, Ltd. 293 setting spacing 338
Full structure searching 408, see also Substructure settings dialog 88
searching, Similarity searching spacing 430
tool 340
G Ground state 297
G Groups, see Alternative Groups Ground state, RHF 298
GAMESS Ground state, UHF 298
minimize energy command 203 Groups
overview 203 colors 79
specifying methods 204 defining 115
Gaussian labeling, in proteins 82
about 27 mapping colors onto surfaces 92
checkpoint file format 149 table 115
compute properties command 200 Guessing parameters 253
cube file format 149 GUI, see User interface
file formats 149
molecular surface types available 86 H
properties tab 200 Hardware stereo graphic enhancement 83
tutorial example 69 Having a Section Appear by Default 748
Unix, visualizing surfaces 93 Headers, delimited text files 401
General Heat of formation, definition 177
CAL commands 483 Heat of formation, DHF 177
commands Help, CAL 435
Commands Help, Windows 25
general 483 Hiding
properties 465 annotations 430
tab, GAMESS 205 atoms or groups 116
General preferences 431 data boxes 349
General tab 174 hydrogens, tutorial example 54
Generic Groups, see Alternative Groups serial numbers 109
Generics, hitting in queries 415 Hiding a Box 675
Geometry field 256 Hiding Fields and Boxes when Configuring a Form
Getting started in E-Notebook 508 675
GIF file format 147 Hiding Fields in a Form 676
GIF, animated, see Save As command Hiding the Box Name 672
GJC file format 144, 149 Hiding the collection tree 528
GJF file format 149 Hiding the Max Button 671
Go To Record command 369 Highest Occupied Molecular Orbital, overview 93
GPT file format 153 Highest Occupied Molecular Orbital, viewing 68
Gradient norm 177 Highlighting, in substructure searches 327
Grid 340 Hit any charge on carbon 415
density 88 Hit any charge on heteroatom 415

Chem & BioOffice 2006/Index xv

 Hit List results 453 log files 398
Hit lists RDFiles 397
Boolean operations 424 SDFiles 397
current 307 security settings 359
Administrator

intersecting 424 structure data and reaction data files 397

joining 425 structures 395
merging 424 tables 439
replacing 424 text files 399
restoring 424 Importing and exporting data 395402
saving 424 InChI strings, exporting 154
saving as text files 424 InChI, copy as 308
Home page, CambridgeSoft 815 InChI strings, exporting 154
HOMO see Highest Occupied Molecular Orbital Inserting
Hooke's law equation 262 custom Autotext 546
Hotkeys links with Autotext 545
select tool 58 new reactants and products 544
Hckel, see Extended Hckel method reactants and products from the stoichiometry
Hydrogens grid 544
in queries 466 Int Coords, see Internal coordinates file
Hydrogens, added to structures 382 INT, see Internal coordinates file
Hydrophobicity, mapping onto surfaces 92 Integer fields 374
Hydrophobicity, scale 89 Integrated products 23
Hyperfine coupling constants 180 Intermediates, in queries 412
Hyperfine coupling constants, example 186 Internal coordinates 48
Hyperpolarizability 180 changing 125
Hyrogen bonding 117 file 227
file format 144, 149
I FORTRAN file format 229
ID queries 405 pop-up information 129
Identity searching, see Exact searching table 133
Implicit hydrogens 471 Internal coordinates file 227
in queries 471 Internal rotations, see Dihedral angles, rotating
on metals 431 Internal tables 44
Implicit hydrogens, added to structures 382 Internet, CambridgeSoft web site 815
Import file command 35 Intersect With Current List command 424
Importing Inverting a model 110
and exporting collections 593 Inverting cis, trans isomers 58
Cartesian coordinates files 189 Ionization field 260
collections 593 ISIS/Draw 97
data 395 ISIS/Graphic files 395
from a specified location 398 ISIS/Sketch files 395
hit lists 424 Isocharge 92
ISIS/Draw structures 97 Isopotential 92

xvi CambridgeSoft
Isospin 92 Keywords, continued
Isotopes 467, 617 TS 173
Isovalues, editing 87 VECTORS 295
Iterations, recording 136 Keywords, automatic 294
Keywords, MOPAC 294
J KS field 258
JDF file format 153
JDF Format 199 L
JDT file format 153 Lab supplies, purchasing online 814
JDT Format 199 Labels 220
Job description file format 153, 199 editing 342
Job description stationery file format 153 fixed 341, 348
Job Type tab fonts 349
GAMESS 204 live 348
Job type tab 204 using 99
using for substructures 58
K using to create models 57
KB field 259 Languages other than English, sorting 381
Keyboard modifiers, table of 213214 Last Record command 369
Keywords Launching ChemFinder 309
BFGS 173 Layout tool 340
BOND 295 Layout, changing 354
DFORCE 295 LDB file format 439
EF 173 Length field 258
ENPART 295 LET keyword 175, 294
LBFGS 173 Limitations 233
LET 175, 294 Limiting collection browsing 528
LOCALIZE 295 Link node 427
NOMM 295 Linking subforms to main forms 361
PI 295 Live labels 348
POLAR 185 LN (link node), special atom type 427, 469
PRECISE 175, 294, 296 LOCALIZE keyword 295
RECALC 175, 295 Localized orbitals 295
RMAX 294 Locating the eclipsed transition state of ethane 175
RMIN 294 Locking plots 388
Log files 398
Logging In 508
Logging in with Internet Explorer 509
Logon, database 368
Lone pairs field 264
Lowest Unoccupied Molecular Orbital, overview
93
Lowest Unoccupied Molecular Orbital, viewing 68

Chem & BioOffice 2006/Index xvii

 LUMO, see Lowest Unoccupied Molecular Orbital
M Managing Stored Document Fields 723
M (metal), special atom type 469
Administrator
MacroModel 229
FORTRAN format 230
MacroModel file format 150
Main form 305
Main toolbar 305
Managing
queries 421
Managing Active Document Field Listeners 700
Managing Active Document Fields 699
Managing AutoText Fields 700
Managing Chemical Query Fields 733
Managing Chemical Structure Field Listeners 703
Managing Chemical Structure Fields 702
Managing Collection Listeners 753
Managing Collection Security 787
Managing Collection Type Form Tools 762
Managing Collection Types 745
Managing Contained Collection Types 749
Managing Contained Reference Types 750
Managing Data Fields 699
Managing Database Table Fields 705
Managing Database Values in Property Lists 716
Managing Database Values in Tables 728
Managing E-Notebook Security 787
Managing Enumerated Values in Tables 729
Managing Enumerated Values in Property Lists 714
Managing Excel Fields 708
Managing Export Templates for Section Types 677
Managing Export Templates of Collection Type
s 779
Managing Fields 697
Managing Fields within a Section Type 656
Managing Form Tools 658
Managing Property List Listeners 719
Managing Property Lists 712
Managing Search Fields 733
Managing Search Types 764
Managing Section Listeners 663
Managing Section Types and Forms 655
xviii
Managing Spectrum Fields 722
Managing States and Transitions 768
Managing Subsection Field Listeners 725
Managing Subsection Fields 723
Managing Summary Fields in a Table of Contents
657
Managing Table Fields 725
Managing Table Listeners 730
Managing Templates 761
Managing the Active Document Form Tool 662
Managing the Add Reactant Table Listener 731
Managing the Add-In Configuration 739
Managing the Analyze Reaction Table Listener 732
Managing the Annotate Transition Listener 772
Managing the Audit Section Listener 666
Managing the Auto Number Collection Listener
755
Managing the Block Reference In State Property
List Listener 721
Managing the Block Reference In State Table Lis-
tener 731
Managing the Button View Subsection Listener 725
Managing the Change Display Collection Listener
756
Managing the Change Display Transition Listener
772
Managing the Chemical Properties Property List
Listener 722
Managing the Final Print Transition Listener 773
Managing the Fixed Name Collection Listener 757
Managing the Fixed Section Name Listener 666
Managing the Insert Reference Form Tool 663
Managing the Locked Container Transition
Listener 774
Managing the New Child Collection Form Tool 763
Managing the New Section Form Tool 661
Managing the New Subsection Section Form Tool
661
Managing the Next Step Form Tool 661
Managing the Owner Full Control Collection
Listener 758
Managing the Parent Prefix Collection Listener 757
CambridgeSoft
Managing the Person Property List Listener 721 Matching stereochemistry 415
Managing the Prevent Delete when Referenced Mathematical operators, in CAL command 486
Collection Listener 759 Maximum Ring Size field 255
Managing the Prevent External Link Active MCM file format 144, 150
Document Field Listener 700 MDB file format 439
Managing the Prevent Reference Copy Collection MDL file format 468
Listener 759 MDL MolFile 231
Managing the Print Multiple Form Tool 663 MDL MolFile format 150
Managing the Products Table Listener 730 MDL MolFile, FORTRAN format 233
Managing the Reactants Table Listener 730 MDL Molfiles 395
Managing the Required Properties Transition MDL RXNFiles 395
Listener 775 Measurement table 131
Managing the Required Section Listener 666 Measurements
Managing the Security Properties of a Collection actual field 49
Type 792 deleting 132
Managing the Security Properties of a Section Type displaying graphically 82
796 editing 131
Managing the Spectrum Form Tool 662 non-bonded distances 130, 132
Managing the Standard Collection Listeners 755 optimal field 50
Managing the Standard Form Tools 660 setting 107
Managing the Standard Search Engines 765 table 49, 59, 131
Managing the Standard Section Listeners 666 Measuring coplanarity 132
Managing the Standard Transition Listeners 772 Memo fields 375
Managing the Unlocked Contents Transition Menu bar 305
Listener 775 Menu commands 479
Managing the User Collection Listener 761 Menu commands, CAL 479
Managing the Validate Value Property List Menu, adding to data box 348
Listener 722 Menus
Managing the Validate Value Table Listener 732 edit 35
Managing the Analyze Reaction Chemical file 35
Structure Listener 703 structure 38
Managing Transition Listeners 770 view 36
Managing Units in Property Lists and Tables 741 Minimize Energy 203
Managing URL Display Fields 732 MOPAC 172
Managing Visual Display of Changes 776 Minimize Energy command
Managing Property Query Fields 736 GAMESS 203, 204
Managing Search Location Fields 738 Minimize Energy dialog
Managing State Query Fields 737 GAMESS 204
Managing Table Query Fields 737 Minimizer 173
Managing Unannotated Version Query Fields 738 Minimum RMS Gradient
Map Property control 92 MOPAC 172
Mapping atoms in reaction queries 411 MM2
Mapping properties onto surfaces 69, 92 applying constraints 50

Chem & BioOffice 2006/Index xix

 MM2, continued mulas
atom types table 252, 263 Molecular formula searches, see Searching, for for-
constants table 252, 262 mulas
editing parameters 289 Molecular orbitals 93
Administrator

overview 157 Molecular orbitals, calculation types required 86

parameters 289 Molecular orbitals, definition 93
references 289 Molecular shape 92
tutorial example 60 Molecular surface displays 84
MM2 force field in Chem3D 290 Molecular surfaces 179
Model, see also Internal coordinates, Cartesian coor- calculation types 85
dinates, Z-Matrix clearing all 88
data 129 definition 179
display 46 dots surface type 87
display control panel 79 grid 88
display toolbar 36, 41 overview 84
settings control panels 75 smoothness 88
settings, changing 75 solid surface type 87
settings, dialog box 45 translucent surface type 87
types 75 types available from extended Hckel 86
Model area 34 types available from Gaussian 86
Model building basics 44 types available from MOPAC 86
Model building controls, setting 95 viewing 68
Model Explorer 48 wire mesh surface type 87
Model Explorer, stacking windows 59 Molecular Weight field 371
Model information panel, see Model Explorer, Mea- Molecular weight, searching by 453
surements table, Cartesian Coordinates table, Z- Monochrome 146
Matrix table MOP file format 144, 150
Model window 33 MOPAC 237
Models AAA file 188
building 95 about 27
docking 65 background 293
editing 95 compute properties command 176
viewing with Chem3D 383 create input file command 189
Modifying data 380 file formats 150
MOL file format 144, 150 FORTRAN format 238
Mol_ID field 371 general tab 174
Molecular Design Limited MolFile (MOL) 150 graph file format 153
Molecular electrostatic potential 92 history 293
Molecular electrostatic potential surface Hyperfine Coupling Constants 173
calculation types required 86 minimizing energy 172
definition 92 minimum RMS gradient 172
dialog 92 molecular surface types available 86
Molecular formula querie,s see Searching, for for- optimize to transition state 174

xx CambridgeSoft
MOPAC, continued MSI ChemNote file format 150
OUT file 188 MSI file format 439
overview 171 MSI MolFile 233
parameters, editing 294 MSI Molfile 395
properties 177 MSM file format 144, 150
references 293 MST file format 439
repeating jobs 190 Mulliken charges 178
RHF 173 Multiple models 106
running input files 189 Multiple structures, adding to forms 376
specifying electronic state 296 Multi-step reactions 410
specifying keywords 174, 294 Multi-user access 367
troubleshooting 188
UHF 173 N
Move Name field 254
to X-Y plane command 123 Name searching 325
to X-Z plane command 123 Name=Struct 97
to Y-Z plane command 123 Naming a selection 115
Move a column 572 Navigation overview 509
Move a row 572 New features 505
Movie control panel 140 New form, creating 340
Movie controller, speed control 141 New in ChemFinder 479
Movie file format 147 New Record indicator 305
Movie toolbar 42 Next Record command 369
Movies NOMM keyword 295
computing properties 63 Non file-based databases, attaching 373
editing 140 Non-bonded distances, displaying 130
overview 139 Non-bonded distances, displaying in tables 132
Moving Normal Searching 406, see also Exact searching,
atoms 118 Similarity searching
atoms to an axis 63 Normalization 469
boxes 352 Normalization, in queries 469
models see Translate Numbers, customizing 350
objects 352 Numeric format 350
Moving a section within a collection 584 Numeric searches 325, 404
Moving collections between container collections
589 O
Moving collections within a container collection Objects
588 aligning 354
Moving forms and databases 377 deleting 353
MOZYME 172 distributing 354
MPC file format 150 spacing 354
MS Access, see Access ODBC, adding structures to existing sources 377
MS Access, workgroup information 356 ODBC, selecting data sources 373

Chem & BioOffice 2006/Index xxi

 Odd-electron systems 298 Oracle, continued
OLE automation, communicating with other using CAL with 447
applications 438 Oracle Cartridge
OLE automation, overview 438 configuration via CF_SETTINGS table 492
Administrator

Online Help, see Help fast-move caching scheme 491

Online Menu pre-setup procedures 491
browse ChemStore.com 814 Order of attachment, specifying 100
CambridgeSoft homepage 815 Ordering objects 353
ChemOffice SDK 815 Organizing collections 588
CS Chem3D technical support 812 Origin atoms, Z-matrix 125
lookup suppliers on ChemStore.com 813 Other applications
register online 811, 815 attaching tables from 373
Open Database button 335 Other applications, communicating with using
Open last form on startup 432 DDE 437
Open shell 298 Other applications, communicating with using
Opening OLE Automation 438
databases 335, 367 Other applications, communicating with using
existing chemical databases 335 scripts 437
hit lists 424 Other fields in a spectrum section 567
options, see Preferences Out-of-plane bending 267
pictures 344 Output panel 44
secured MS Access databases 337 Overlays 63
specific databases 327 Overlays, hiding fragments 65
Opening a database, tutorial 317 Overriding security 360
Opening ChemFinder, see Launching ChemFinder Overview 510
Operators, in CAL commands 486
Optimal field 50, 132 P
Optimal measurements 131 Packbits, compression 147
Optimizing to a transition state 174 Page Breaks 681
Options 388 Page size 143
OR operator, hit lists 425 Pan, see Translate
OR operator, queries 403 Paradox 373
Oracle Parameter table fields 252
attaching tables 373 Parameter tables, overview 251
handling lists in 443 Parameters
indexing 446 creating 253
loading 445 estimating 253
opening a database 442 MM2 289
overview 441 MOPAC 294
searching in 443 Partial charge
setting preferences 444 atom size control 78
setup 441 definition 71
updating and adding data 444 pop-up information 129, 130

xxii CambridgeSoft
Password, for secured forms 368 Precision, in numerical queries 404
Paste command 154 Pre-defined substructures 58
Paste special 35 Preferences
PDB file format 144, 153 color 430
Performing a collection transition 597 date display 405
Periodic Table 466 display 429
Periodic table 434 general 431
Perspective rendering 80 grid spacing 430
Pi atoms table 260 opening 431
Pi bonds table 251, 261 picture display 430
PI keyword 295 recent file list size 432
Pi orbital SCF computation 291 registration 431
PIATOMS.TBL, see Pi atoms table search details 414
PIBONDS.TBL, see Pi bonds table search type 413
Picture boxes, creating 343 setting 429
Picture fields 374 stereochemistry 415
Picture tool 343 structure display 429
Pictures 343 Preferences in ChemFinder/Office 460
framing 430 Previous Record command 369
of structures 383 Previous Users, help for 31
preferences 430 Print command 144
reading 344 Printing 144
saving 344 background color 81
saving ChemDraw drawings as 383 collections 597
searching 383 multiple collections at once 597
updating 344 sections 585
Plain text tool 342 Processing the reaction template 498
Planarity 132 Product sheets 501
Plates, browsing 502 Products
Plates, configuring 501 in queries 412
Plotting searches 392 searching for 410
PNG file format 147 Products Only option 501
POLAR keyword 185 Program Execution commands 482
Polarizability 179, 180 Program Execution commands, CAL 482
Pop-up information 129 Properties
Portal database 377 dialog box, opening 358
Positioning by bond angles 127 tab, GAMESS 205
Positioning by dihedral angle 127 tab, Gaussian 200
Positioning example 126 Property lists 547
PostScript files, background color 81 Pro-R 126
Potential functions parameters 293 Pro-S 126
PowerPoint, embedding models in 155 Protein Data Bank File
PRECISE keyword 175, 294, 296 FORTRAN format 240

Chem & BioOffice 2006/Index xxiii

 Protein Data Bank file 239 Queries, continued
Protein Data Bank file format 153 multiple fragments 407
Protein Data Bank Files 239 multiple substructures 427
Protein residues, labeling 82 no highlighting 418
Administrator

Proteins, highlighting binding sites 116 normalization 469

Providing required annotation 603 numbers in 404
Providing unprompted, optional annotation 604 overlapping fragments 415
Publishing formats 145 overview 403
precision 404
Q products 412
Q (heteroatom), special atom type 469 progress display 417
QRY indicator 305, 307 radicals 466
Quality field 252 ranges 404, 405
Quartic stretching term 291 reactants 412
Queries reactions 410
anchored substring 403 red highlighting 417
atom lists 426, 469 refining 417
atom not-lists 470 similarity 407
atom properties 465 similarity rules 477
atom properties in 469 special atom types in 469
atom types 426, 465 special bond types 472
bond properties 472 SQL 403, 413
bond types 426, 465 stereochemistry 408, 467
Booleans 403 stopping 417
charges 466 structural similarity 407
context menu 422 structures 406
dates 405 subforms 365
entering 307, 413, 416 submitting 416
exact structure 408 substituents 466, 470
exact text match 403 text 403
finding current structure 418 unsaturation 471
formulas in 404 using current structure 418
free sites 471 wildcards 403
full structure 408 Query operators
hydrogens in 466 - 405
ID 405 ( 405
identity 407 < 405
implicit AND between fields 403, 412 = 403, 405
implicit hydrogens 471 > 405
inequalities 405 \ 413
intermediates 412 Query properties
isotopes 467 conflicting 465
multiple fields 412 overview 465

xxiv CambridgeSoft
Questel F1D files 395
Questel F1Q files 395
Quick Reference Card, description 25
QuickTime file format 147
R Read File command 344
R Groups, see Alternative Groups
R* field 264
R, special atom type 469
Radicals, in queries 466
Ranges, in queries 404
RDFiles 359, 397, 400
RDL file format 144, 153
Reactant lists 499
Reactant sheets 501
Reactants, in queries 412
Reactants, searching for 410
Reaction
center 620, 621
drawing 531
drawing and analyzing 532
searching 621
Reaction Centers 472
bond type 477
bond types 472
Reaction centers 410
bond types 475
display preferences 429
overview 410
Reaction queries 410
atom-atom mapping 411
creating 418
hitting reaction centers 411, 415
intermediates 412
products 412
reactants 412
Reaction queries, tutorial 327
Reaction searches 410
Reaction template
adding to a worksheet 498
basics 495
processing 498
Reaction template basics 461
Chem & BioOffice 2006/Index
Reaction worksheet, adding a template 498
Reactions
multiple-step 410
Reactions, MS Word, MS Excel, and other sections
527
READ indicator 305, 307
Read Structure command 399
Reading a Structure 398
Read-only access 367
Real fields 374
Rearranging Boxes in a Form 670
RECALC keyword 175, 295
Recent file list size, setting 432
Reconfiguring an Existing Form 669
Record number dialog box 369
Record order 258, 260, 261, 267, 268
Record tool 369
Record toolbar
browsing with 369
description 305
illustration 367
Records
adding 307, 378
current 305, 307
deleting 384
duplicating 379
moving between 369
Rectification 48
Rectification type field 255
Rectification, when deselecting 114
Rectifying atoms 112
Red-blue anaglyphs 80
Redo command 353, 384
Redoing changes 384
Reduct field 264
Reference description field 257
Reference field 253
Reference number field 257
References table 252, 257
References, MM2 289
References, MOPAC 293
Refining a model 111
xxv
 Refining queries 417 Replacing
Refining your search atoms 56
overview 457 atoms with substructures 103
Refining your search, search options 457 Replacing a spectrum 567
Administrator

Refining your search, search tools 457 Repulsion field 260

Reflecting a model through a plane 111 Reserializing a model 109
Refreshing E-Notebook 654 Resetting defaults 139
Registration preferences 431 Resetting the database 381
Registration, online 811 Resizing
Relational data and subforms 361 boxes 352
Relational databases 361, 373 models 124
Relative Tetrahedral Stereochemistry 468 objects 352
Relative tetrahedral stereochemistry 416 Resizing Boxes in a Form 673
Removing Resizing models 213
bonds and atoms 98 Resolve density matrix 295
filters 535 Resonance, forms 469
measurements from a table 132 Restore List command 424
properties from the field 625 Restoring a hit list 424
reactants and products from the stoichiometry Restoring changes 353
table 537 Reversing and restoring changes 353
sections 584 RGB indexed color 146
Removing a Collection Listener from a Collection R-group tables 370
Type 754 RHF spin density 181
Removing a Contained Collection Type from a RHF spin density, example 188
Collection Type 750 Ribbons display 77
Removing a Contained Reference Type from a Ring bonds 472
Collection Type 752 Ring closure 100
Removing a Form Tool from a Section Type 660 RMAX keyword 294
Removing a Section Listener from a Section Type RMIN keyword 294
665 ROSDAL 242
Removing a Section Type from a Collection Type ROSDAL file format 153
748 Rotating
Removing a Transition Listener from a Transition around a bond 122
771 around a specific axis 122
Renaming dihedral angles 120, 122
tabs 344 fragments 120
Renaming a collection 591 models 119
Renaming a section 584 two dihedrals 62
Rendering types 75 using trackball 120
Reorienting a model 63 with mouse buttons 213
Repeating a GAMESS Job 206 X/Y-axis rotation 120
Repeating MOPAC Jobs 190 Z-axis rotation 120
Replace Current List command 424 Rotating fragments 64

xxvi CambridgeSoft
Rotation bars 34 Scripts, continued
Rotation dial 61 executing 436
Rules 475 in subforms 365
Run GAMESS Input File command 206 writing 435
Running Scroll bars, adding 349
GAMESS jobs 206 SDFiles
MOPAC input files 189 exporting 400, 402
MOPAC jobs 190 SDFiles, importing 359, 397
SDK Online, accessing 815
S Search
Sample code, SDK web site 815 examples 425
Sample databases 313 toolbar 305, 413
Save All Frames checkbox 151 type 406
Save As command 145 type preferences 413
Save command 379 Search Details preferences 414
Save command, effect on changes 339 Search Engines 803
Save dialog box 339 Search options 457, 625
Save List command 424 Search Over List command 330
Save Structure command 401 Search results 453
Saving Searching 609, see also Queries
and restoring lists 423 a database, tutorial 321
changes through backup and restore 602 .dsd files 455
changes to a collection 601 by chemical formula 452
changes, by browsing to another collection 602 by chemical structure 451
changes, through Autosave 602 by molecular weight 452
customized job descriptions 205 by multiple properties 452
data sources 454 by reaction type 329
directory paths to search 454 by selected files 453
files 454 combined
forms 339 databases 499
hit lists 424 directory paths 454
pictures 344 enter query 457
search results 454 for conformations 63
structures 401 for dates
subforms 339 for formulas 323, 404
vs. committing 339 for intermediates 412
Scaling a model 124 for names 325
Scaling structures 430 for numbers, 325404
Script-only commands 487 for products, 328412, 623
Script-only commands, CAL 487 for reactants 328, 412, 622
Scripts for substructures 326
communicating with other applications 437 for text, with the query text field 626
debugging 436 formula element ranges 405

Chem & BioOffice 2006/Index xxvii

 Searching, continued Security, continued
formula query rules 404 overriding 360
Fullerenes 426 setting options 356
link nodes and multivalent Rs (MVRs) 426 Security overview 509
Administrator

more than one substructure 427 Select Fragment command 115

online for chemical information 812 Select fragment command 36
overview 403 Select tool 113
parentheses in formulas 405 Select tool, hotkey 58
procedures 413 Selecting
refining 457 adding atoms to a selection 114
restore previous query 457 all children 117
save results 454 atoms 113
search options 457 atoms and bonds 113
search tools 457 bonds 113
start 457 boxes 352
subforms 365 by clicking 113
with collection attributes 623 by distance 116
with the property query and table query fields by double click 115
624 by dragging 114
with the search location field 623 by radius 116
with wildcards 627 data to display 336
Section databases 335
changing a 583 defining a group 115
cutting and pasting 584 fragments 115
duplicating between collections 585 moving 118
duplicating within a collection 585 multiple atoms or bonds 114
exporting to MS Word 585 objects on a form 352
moving within a collection 584 selection rectangle 114
names as categories 548 Selection rectangle 114
printing 585 Selection tool 352
reactions, MS Word, MS Excel 527 Send to Back command 353
removing 584 Sending to another application 455
renaming 584 Separating fragments 63
spectrum, other fields in 567 Serial numbers, displaying 81
Section Listeners 802 Serial numbers, tutorial example 55
Section Metadata Tags 679 Set Z-Matrix commands 127
Section Search Engine 766 Setting
Section Type Security 796 alerts 431
Secured access 368 bond angles 108
Securing forms 356 bond lengths 108
Security bond order 105
disabling 360 box properties 345
MS Access workgroup information 356, 357 changing structural display 75

xxviii CambridgeSoft
Setting, continued Showing and hiding collections 528
charges 109 Showing and Hiding the Max Button for a Box 671
color 351 Showing and Hiding the Name of a Box 672
constraints 109 Showing the Max Button 671
data box styles 345 Showing the Name of a Box 673
default atom label display options 81 Similarity rules 477
dihedral angles 108 Similarity searching 407, see also Exact searching,
fixed and live data 348 Normal searching
measurements 107 Single point calculations, MOPAC 176
measurements, atom movement 108 SM2 file format 144
model building controls 95 SM2, see SYBYL MOL2 File
molecular surface colors 88 SMD 242
molecular surface isovalues 87 SMD file format 144, 153
molecular surface types 86 SMD files 242, 395
non-bonded distances 108 SMILES notation, exporting 154
numeric format 350 SML file format 144, 153
origin atoms 127 Solid spheres, size by control 78
preferences 429 Solid spheres, size% 78
recent file list size 432 Solid surface type 87
search details preferences 414 Solution effects 180
search type preferences 413 Solvent accessible surface
security options 356 calculation types required 86
serial numbers 109 definition 91
solid sphere size 78 dialog 91
solvent radius 88 map property 92
stereochemistry search preferences 415 mapping atom colors 92
surface mapping 89 mapping group colors 92
surface resolution 88 mapping hydrophobicity 92
Setting the Fields in Boxes 668 solvent radius 89
Sextic bending constant 263 Sort data by a property 572
Shift+selecting 114 Sorting 390
Show Internal Coordinates command 125 data 380
Show Surface button 86 data tables 380
Show Used Parameters command 253 fields 380
Showing formulas 380
all atoms 117 from the data table 380
annotations 430 in reverse order 380
atoms or groups 116 languages other than English 381
data boxes 349 permanently 439
Hs and Lps 117 structures 380
opening dialog 432 text 380
reaction centers 429 Space filling display 77
serial numbers 109 Special atom types 617

Chem & BioOffice 2006/Index xxix

 Special atom types, list of 469 Stereochemistry, continued
Special bond types 472, 620 stereochemical relationships 219
Special structure searches 419 tetrahedral 467
Specification of Units 743 trigonal bipyrimidal 467
Administrator

Specifying Steric energy

electronic configuration 296 tutorial example 60
general settings 205 Sticks display 76
print options 143 STN Express 153
properties to compute 205 Stopping
Specifying an annotation through the history pane queries 417
605 Stretch-bend parameters 263
Spectra, replacing 567 Struct=Name 308
Spectrum viewer 193 Structural query features 465
Speed control 141 Structure
Spin about selected axis 140 columns 376
Spin density 181 deleting a 574
Spin density, tutorial example 69 display preferences 429
Spinning models 140 displays, changing 75
SQL 413 displays, overview 75
SQL searches 413 drawing 531
Standard Field Types 679 editing 574
Standard measurement 251 registration options 431
Standard measurements, applying 48 searches 406
Standard measurements, bond angle 258 Structure field 371
Standard measurements, bond length 257 Structure menu 38
Standard Molecular Data file format 153 Structures
Start menu login 508 adding 378
Starting ChemFinder 309 adding to non-chemical database 377
Statistical analysis, see BioViz as pictures 383
Status bar 305, 307 checking chemistry 382
Stereo pairs 83 chemically-significant text 382
Stereochemistr cleaning 381
, inversion 110 editing 381, 382
Stereochemistry 408, 467 entering 382, 431
allenic 467 file formats 395
changing 110 importing 395
cis/trans double bonds 467 queries 406
octahedral 467 query properties 465
overview 408 red highlighting in queries 417
queries 467 scaling 430
relative tetrahedral 416, 468 sorting 380
search preferences 415 viewing related 502
square planar 467 Style, box, changing 346

xxx CambridgeSoft
Style, definition 388 T
Styled text 383 Tabbed windows 308
Subform fields, exporting 402 Table
Subforms editor 100
changes in ChemFinder 9 362 numerical units, working with 575
creating 363 Tables 547
data table 365 adding 365, 384, 439
linking fields 361 changing names 439
overview 361 creating 372
searching 365 deleting 372
switching between forms and data tables 365 exporting 439
tutorial 332 headers 306
using scripts 365 importing 439
Subforms, tutorial 332 internal and external 44
Submitting queries 416 Tabs, creating and editing 344
Substituents 466, 616 Tabs, renaming 344
exactly 470, 618 Tanimoto similarity 477
free sites 471, 619 Technical support 809
in queries 466, 470 Templates, entering 461
up to 470, 618 Temporary database 377
Substructure searching 326, 407 Terminology 506
Substructure similarity 478 Tetrahedral stereo center hits 416
Substructures 211 Text
Substructures table 58, 257 as structures 382
Substructures, adding to model 103 building tool 99
Summary file, see MOPAC out file building tool, tutorial example 56
Summary of the Standard Add-Ins 801 creating 342
Suppliers, finding online 813 customizing 349
Supported file formats 395 fields 374
Surface types 85 format toolbar 349, 383
Surfaces toolbar 41 number (atom type) 255
Surfaces, mapping properties onto 69 queries 403
SYBYL file format 153 searches 323, 403
SYBYL MOL File 245 sorting 380
SYBYL MOL2 File 247 styled 383
FORTRAN format 250 tool, specifying order of attachment 100
SYBYL MOLFile 245 Text files, importing 399
FORTRAN format 247 Theory tab 204
SYBYL2, see SYBYL MOL2 File TIF file format 146
Symbol 254 Time Settings 740
Synchronization 392 Title bar 306
Synchronizing ChemDraw and Chem3D 96 Toolbars
building 40

Chem & BioOffice 2006/Index xxxi

 calculation 42 tutorial example 51
customizing 433 Z-axis rotation 120
description 305 Transferring information
form 306 to ChemDraw 154
Administrator

main 306 to other computers 377

model display 36, 41 Transferring information to other applications, see
movie 42 Exporting
record 307 Transition Listeners 802
search 307 Transition Security 791
standard 40 Transition security 595
surfaces 41 Translate 119, 213
text 307, 383 Translate tool 119
Toolbars, Demo 42 Translucent surface type 87
Tools Trigger scripts 437
Alternative Group 409 Triple bonds field 256
attachment point 409 Troubleshooting
data box 341 atoms shift on MOPAC input 189
eraser 98 background color 81
frame 341 Chem3D 809
framed box 341 MOPAC quits 188
grid 340 online 812
layout 340 Type 2 (-CHR-) bending force parameters for C-C-
picture 343 C angles 262
plain text 342
record 369 U
select 113 UHF spin density 181
select, hotkey 58 UHF spin density, example 187
Tools palette, see Building toolbar Uncoordinated bonds, creating 98
Topology 472, 620 Understanding forms and databases 311
Torsional parameters table 265 Undo 353
Torsional parameters table, 4-membered ring 265 Undoing changes 384
Torsionals table 252 Undoing data entry 379
Total charge density 92 Uniform bond length 430
Total charge density surface, calculation types Union with current list 425
required 86 Unix, Gaussian files 93
Total charge density surface, definition 92 Unsaturation 471, 619
Total spin Unsaturation, in queries 471
calculation types required 86 Use Current Z-Matrix button 149
definition 92 Use tight convergence criteria 204
density 92 User Administration 783
density surface dialog 92 User collection
Trackball tool adding a new collection to 514
overview 120 adding a reference within 514

xxxii CambridgeSoft
User collection, continued Using the zoom control 124
working with 514 UV energies 295
User guide, online 812
User interface 33 V
Username, for secured forms 368 V1 field 265
Using V2 field 265
atom lists 426 V3 field 266
bond tools, tutorial example 51 Valence
ChemDraw to create models 59 charged atoms 466
ChemFinder with databases 309 checking 431
current molecule as a query 418 non-standard state 431
display mode 139 unfilled 466
double bond tool, tutorial example 54 van der Waals
form tools 340 cutoff distance 263
grids 340 cutoff term 291
hardware stereo graphic enhancement 83 radius field 255
keyboard shortcuts 430 surface, definition 91
labels 99 Van der Waals radii
labels for substructures 58 atom size control 78
labels to create models 57 dot surfaces display 78
log files 398 Variable Commands 485
measurements table, tutorial example 59 Variable Commands, CAL 485
MM2, tutorial example 60 VDW interactions 268
MOPAC keywords 294 VDW interactions table 252
MS Access with ChemFinder 439 VECTORS keyword 295
Name=Struct 97 Vibrational energies 295
periodic table 434 View focus 107
rotation dial 61, 120 View format for structures, selecting 346
scripts 437 View menu 36
scripts in subforms 365 Viewing
selection rectangle 114 collection properties 592
stereo pairs 83 Highest Occupied Molecular Orbitals 68
substructures 100 Lowest Unoccupied Molecular Orbitals 68
table editor to enter text 100 models with Chem3D 383
text building tool 99 molecular surfaces 68
text building tool, tutorial example 56 parameters 289
trackball tool, tutorial example 51 related structures 502
Visual Basic 438 results 417
Using quick add to add a structure 533 structures 346
Using the add dialog to add a structure 533 structures in Chem3D format 347
Using the Batch Import Facility 807 user information 654
Using the Session Manager 798 Viewing and Editing the Properties of a Collection
Using the session manager 653 Listener 754

Chem & BioOffice 2006/Index xxxiii

 Viewing and Editing the Properties of a Form Working with, continued
Tool 659 the inbox 517
Viewing and Editing the Properties of a Search the reaction toolbar 532
Engine 767 the stoichiometry table 535
Administrator

Viewing and Editing the Properties of a Section the user collection 514
Listener 664 the user configuration folder 518
Viewing and Editing the Properties of a Transition Working with reaction templates 461
Listener 771 Working with structures using ChemDraw 382
Viewing subform data in a table 365 Working with subforms 365
Visual Basic 438
Visual display of changes 606 X
Visualizing surfaces from other sources 93 X (halogen), special atom type 469
X- Y- or Z-axis rotations 120
W XH2 field 260
Wang-Ford charges 179 XR2 field 259
Web pages, embedding models in 155 XRH field 259
Web site, CambridgeSoft, accessing 815
Whats New in ChemFinder 10? 301 Z
Wildcard Zero point energy 295
% 403 Z-matrix 48
* 403 changing 125
Wildcard searching 627 overview 133
Windows help 25 pop-up information 129
Windows metafiles 341, 343, 344 ZMT file format 150
Wire frame display 76 Zoom 393
Wire mesh surface type 87 Zoom on drag 389
WMF and EMF 146 Zooming in on a spectrum peak 567
WMF file format 344 Zwitterion, creating a 102
Word files, exporting 401
Word, embedding models in 155
Working with
Autotext 543
experiments 501
folders 517
multiple hit lists 425
numerical units in tables 575
pages and experiments 516
reactant lists 499
reactants collections 518
reaction templates 495
subforms, tutorial 332
the changes icon 601
the history pane 604

xxxiv CambridgeSoft
CambridgeSoft
Solutions

D ESKTOP S OFTWARE
E NTERPRISE S OLUTIONS

C HEMICAL I NFORMATICS
B IOLOGICAL I NFORMATICS

K NOWLEDGE M ANAGEMENT
S CIENTIFIC D ATABASES
 CAMBRIDGESOFT

ChemOffice Desktop to
KNOWLEDGE CHEMICAL
MANAGEMENT INFORMATICS

Desktop

E-Notebook CombiChem Inventory Registration

Enterprise Enterprise Enterprise Enterprise

E-Signatures 21CFR11 GxP

IP Protection Compliance Validation

Enterprise
WebServer

DESKTOP TO ENTERPRISE
Chem & Bio Office Just as Chem & Bio Office supports the daily work of the individual scientist,
ChemOffice Workgroup ChemOffice Enterprise, with Oracle Cartridge, and ChemOffice Workgroup, based
on SQL Server, help organizations from small workgroups to large enterprises
ChemOffice Enterprise
collaborate and share information more effectively.

KNOWLEDGE MANAGEMENT
E-Notebook Enterprise Research organizations thrive when information is easily captured, well organized, and
Reaction Explorer readily available. E-Notebook Enterprise streamlines record keeping with rigorous
security and efficient archiving, and facilitates text and structure searching. Reaction
CombiChem Enterprise
Explorer can display the ancestors and descendants of a particular batch in seconds,
E-Signatures while CombiChem Enterprise provides the power of combinatorial chemistry.
21CFR11 Compliance E-Signatures provides intellectual property protection and 21CFR11 Compliance
implements an organizations regulatory compliance process.

CHEMICAL INFORMATICS
Inventory Enterprise Managing huge data streams is a key challenge. Registration Enterprise organizes
GxP Validation information about new compounds according to an organization's business rules,
while Inventory Enterprise provides complete management of chemical and biological
Registration Enterprise
inventories, including GxP validation. DocManager Enterprise is an important part
DocManager Enterprise of collaborative research data management. Oracle Cartridge adds chemically
Oracle Cartridge intelligent searching to Oracle, integrating with ChemOffice Enterprise applications.
SOLUTIONS

Enterprise Solutions
BIOLOGICAL SCIENTIFIC
INFORMATICS DATABASES

DocManager BioAssay ChemACX The Merck

Enterprise & BioViz Database Index

BioSAR Sigma-Aldrich Scientific

Oracle Cartridge Enterprise MSDS Databases
or SQL DB

BIOLOGICAL INFORMATICS
BioAssay Enterprise Finding structural determinants of biological activity requires processing masses of
biological assay data. Scientists use BioAssay Enterprise and BioSAR Enterprise to set
BioViz
up biological models and visualize information, to generate spreadsheets correlating
BioSAR Enterprise structure and activity, and to search by structure. The BioViz application allows you to
BioDraw create graphical representations of data.

DESKTOP SOFTWARE
ChemDraw & Chem3D Success begins at the desktop, where scientists use ChemDraw, ChemOffice, and
ChemFinder & ChemInfo BioOffice to pursue ideas and communicate with the natural language of chemical
structures, biological pathways, and models. Scientists organize information and
BioAssay & BioViz
manage data with E-Notebook and Inventory. Chem3D provides modeling, ChemFinder
BioDraw aids searching, while BioOffice adds BioAssay, BioViz and BioDraw. Integrated with
Inventory & E-Notebook Microsoft Office to speed research tasks.

SCIENTIFIC DATABASES
The Merck Index Good research depends on reference information, starting with the structure-
Scientific Databases searchable ChemACX Database of commercially available chemicals and Sigma-
Aldrich MSDS. The Merck Index and other scientific databases provide necessary
ChemACX Database
background about chemicals, their properties, and reactions.
Sigma-Aldrich MSDS
PROFESSIONAL SERVICES
Development CambridgeSoft's scientific staff has the industry experience, and chemical and
Training & Support biological knowledge to maximize the effectiveness of your information systems.
 Av Ch C E- Th
em Che hem Ch Bi Bi Bi In N e Ch
ai e Ch o o o v ot M em
la O m D m e O D A Bi en eb e
m
bl
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ffi
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*ChemDraw Ultra Win/Mac
*ChemDraw Pro Win/Mac
*ChemDraw Std Win/Mac
*ChemDraw ActiveX/Plugin Pro Win/Mac
*Chem3D Ultra Win
*Chem3D ActiveX Pro Win
Software

*Chem3D & E-Notebook Pro Win

Chem3D & E-Notebook Std Win
ChemFinder Pro Win
ChemFinder Std Win
*BioDraw Pro (Pathworks) Win
*BioAssay Pro Win
*Inventory Pro Win
*E-Notebook Ultra Win

BioViz/Chem & Bio Finder Win

CombiChem/Excel Win
ChemFinder/Oracle Win
ChemFinder/Office Win
ChemDraw/Excel Win
Struct<=>Name Win/Mac
Applications & Features

ChemNMR & ClogP Win/Mac

Stoichiometry Grid Win/Mac
TLC PLate Tool Win/Mac
Mass Fragmentation Tool Win/Mac
Structure Clean Up Win/Mac
Polymer Draw Win/Mac
LabArt & BioArt Win/Mac
Tinker/Chem3D Win
MOPAC Client Win
GAMESS Client Win
Gaussian Client Win
Jaguar Client Win

The Merck Index Win/Mac

Databases

*ChemACX Ultra (1 Year) Win

*ChemINDEX Ultra Win
ChemRXN, NCI & AIDS Win
*Available Separately
 Chem & Bio Office
Software Standard for Scientists
the ultimate ChemOffice is a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder
software suite and ChemACX for chemists, BioOffice, BioAssay, BioViz, and BioDraw for biologists, and
for scientists Inventory, E-Notebook and The Merck Index for scientists. ChemOffice and BioOffice are available
for Microsoft Windows.
the standard ChemDraw includes Struct <=> Name, ChemDraw/Excel and ChemNMR. Create stereo-
achieves the chemically correct structures from chemical names, and get accurate IUPAC names for structures.
ultimate Estimate NMR spectra from a ChemDraw structure with direct atom to spectral correlation.
The ChemDraw ActiveX/ Plugin adds chemical intelligence to your browser for querying databases
and displaying information.
computational Chem3D provides visualization and display of molecular surfaces, orbitals, electrostatic potentials,
chemistry charge densities and spin densities. Chem3D utilizes MOPAC, Gaussian, GAMESS and extended
made easy Hckel to compute molecular properties. ChemProp computes Connolly surface areas, molecular
volumes and properties, including Tinker, ClogP, molar refractivity, critical temperature & pressure.
desktop to ChemFinder is a chemically intelligent database manager and search engine. ChemDraw/Excel
enterprise creates searchable spreadsheets. ChemFinder/Word searches documents, spreadsheets, and files for
searching chemical structures and references. ChemFinder includes CombiChem/Excel for combinatorial library
generation in chemical spreadsheets. ChemFinder/Oracle provides enterprise solution integration.
ultimate suite BioOffice is the ultimate suite for management, analysis and visualization of biological data
for biologists using BioAssay and BioViz. Use BioDraw for drawing pathways. Includes Chem3D, Inventory
and E-Notebook.
draw BioDraw, formerly called Pathworks, makes drawing and annotating your biological path-
pathways ways straight-forward and quick, adding a level of uniformity and detail which is unmatched.
screening BioAssay manages both high and low throughput biological screening data. Designed for
data complex lead optimization experiments, the software supports the quick set-up of biological models.
visualize BioViz offers automated calculations, curve fitting, and customized structure activity reports,
data including a user friendly interface for importing, viewing, validating & plotting biological assay data.
handle Inventory manages your reagent and biological tracking needs. Using MSDE as the desktop
reagent database, you organize, store and search over your inventory. Inventory integrates with the
tracking ChemACX database of available chemicals and ChemMSDX safety data providing chemical
sourcing and purchasing.
efficient E-Notebook is the efficient, accurate way to write lab notebooks. It stores MS Office docu-
notebook ments, ChemDraw structures and reaction drawings, and related data in a notebook searchable
keeping by text or chemical structure. Organize pages by project, experiment, or in your own style. Use
CombiChem/Excel to build libraries.
access info Databases include The Merck Index and ChemINDEX, including the NCI and AIDS databases.
with ease The ChemACX Database contains nearly 400 catalogs from leading suppliers and ChemMSDX
Database contains over 20,000 material safety data sheets for commonly used laboratory chemicals.
 ENTERPRISE &

Chem & Bio Office Workgroup

Integrated Research, Discovery, Development,
Research & Discovery - Search for Products
Since the companys founding, CambridgeSofts
desktop software, starting with its industry-leading
ChemDraw, has been the cornerstone application for
scientists who draw and annotate molecules, reactions,
and pathways. The suite of applications has devel-
oped and CambridgeSoft now provides solutions in
virtually all areas of discovery. Researchers can record
and share their experimental information using
E-Notebook, while protecting intellectual property
with digital signatures and 21CFR11 compliance.
They can design both single experiments or design
combinatorial libraries of compounds. They find
and purchase reagents in ChemACX database, store
and use them from Inventory, record newly made
compounds within a proprietary Registration system,
record the results from biological testing in BioAssay,
analyze the results with BioViz, and generate reports
linking activity and structure with BioSAR.
Virtually every aspect of discoveryfrom synthesis
planning, library enumeration, reagent selection,
primary and secondary screening, in vivo testing,
through to analysis of results and reporting is covered
by this integrated application suite.
Development - Converting Leads into Testing
Building on productivity software, CambridgeSoft
created enterprise applications to meet the needs of an

En En En W W W
ChemOffice ter ter ter or or or
pr pr pr kgr kgr kg
ise ro
Ul ise is ou ou up
tra Pr e Std Ultr p Pr p
Std
Includes
o a o

E-Notebook Enterprise or Workgroup

BioAssay Enterprise or Workgroup
BioSAR Enterprise
BioViz Desktop

Registration Enterprise
Inventory Enterprise or Workgroup
ChemACX Database

ChemINDEX Database
Oracle Cartridge
SQL Server Compatible
ChemFinder Ultra

All specifications subject to change without notice.

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WORKGROUP
and Enterprise Solutions
Trials and Manufacturing Workflow
ever expanding research and development community
that relies on data sharing across scientific disciplines,
research campuses, and even oceans as globalization
has increased demands. Since it is web-based, the
software is deployed readily throughout a research
and development organization. Using Registration, E-
Notebook, BioAssay, and BioViz, in conjunction with
DocManager and DrugDeg, scientific teams are well
armed to solve the daily challenges of development.
These teams include scientists who scale up and
design manufacturing procedures, toxicologists who
determine the metabolic fate of drug candidates, for-
mulation scientists who determine drug dosing and
delivery systems, as well as many others.
Trials & Manufacturing - Last Steps to Success
A suitable drug candidate is one that has the desired
activity to provide disease therapy while still meeting
drug safety requirements, can be manufactured in a
cost effective and reproducible fashion under
21CFR11 and GMP guidelines, and is stable under
normal formulation and storage conditions. With a
drug candidate in hand, the final challenge is to deter-
mine safety and efficacy, beyond the laboratory, in a
patient population.
Manufacturing requires the hand off of data and
batch process records from the pilot plant studies
using Inventory, E-Notebook, and Registration systems
under Good Laboratory and Manufacturing
Processes (GxP).
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The handling of materials, including chain of custody
requirements, material documentation, material
workflow, such as availability states and recertification
dates, are tracked and handling by the system. The
systems meet these requirements and provide the
basis to manage materials and records during clinical
trials. Clinicians can design and record results from
protocols, and all of these web based software systems
provide the access required by clinicians who are
removed from the sponsoring company.
ChemOffice Enterprise is a comprehensive
knowledge management and informatics solution,
covering electronic notebooks, biological screening,
chemical registration and more over your intranet.
Enterprise Ultra includes E-Notebook for record keep-
ing, BioAssay for low and high throughput screening
with integrated plate inventory, BioSAR for SAR
reports, Registration system, Inventory for reagents
and ChemACX database of available chemicals.
Technologies include ChemDraw ActiveX and Oracle
Cartridge.
ChemOffice Workgroup is a comprehensive
knowledge management and informatics solution,
covering electronic notebooks, biological screening
and more over your intranet. Workgroup Ultra
includes E-Notebook for record keeping, BioAssay for
low and high-throughput screening, BioViz for
visualization, Inventory for reagents and ChemACX
database of available chemicals. Technologies include
SQL Server for affordability and ease of administration.
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0120 731 800 WWW www.cambridgesoft.com

E-Notebook, Reaction Explorer,
Electronic Journal and Record Keeping
E-Notebook
E-Notebook provides a smooth web-based interface
designed to replace paper laboratory notebooks, with
a fully configurable, secure system for organizing the
flow of information generated by your organization.
You can enter reactions, Microsoft Word documents,
spectra and other types of data, and search this data
by text, substructure or meta data. You can organize
your electronic pages by projects, experiments or any
other classification that conforms to your workflow.
E-Notebook Enterprise
E-Notebook Enterprise edition integrates notebook
keeping at group and enterprise levels to promote lab
productivity and information sharing. Oracle
Cartridge manages chemical structures in a common
data repository with detailed security and 21CFR11
Compliance. The enterprise edition also works with
procurement and inventory management systems to
save time locating chemicals and entering structures.
E-Notebook Workgroup
E-Notebook Workgroup, intended for use with a
medium number of users, offers much of the func-
tionality delivered in E-Notebook Enterprise while
using SQL Server as the database. Learning to use
and administer the application is quick and straight-
forward. E-Notebook applies various data types to
suit different disciplines with an unlimited number
of workflows.
All specifications subject to change without notice.
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005
KNOWLEDGE
E-Notebook offers custom organization of
notebook pages at personal or enterprise levels
Quick access to important data by searching
on keywords, dates, chemical structures and
more
Reaction Explorer can display the ancestors
and descendants of a batch in seconds
E-Notebook Ultra
E-Notebook Ultra is the efficient, accurate way to
write lab notebooks entries as you work. It stores
Microsoft Office documents, ChemDraw structures
and reaction drawings, and related data in an elec-
tronic notebook you can search by text or chemical
structure. Organize pages by project, experiment or
your own style with the MSDE database.
CombiChem/Excel builds combinatorial libraries.
Reaction Explorer
Reaction Explorer is a powerful application that
assembles a vast amount of information into a lucid
synthesis map. The map provides reaction informa-
tion, as well as quick access to experiments. Reaction
Explorer displays two types of relationships between
compounds: relationships grouped by batch and
those grouped by compound. Both types of displays
are configurable, allowing scientists to create a look
and feel that they are comfortable with.
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MANAGEMENT

E-Signatures & 21CFR11 Compliance

Property Protection and Regulatory Compliance
The batch display tracks the history of a particular E-Notebook also provides the capability to scale reac-
entity through several subsequent reactions and tions by virtually any parameter from reagent
experiments. This might be of interest to a chemical amount to vessel size. Individual reactions may be
auditor or patent attorney needing to track down the scaled as well as total syntheses. Batch procedures cre-
original source of material. ated with E-Notebook can be used to produce auto-
matically batch record worksheets.
The compound display is more general, and shows all
possible pathways to and from a compound. This is
ideal for chemists working to optimize a process, or a
patent attorney trying to link a product to discovery,
or a scientist trying to compile work done by several
other scientists.

Process Chemistry
The objective of process research is
to identify efficient processes for the
synthesis of active pharmaceutical
agents at the scale required for
clinical trials and commercial use. It
is necessary to provide precise Display Ancestors
descriptions of these processes so
that they can be executed by differ-
ent groups in different locations.
E-Notebooks process chemistry mod-
ules are designed to support these
dual workflow and regulatory-
compliance needs of process Authenticate Work
chemists. After the steps in a synthe-
sis have been optimized, either indi-
vidual steps or the entire synthesis
must be scaled.

All specifications subject to change without notice.

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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005
 KNOWLEDGE

E-Notebook, Reaction Explorer,

Electronic Journal and Record Keeping
CombiChem Enterprise
Highly flexible and configurable to match
Combinatorial chemistry, in particular the technique
an organizations workflow
of parallel synthesis, has become an essential element
of the drug discovery process. By using parallel Consulting teams analyze and adapt
synthesis techniques, chemists are able to multiply existing procedures to comply with new
their productivity by a factor of between 5 and 100. regulations
CombiChem Enterprise has been developed to provide
Systems include authentication and digital
the tools required by the combinatorial chemist
signatures and adapt to changing
to manage and document parallel synthesis regulations and demands for intellectual
experiments. property protection
Flexibility is the key when dealing with databases of
chemical compounds. CombiChem Enterprise can use
reagent lists from a variety of different sources: SD associated metadata. Managers, patent attorneys,
files, ChemFinder databases, ChemFinder hit lists, and scientists can retrieve records based on searches
ChemACX Database, or directly from the user via over the metadata.
ChemDraw. Regardless of the source, CombiChem
produces a list of reagents which match a particular E-Signatures also manages the signature workflow for
generic reactant. electronic records and documents in process. Digital
signatures are captured at the time of record
E-Signatures IP Protection
creation, which can later serve to prove the authen-
E-Signatures provides data storage and access func- ticity of the stored electronic records. Reviewers,
tions for electronic records. It is used in conjunction
witnesses, and other individuals can countersign
with E-Notebook as a long-term storage system.
records for various business purposes, including wit-
While E-Notebook is intended to capture and record
ness records necessary to meet the needs of 37 CFR
data as the experiments are carried out, E-Signatures
and similar regulations worldwide.
serves as the repository for finished experiments and
other documents. Electronic records must be 21CFR11 Compliance
available indefinitely, and their authenticity must be
Large and growing enterprises are facing a challenge
verifiable independently of the E-Notebook system. In
to their core missions of developing and producing
addition to the record, E-Signatures long-term
archive includes a digital signature, a timestamp, and new products including food, therapeutic pharma-
ceuticals, medical devices, cosmetics or other health

All specifications subject to change without notice.

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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005
MANAGEMENT

E-Signatures & 21CFR11 Compliance

Property Protection and Regulatory Compliance
enhancing items. The complexity lies in complying
with government regulations designed to protect
public health and safety. The most notable of these
is Title 21 of the Code of Federal Regulations
governing Electronic Records and Signatures
(21CFR11).
Once you have determined how your enterprise will
comply with these new regulations, implementing
those decisions needs to be done quickly, efficiently
and with the understanding that the rules for
compliance are in flux. In order to succeed, you must
be able to respond to change. CambridgeSofts
21CFR11 Compliance consulting has both the tools
and the expertise to provide complete solutions, carry
out integration with existing systems, and help exe-
cute the process as quickly as your organization
demands.

All specifications subject to change without notice.

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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005

Inventory, Registration,
Chem and Bio Inventory and Registration
Chem & Bio Inventory
Inventory is an application designed to manage the
chemical and reagent tracking needs of laboratories
and research centers. The system manages data
associated with both commercially procured and
internally produced chemical substances from
procurement or initial production through depletion
and disposal. To meet the needs of institutions
of all sizes, Inventory comes in an Enterprise edition,
a Workgroup edition and two Desktop editions.
Inventory Enterprise is an Oracle-based, ChemOffice
Enterprise product. Designed for large organizations,
it comprises a number of features not included in the
desktop or workgroup versions. Inventory Enterprise
conveniently manages plate information. In addition
to storing, moving, and deleting plates, the applica-
tion allows users to create daughter plates and
reformat plates. Inventory Enterprise can be tightly
integrated with Registration Enterprise and ChemACX
Database.
Inventory Workgroup is a thick-client SQL Server-
based product. This version is suitable for larger
organizations that do not have the interest or desire to
maintain an Oracle server.
Inventory Ultra is the same MSDE based product,
while also including the ChemACX Database,
CambridgeSofts collection of nearly 400 catalogs
from suppliers of chemical reagents.
All specifications subject to change without notice.
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CHEMICAL
Inventory offers plate handling for high-
throughput experimentation
Inventory is GxP Compliant with validated
audit trails
Registration has flexible business rules for
registration, salt handling, and batch fields
with chemical intelligence that includes
advanced stereochemistry
Inventory Pro is an all-inclusive desktop product. It
includes Microsoft SQL Server Desktop Edition
(MSDE ), the re-distributable database for SQL
Server. No additional licensing is required.
Registration Enterprise
Registration Enterprise includes a robust data model
for pure compounds, batches, salt management,
automatic duplicate checking and unique ID assign-
ments. Compounds may be entered individually or
through the use of a batch loader. The data model
resides entirely in Oracle and uses Oracles security
and transaction framework. Registration is easily
adapted to any workflow.
New compound chemical and non-chemical data is
entered into a temporary storage area through a web
form. When the compound is registered, it is
compared for uniqueness via a configurable, stereo-
selective duplicate check, and assigned a registry
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I N F O R M AT I C S

DocManager & Oracle Cartridge

Document Searching and Enterprise Infrastructure
number. All information about the compound, systems are designed for registration of single mole-
including its test data and other syntheses, is tracked cules, with little thought for the world of formulations
by the registry number. When a compound is regis- and mixtures. CambridgeSoft has developed a system
tered, the structure is checked for novelty. If a dupli- specifically designed for this registration need called
cate already exists in the database, the user can elect Formulations & Mixtures.
to register the information as a new batch of the
existing compound, or assign it a unique registry
number.
Registration Enterprise is the only true n-tiered appli-
cation of its kind that is designed around thin clients
and thin servers. This translates into ultimate flexibil-
ity on both the client and server side. Oracle is
supported on a variety of platforms and operating
systems. Using Oracle keeps your proprietary data
secure through the use of Oracles
role based security and allows all
chemical and non-chemical data to
be stored directly in the Oracle Index Documents
tables.
Formulations & Mixtures
Formulation scientists face different
challenges from those working with
individual molecules, yet many of
the tools they are forced to use
emerge from the drug-discovery Manage your Inventory
world, where single-molecule
research is the norm. Take an essen-
tial task such as compound registra-
tion and you will find that most

All specifications subject to change without notice.

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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005

Inventory, Registration,
Chem and Bio Inventory and Registration
DocManager Enterprise
Web browser based, DocManager Enterprise extends
the capability of standard search engines to include
full free text searching and chemically intelligent
structure searching of electronic documents includ-
ing Text, Microsoft Word, Excel, PowerPoint, and
Adobe PDF.
The DocManager Enterprise interface allows users to
easily submit documents through a series of simple to
navigate web forms. When a new document is
submitted, DocManager builds a free-text index of
the document, and extracts chemical information
into a chemically-aware, substructure searchable
database. Chemical information can originate from
either ChemDraw or ISIS Draw.
DocManager Enterprise includes a batch loading
utility for administration level users to load multiple
documents at one time. The system can be
configured to submit a batch of documents as one
event, or as a reoccurring submission to be executed
daily. The administrator simply specifies a time
for the submission to take place and the location of
the files.
DocManager Enterprise utilizes the searching intelli-
gence of the ChemOffice Enterprise suite. In addition
to standard textual and numerical searching,
DocManager searches the submitted documents for
chemical structure or reaction.
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CHEMICAL
DocManager parses Word, Excel and
PowerPoint documents, including free text
DocManager has a web based interface and
a file drop folder for quick submissions
Oracle Cartridge is compatible with Linux,
Solaris, AIX and Windows and includes
structure searching, property predictions
and nomenclature
Oracle Cartridge
The CambridgeSoft Oracle Cartridge is used by all
ChemOffice Enterprise applications for storing, search-
ing over, and analyzing chemical data. It can also be
used in the development of your custom Oracle
applications. Chemical structure information is
difficult to manipulate without utilizing special
software. Oracle data cartridges define new, recognized
datatypes. CambridgeSofts Oracle Cartridge utilizes
this technology making it possible to manipulate
chemical structure and reaction data from within
Oracle, improving portability and consistency in
applications. Since the Oracle Cartridge is accessed
through Oracle, this allows the programmer to interact
with chemical structure data directly in Oracle. The
CambridgeSoft Oracle Cartridge supports CDX ,
CDXML , MolFile, RXN , and SMILES formats
making it flexible enough to be included with both
new and legacy data, without the need for conversion.
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I N F O R M AT I C S

DocManager & Oracle Cartridge

Document Searching and Enterprise Infrastructure
ChemFinder Enterprise
ChemFinder Enterprise is a multiple-user system
designed for sites with heavy-duty chemical and
biological data needs. ChemFinder Enterprise contains
its own engine for working with local and shared
databases and it is also delivered with the
CambridgeSoft Oracle Cartridge, the powerful
Oracle-hosted structure engine based on ChemFinder
search technology. So, the face of ChemFinder
Enterprise is the same friendly form-oriented interface
as the desktop version, but underneath is a fast direct
connection to Oracle and the robust, scalable Oracle
Cartridge running on the server.

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BioAssay
Biological assay data comes in many forms, from a
scientists observations to output from a plate reader.
Software designed to store and analyze this data must
provide a solution for both the ultra-high volume
laboratories, including laboratory automation,
calculation, and statistics, as well as the very compli-
cated low and medium throughput assays such as
animal models and in vivo experiments. Organizing,
analyzing, and sharing data can be a challenge for
screening biologists, regardless of the amount of
automation or manual data manipulation employed.
BioAssay was designed to tackle the needs of high and
low throughput screening biologists alike by provid-
ing an application flexible enough to model any
assay, regardless of complexity, while robust enough
to provide an easy to use interface for importing,
storing and analyzing the data. The software supports
the quick set-up of biological models, automated cal-
culations and curve fitting, data validation, and the
creation of customized structure activity reports.
BioAssay Enterprise offers a scalable, flexible biological
screening solution utilizing Oracles role based securi-
ty and the Oracle Cartridge. As part of ChemOffice
Enterprise, BioAssay is easily integrated with Inventory
Enterprise for plate tracking and management,
Registration Enterprise for the registration of new
compounds and BioSAR Enterprise for customized
reporting.
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BIOLOGICAL
BioAssay, BioViz,
Assay Screening and Visualization
BioAssay effectively manages data from com-
plex biological assays involved with lead
optimization
BioViz provides a flexible reporting and plot-
ting engine for your scientific data
BioViz integrates with BioSAR for one step in-
depth data analysis from a BioSAR report
BioAssay Workgroup, intended for single site deploy-
ment, uses SQL Server as a database, instead of
Oracle. This solution offers affordability and ease of
maintenance, but still remains a robust solution suit-
able for a smaller groups needs. Organize and share
your biological screening data with minimal admin-
istrative costs.
BioAssay Ultra is designed to deliver much of the func-
tionality of our enterprise level applications, without
a widespread roll out. MSDE database compatible,
BioAssay Ultra, coupled with BioViz, offers a user
friendly interface for importing, viewing, validating,
and plotting your biological assay data from your
desktop.
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I N F O R M AT I C S

BioSAR & BioDraw

Data Mining and Pathway Drawing
BioViz
BioViz, with ChemFinder, transforms the numbers in
your database into graphics on your screen. Retrieve
or search for a set of compounds, choose the data you
want to see, whether it is biological test results in
Oracle tables, physical property values calculated
automatically or prices in a catalog, and BioViz will
generate an interactive window showing a scatterplot,
histogram, or other useful data graphic.
The Plot Window, the key to data visualization in
BioViz, shows two variables plotted against each
other in a scatterplot with each point representing a
structure from the current hit list.
If you modify the list, for example
Draw Biological Pathways
by performing a search, the plot
updates to show the new set of
points. You can drag a rectangle
around a set of points to select
them, or zoom in to see them
more closely.

Plot Assay Data

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BioSAR
BioSAR Enterprise, a strategic must for any discovery
organization interested in serious data mining, is a
data-dictionary driven structure-activity analysis
program. Users may choose among assays registered
in the dictionary or search for assays of interest. The
power of BioSAR lies in the researchers freedom from
dependence on IT support. Once an assay is
registered into the data-dictionary, it is automatically
included in the powerful analysis framework. By
reducing the time between question and answer,
BioSAR gives researchers the ability to explore new
ideas, the bottom line for discovery information sys-
tems. Systems that provide answers after questions
have become irrelevant are of no use. BioSAR avoids
this issue by placing application development in the
researchers control.
BioSAR Enterprise allows the researcher to create cus-
tom reports and views of their data. You decide what
is displayed, and BioSAR takes care of the rest. While
most SAR tools provide only a table-based interface,
BioSAR provides a both a form view and table view.
The form view provides highly detailed information
about one compound, whereas the tabular view
makes viewing comparisons between compounds
more feasible. There is often a tradeoff between
power and simplicity, and most SAR tools opt for the
former at the expense of the latter. BioSAR, however,
merges the sophistication of a powerful data catalog
technique with knowledge gained through years of
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BIOLOGICAL
BioAssay, BioViz,
Assay Screening and Visualization
BioSAR is a catalog driven data mining and
structure- activity analysis program
BioSAR provides both form and table views
within a simple and powerful web interface
BioDraw makes it easy to draw and annotate
biological pathways including common
elements such as membranes, enzymes,
receptors and DNA
working closely with users. The result is a SAR
application that is as intuitive as it is powerful.
Security within BioSAR Enterprise is highly granular.
Different roles exist for administrators, publishers,
and browsers. Administrators may add assays to the
data catalog engine, publishers may create reports
and publish them, and browsers may use data query
and analysis. Most data mining tools provide a
mechanism to store queries, but the interface for
creating queries is too complex. With BioSAR, each
set of assays is a complete report with a query form,
a view form, and a table view, combining the
convenience of a ChemFinder or ISIS application with
the power and flexibility of a data catalog-driven
mining program.
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I N F O R M AT I C S

BioSAR & BioDraw

Data Mining and Pathway Drawing
BioDraw
Reporting on and presenting findings is a task familiar The drawing and data organization offered by
to every biologist. Making this process easier and BioDraw gives any biologist an advantage. Sharing
more effective benefits everyone involved. BioDraw, this advantage assists the community as a whole.
formerly called Pathworks, is doing for biologists BioDraw offers many ways to share your drawings
what ChemDraw has done for chemists for years and accompanying data. Users can export data to
saving time, and resulting in a more professional Microsoft Office applications for inclusion in
presentations and grant proposals or save data as an
representation of the science at hand.
image file for use in journal article submission.
BioDraw makes drawing and annotating biological
pathways quick and easy, adding a level of uniformi-
ty and detail which is unmatched. Typical drawings
of biological pathways include many elements that
are difficult to draw with the standard presentation
and word processing software that is on the market.
Common pathway elements such as membranes,
enzymes, receptors, DNA and reaction arrows are
built into the BioDraw toolbar. BioDraw also allows
users to import images in GIF, PNG or JPEG format.

Keeping data organized is of utmost importance in

any lab. BioDraw reflects that importance by allow-
ing users to store annotations for each element in a
drawing. Annotation data ranges from manually
entered text to attached documents, restriction maps,
microarrays, sequence information, literature refer-
ences, or links. Any data, regardless of format, is
stored side-by-side with the drawing for future
retrieval.

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 DESKTOP

ChemDraw, Chem3D,
Structure Drawing and Molecular Modeling
ChemDraw Ultra adds Struct<=>Name,
ChemDraw/Excel, ChemNMR, CLogP, tPSA and ChemDraws improved Struct<=>Name
ChemFinder/Word to ChemDraw Pro. With rich feature produces names for more types of
polymer notation, atom numbering, BioArt templates, compounds
and modern user interface, ChemDraw is more
Live ChemDraw window embedded in
powerful than ever before. Create tables of structures, Chem3D application allows simultaneous
identify and label stereochemistry, estimate NMR 2D and 3D editing
spectra from a ChemDraw structure with structure-
to-spectrum correlation, obtain structures from Chem3D brings workstation-quality
molecular graphics and rigorous
chemical names, assign names from structures, and
computational methods to your desktop
create multi-page documents and posters.
ChemDraw Pro will boost your productivity
more than ever. Draw publication-quality structures
and reactions. Publish on the web using the
ChemDraw Plugin. Create precise database queries by
specifying atom and bond properties and include ChemDraw/Excel allows the user to create
stereochemistry. Display spectra, structures, and chemically knowledgeable spreadsheets within the
annotations on the same page. Use the Online Menu familiar Microsoft Excel environment. You can build
to query ChemACX.Com by structure and identify and manipulate chemical structures within Excel,
available vendors. compute chemical properties and perform database
Struct<=>Name contains the leading compre- searches.
hensive methods for converting chemical structures
ChemNMR can be used to accurately estimate 13C
into chemical names and names to structures. It can
and 1H (proton) chemical shifts. The molecule and
be used for many types of compounds, including
charged compounds and salts, highly symmetric the spectrum appear in a new window. The chemical
structures and many other types of inorganic and shifts are displayed on the molecule and the spectrum
organometallics. Struct<=>Name is available in two is linked to the structure so that clicking on a peak in
forms: a batch application, and an interactive version the spectrum highlights the related fragment on the
that is also available in ChemDraw Ultra. molecule.

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S O F T WA R E

ChemFinder & ChemInfo

Structure Searching and Scientific Databases
Chem3D Ultra includes a number of molecular It can also be used to predict a number of chemical
modeling capabilities such as molecular overlay, and physical properties. Chem3D contains an
conformational searching and dihedral driver support. interface to the MOPAC package.
It also includes interfaces for optional use of
Gaussian is a collection of semi-empirical and
MOPAC , Gaussian and GAMESS . The user can also
ab initio molecular orbital (MO) computational
compute advanced physical properties such as CLogP
methods which can be used to predict energies,
and ChemProp. These properties can be used to
molecular structures, molecular properties, as well
create SAR tables. ChemSAR/Excel can then be used
as molecular spectra. Chem3D enables the user to
to explore structure activity relationships. High
transparently create input and analyze output resulting
quality Chem3D graphics can be viewed on the web
from Gaussian.
using the Chem3D ActiveX.
Chem3D Pro brings workstation quality molecular
visualization and display to your desktop. Convert
ChemDraw and ISIS/Draw sketches into 3D models.
View molecular surfaces, orbitals, electrostatic
potentials, charge densities and
spin densities. Use built-in extended
Hckel to compute partial atomic
charges. Use MM2 to perform
rapid energy minimizations and
molecular dynamics simulations.
Molecular Modeling
ChemProp estimates physical prop-
erties such as logP, boiling point,
melting point and more. Visualize
Connolly surface areas and molec-
ular volumes.
MOPAC is a semi-empirical Estimate Spectra
quantum mechanics package which
can be applied to the study of
chemical properties and reactions.

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ChemDraw, Chem3D,
Structure Drawing and Molecular Modeling
ChemFinder Enterprise is a multiple-user
system designed for chemical and biological data
management. ChemFinder Enterprise contains its own
engine for working with local and shared databases
and it is also delivered with the CambridgeSoft
Oracle Cartridge, the powerful Oracle-hosted
structure engine based on ChemFinder search
technology. So, the face of ChemFinder Enterprise is
the same friendly form-oriented interface as the desk-
top version, but underneath is a fast direct connec-
tion to Oracle and the robust, scalable Oracle
Cartridge running on the server.
BioViz, included in ChemFinder Enterprise, provides
a new set of data visualization features. These features
allow you to plot structural and biological data in a
variety of styles, filter plots based on your criteria,
highlight lists and intersecting sets on plots, generate
histograms of data distributions, and more.
ChemFinder Pro is a fast, chemically intelligent,
relational database search engine for desktop, work-
group or enterprise applications. Extended integra-
tion with Microsoft Excel and Word adds chemical
searching and database capability to spreadsheets and
documents.
Today, an ever-increasing number of chemical data-
bases are available in ChemFinder format. Compatibility
with MDL ISIS databases is provided by SDfile and
RDfile import/export. ChemFinder provides network
server workgroup functionality when used with
ChemOffice Workgroup and Enterprise.
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DESKTOP
ChemFinder offers improved searching and
hitlist management, along with new property
generation
ChemFinder is tightly integrated with
CambridgeSofts Oracle Cartridge
Search ChemACX and other CambridgeSoft
databases for important chemical information
The Merck Index is an encyclopedia of chemi-
cals, drugs and biologicals, with over 10,000 mono-
graphs covering names, synonyms, physical proper-
ties, preparations, patents, literature references, ther-
apeutic uses and more.
ChemACX Database includes 500,000 chemi-
cal products from nearly 400 supplier catalogs,
searchable with a single query by structure, substruc-
ture, name, synonym, partial name, and other text
and numeric criteria. ChemSCX is a compilation of
searchable catalogs from leading screening compound
suppliers.
ChemMSDX Database provides material safe-
ty data sheets for 7,000 pure compounds.
ChemINDEX Database includes 100,000
chemicals, public NCI compounds, AIDS data, and
more.
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S O F T WA R E

ChemFinder & ChemInfo

Structure Searching and Scientific Databases
NCI Database contains over 200,000 com-
pounds with anti-cancer drug dose-response data.
AIDS Database is an NCI compiled database for
AIDS anti-viral compounds.
ChemRXN Database is a collection of 30,000
fully atom-mapped reactions selected and refined from
the chemical literature. It includes reactions from
InfoChems ChemSelect database and ISIs
ChemPrep database.
ChemFinder.Com is the award-winning web site
with information and WWW links for over 100,000
chemicals. Users can search by name or partial name,
view structure drawings, or use the ChemDraw
ActiveX/Plugin for structure and substructure search-
es. In addition, users can view live ChemDraw files on
Windows and Macintosh clients.

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BioDraw, BioAssay, BioViz
Pathways, Biological Assay and Visualization
BioAssay Ultra
BioAssay Ultra, the cornerstone of BioOffice, provides
flexible storage, retrieval, and analysis of biological
data. BioAssay easily manages both high and low
throughput biological screening data. Designed for
complex lead optimization experiments, the software
supports the quick set-up of biological models, auto-
mated calculations and curve fitting, and the creation
of customized structure activity reports. BioAssay
brings all of this functionality to your desktop.
BioAssay Ultra, compatible with MSDE database,
offers a user friendly interface for importing, viewing,
validating and plotting your biological assay data.
BioViz
Combining biological data with the chemical
structure is of utmost importance in any drug discovery
environment. BioViz allows you to analyze structure-
related data combined with biological data visually.
BioViz, within ChemFinder, provides a graphical rep-
resentation of the data loaded into a ChemFinder
form. Users can search over data and construct a
scatterplot, histogram, or other useful data charts.
Plots are interactive to allow you to select subsets of
your data.
BioDraw
BioDraw, formerly called Pathworks, makes drawing
and annotating your biological pathways quick and
easy, adding a level of uniformity and detail which is
unmatched. Typical drawings of biological pathways
include many elements that are difficult to draw with
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DESKTOP
BioAssay offers flexible storage, retrieval and
analysis of biological data
BioViz provides a graphical representation of
the data loaded into a ChemFinder form
BioDraw allows for quick and easy drawing
and annotating of biological pathways, includ-
ing importing of images in GIF , PNG or
JPEG format
the standard presentation and word processing
software on the market. Common pathway elements
such as membranes, enzymes, receptors, DNA and
reaction arrows are built into the BioDraw toolbar
and including them in your document is as easy as
including a rectangle. Click on the toolbar shortcut
and drop the element into your document. Resize
and move elements by clicking and dragging and
create an accurate and concise drawing in minutes.
BioDraw allows the import of images in GIF , PNG
or JPEG format. ChemDraw users are also able to
include ChemDraw structures in drawings without
difficulty.
Keeping data organized is of utmost importance in
any lab. The BioDraw application reflects that impor-
tance by allowing you to store annotations for each
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S O F T WA R E

Inventory & E-Notebook

Materials Management and Electronic Journal
element in your drawing. Annotation data ranges
from manually entered text to attached documents,
literature references, or links. Any data, regardless of
format, is stored side-by-side with the drawing for
future retrieval.
The drawing and data organization offered by
BioDraw gives any biologist an advantage. Sharing
this advantage assists the community as a whole.
BioDraw offers many ways to share your drawings
and accompanying data.

Notebook Pages

Data Visualization

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BioDraw, BioAssay, BioViz
Pathways, Biological Assay and Visualization
Inventory Ultra
Inventory is an application designed to manage the
chemical and reagent tracking needs of laboratories
and research centers. The system manages data
associated with both commercially procured and
internally produced chemical substances from their
procurement or initial production through their
depletion and disposal.
Inventory Ultra is an MSDE based product and
includes the ChemACX Database with nearly 400
catalogs of chemical reagents. The three primary
entities in an Inventory system are locations, containers,
and substances. Users or administrators configure
a network of locations, which represent locations
within an organization.
Containers are created to represent actual containers
in your facility. Each container is assigned a unique
barcode, which can be printed, using a customized
template, from the Inventory interface. Each container
stores a substance. Additional text fields are available
to track other chemical contents such as the solvent,
and custom fields may also be defined. To keep
track of substances, the system maintains its own
internal chemical structure database containing
unique substances that can be associated with
inventory containers. Advanced duplicate checking is
incorporated in the system.
Every field in a record, including chemical structure,
molecular formula and molecular weight are search-
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DESKTOP
Inventory manages the chemical and reagent
tracking needs of laboratories and research
centers
Inventory maintains its own internal chemical
structure database with advanced duplicate
checking
E-Notebook stores Microsoft Office documents,
ChemDraw structures, reaction drawings and
related data in a convenient, searchable format
able. The application includes a number of specially
designed inventory search forms. Search results are
returned in list form and can be exported into a doc-
ument (PDF , RTF , HTML ) using the report engine.
The Inventory interface allows for printing labels as
well as generating elaborate reports. Inventory uses a
report application that incorporates wizards that allow
for the quick creation of simple report and label
templates that can be shared across an organization.
Inventory Pro
Inventory Pro contains the same features as Inventory
Ultra without the ChemACX Database.
E-Notebook Ultra
E-Notebook Ultra is the efficient, accurate way to
write lab notebooks entries as you work. It stores
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S O F T WA R E

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Materials Management and Electronic Journal
Microsoft Office documents, ChemDraw structures
and reaction drawings, and related data in an elec-
tronic notebook that is searchable by text or chemi-
cal structure. You can organize pages by project,
experiment, or in your own style with the MSDE
database . CombiChem/Excel builds combinatorial
libraries.
E-Notebook is configured exactly like a chemist would
like his or her own notebook to be. Reactions can be
easily drawn into the reaction template by either
selecting from the generous list of preloaded reagents
or by entering or drawing ones own chemicals.
Commonly used reagents can be stored in a separate
folder for easy access. Another fantastic feature is the
procedural section. This section contains prewritten
procedural sentences with the ability to easily drop in
the specific names of reagent chemicals present in the
reaction. One can also easily add other data to the
notebook page such as spectra and Word or Excel
documents.

CombiChem/Excel
CambridgeSoft provides you with the tools to effec-
tively plan combinatorial chemistry experiments in
Excel. The CombiChem/Excel add-in introduces addi-
tional functionality for handling combinatorial
chemistry. Users can generate products from a reac-
tion and lists of reagents, you can view all the prod-
ucts arising from a given reagent or all the reagents of
a given product, and you can lay out reagent and
reaction plates.

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The Merck Index, NCI, AIDS,
Scientific Reference, Chemical Reactions and Patents
The Merck Index
Among printed chemical reference works, one that
stands out for its integrity, detail and longevity is The
Merck Index. The Merck Index database is a structure-
searchable encyclopedia of chemicals, drugs, and
biological agents which includes the complete
10,250 monographs of the 13th edition, 230 new
monographs unavailable anywhere else, as well as 540
monographs retired from the 12th Edition.
The Merck Index is available in many forms to suit the
various needs of both individuals and institutions.
Personal subscriptions are available in one-year and
one-month time periods. A stand-alone package,
requiring no other applications, is also available for
personal use.
The subjects covered include human and veterinary
drugs, biological agents and natural products, indus-
trial and laboratory chemicals, and environmentally
significant compounds. In addition to the standard
searches, compound monographs can be searched by
ChemDraw structure as well as substructure.
Traditional Chinese Medicines
Many of todays well-known drugs have their origins
from natural sources. Access to this wealth of
knowledge is now available with the Traditional
Chinese Medicines database. The database consists of
monographs for 10,458 chemicals isolated from 4,625
natural sources used in traditional Chinese remedies.
The monographs feature bio-activity data for many
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SCIENTIFIC
The Merck Index offers encyclopedic reference
for over 10,000 chemicals, drugs and
biological agents
Traditional Chinese Medicines provides
chemical information and their biological
effects of complex compounds isolated from
natural sources
All electronic databases are updated,
contain information unavailable in print,
and are searchable by structure, as well
as text and numeric range
of the compounds, effects and indications of the
medicines, English, Latin, and Chinese names for the
natural sources, and over 2,000 references. This
information is also available as an SD file to facilitate
in silico research.
ChemINDEX
The ability to quickly look up data such as chemical
properties, biological assay results and toxicological
information is no longer a luxury item, but instead a
requirement. Scientists have used the award-winning
ChemFinder.Com database since 1995. Now, the data
on ChemFinder.Com is integrated into ChemOffice as
ChemINDEX. ChemINDEX contains data on over
75,000 compounds including structures, names and
synonyms, physical properties, and Internet links.
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D ATA B A S E S

ChemACX & Sigma-Aldrich MSDS

Available Chemicals and Material Safety Data Sheets
NCI, AIDS & Cancer ChemReact68
Three informative databases have been integrated ChemReact68, from InfoChem GmbH, is a database of
into one powerful application with the NCI and sample reactions comprising essential information on
AIDS database collections. The application starts 68,000 reactions. These reactions have been selected
with a collection of over 200,000 molecules collected because they have greater than 50% yield and have
by the National Cancer Institute. Searchable fields appeared in more than five example reactions.
include structure, synonym, CAS RN, formula, and The database consists of reaction information and
molecular weight. literature references.
ChemRXN
ChemPrep and ChemSelect are the two reac-
tions databases that make up ChemRXN. Scientific Databases
ChemPrep is a reaction database assembled REFERENCE DATA
by the Institute for Scientific Information
The Merck Index 11,000 monographs
(ISI). This reaction database is designed to
help organic chemists find reactions easily. Traditional Chinese Medicines 10,000 substances
It includes full literature citations. ChemINDEX Database 75,000 substances
ChemSelect, licensed from InfoChem NCI, AIDS & Cancer 270,000 substances
GmbH, is a reaction database containing
Drugs: Synonyms & Properties 8,000 drugs
13,000 important organic reactions.
Medicinal Chemistry 540,000 substances
ChemSynth SOURCING & SAFETY DATA

ChemSynth, from InfoChem GmbH, is a ChemACX Database 380 catalogs

database of sample reactions comprising ChemMSDX Database 23,000 MSDSs
essential information on 180,000 reactions.
Sigma-Aldrich MSDS 130,000 MSDSs
These reactions have been selected because REACTION & SYNTHESIS DATA
they have greater than 50% yield and have ChemRXN Database 28,000 reactions
been sited in leading journals more than
ChemSynth 178,000 reactions
once. The database consists of reaction
information and literature reference. ChemReact68 68,000 reactions

All specifications subject to change without notice.

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Development, Deployment,
Custom Development and System Deployment
In order to provide our customers with a total
solution for scientific informatics, CambridgeSoft
offers the following services to assist our clients in
maximizing the productivity of their research and
discovery organizations.
Informatics Planning
Strategic and Operational Planning
A formal analysis is conducted to provide a roadmap
for successful technology utilization. This process
includes:
An analysis of the current state of the science
technology environment, including architecture and
operational processes
A view of the strategic goals and the barriers to
achievement
The delivery of a phased technology transition plan
Requirements Analysis & Proof of Concept
CambridgeSoft consultants can create or refine
requirements to produce an environment that will
ensure success. With years of experience meeting the
needs of the scientific community, CambridgeSoft
understands the user. The prototyping process
allows definition and testing of the functional and
technical feasibility of potential technology solutions.
The process provides a baseline for the future
development and deployment of a tailored solution.
Users gain valuable first hand knowledge in
experiencing how the system can help achieve
individual and workgroup goals.
All specifications subject to change without notice.
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005
PROFESSIONAL
With custom development, CambridgeSoft
works collaboratively with your team to create
a system that meets your needs while executing
our quality driven software development
process. We deliver what you need, on time
and within budget, without surprises.
Project Readiness Assessment
Is your project set up for success? Is it well defined
into measurable deliverables? Are the roles of project
members clearly defined? CambridgeSofts Project
Readiness Assessment has one goal in mind
to create or assess current plans and make recommen-
dations to ensure that results are achieved.
21CFR11 Compliance
Successfully implemented, a traceable and usable
system is essential to any organization involved in the
creation and management of data in a regulated
environment. As an integral part in creating 21CFR11
and GxP validated applications, CambridgeSoft offers
services to:
Audit the software and process
Create conforming systems design specifications
Generate test plans and validation matrices
Insure systems compliance with functional guide-
lines
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SERVICES

Training & Support

Educational Training and Technical Support
Product Development but would like to customize it for a unique environ-
Data Conversion and Integration ment. Our professional services teams can provide
those specific features by making custom modifica-
When developing a new system, the process of tions that will be supported in the future.
converting existing data and creating interfaces with
Systems Deployment
other data systems is an essential part of the process.
Installation and Configuration
CambridgeSofts professional services staff is equipped
to seamlessly incorporate existing data into the devel- CambridgeSoft will install and configure applications
opment of a new enterprise system. Organizations to meet the needs of your user community. For
unique environments, we build custom installers that
will be able to capitalize on historical scientific data
allow us to productively deploy software across an
while setting the platform for future success.
enterprise.
Custom Development
You have discovered a unique application
need in your organization, but cannot find a PLANNING DEVELOPMENT DEPLOYMENT MANAGEMENT
solution that will meet your functionality or
cost requirements. With custom development, Strategic/Op Data Installation & Managed
CambridgeSoft works collaboratively with Planning Integration Configuration Informatics
your team to create a system that meets your
needs, while executing our quality driven Requirements Systems
software development process. We deliver Analysis Custom Optimization Ultra
Application Services
what you need, on time and within budget,
Development Plans
without surprises. Proof of Pre-Release
Systems Integration Concept Programs

The ability to integrate core applications Systems Technical

with other systems in the technology envi- Project Integration Software Support
Readiness Evaluations
ronment is a competency required to deliver
the functionality of a new application.
Product Tailoring 21CFR11 Product Training Remote DBA
Compliance Tailoring Services Services
Your organization can see the benefit from
implementing a CambridgeSoft application,

All specifications subject to change without notice.

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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005

Development, Deployment,
Custom Development and System Deployment
Systems Optimization
CambridgeSofts systems deployment team will work
with you to make sure that your computing environ-
ment has been optimized for high performance.
Your systems, networks, applications and databases
are assessed and designed to deliver maximum
achievement.
Beta and Pre-Release Programs
CambridgeSoft is committed to maximizing your
productivity through the use of our products, as well
as exposing you to the newest technologies. Our beta
and pre-release programs provide you with that
knowledge, allowing CambridgeSoft to improve
applications with your customer feedback.
Pilot Software Evaluations
It often makes sense to pilot an application before a
major commitment for an enterprise wide implemen-
tation is made. CambridgeSoft will work closely with
you to plan the evaluation, deploy the application,
and gather critical feedback regarding systems design,
APIs and technology specifications.
Training
Effective user, administrator and help desk training is
often an afterthought in many systems deployments.
However, the productivity returns generated by
an investment in systems training can provide
dramatic returns. CambridgeSoft offers training in
the following ways:
On-site real time training through our profes-
All specifications subject to change without notice.
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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005
PROFESSIONAL
Managed Informatics allows your organization
to focus on science, allowing CambridgeSoft to
plan, implement and manage your technology
environment.
sional services staff supporting your systems
environment
On-site formal classroom training
Webinars for multi-location instruction
Off-site at CambridgeSoft facilities
Systems Management
Managed Informatics
There is no longer a need to worry about licensing
fees, maintenance contracts, systems administration
work or database support. Informatics Outsourcing
provides the people, processes and technology to
develop a unique level of service for your organization.
For a monthly fee, CambridgeSoft will deliver the
informatics applications and the technology staff
required to maximize productivity. This service
allows your organization to focus on science, while
CambridgeSoft plans, implements and manages your
technology environment.
Ultra Services
The Ultra Services program is CambridgeSofts
personalized, premium service for supporting our
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SERVICES

Training & Support

Educational Training and Technical Support
customers. Organizations can take advantage of both
telephone and electronic access to CambridgeSofts
support scientists who can address:
Usage and installation questions
Product compatibility and interoperability
questions
Diagnostic review to help isolate the cause of a
problem
Configuration assistance
Planning information for software updates and
upgrades
Assistance with problem resolution
Technical Support & Remote DBA Services
To complete our Management Services offerings,
Technical Support and Remote DBA Services, for
Oracle and SQL Server, are also available.

All specifications subject to change without notice.

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ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft Corporation 2005
Chem & Bio Office
Desktop Software to Enterprise Solutions

KNOWLEDGE CHEMICAL BIOLOGICAL SCIENTIFIC

MANAGEMENT INFORMATICS INFORMATICS DATABASES

Desktop

E-Notebook CombiChem Inventory Registration DocManager BioAssay ChemACX The Merck

Enterprise Enterprise Enterprise Enterprise Enterprise & BioViz Database Index

E-Signatures 21CFR11 GxP Oracle Cartridge BioSAR Sigma-Aldrich Scientific

IP Protection Compliance Validation or SQL DB Enterprise MSDS Databases

Enterprise Enterprise

Research, Discovery, Development, Trials & Manufacturing

Enterprise Solutions include ChemOffice, with Oracle Cartridge, and ChemOffice Workgroup, based on SQL Server to help
organizations from small workgroups to large enterprises collaborate and share information more effectively.
Desktop Software includes ChemOffice, a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and
ChemACX for chemists, BioDraw, BioAssay and BioViz for biologists, and Inventory and E-Notebook.
Knowledge Management with E-Notebook, including Reaction Explorer, CombiChem, E-Signatures for intellectual property
protection and 21CFR11 Compliance, streamlines daily record-keeping with rigorous security and efficient archiving.
Chemical Informatics, including Registration, organizes new compound information. Inventory provides complete management
of chemical and biological inventories including GxP Validation. DocManager indexes chemical structures in documents.
BioIogical Informatics scientists use BioAssay, BioViz, BioSAR and BioDraw to set up biological models and visualize
information, generate spreadsheets correlating structure and activity, search by structure, and draw and annotate pathways.
Scientific Databases include the ChemACX Database of commercially available chemicals and Sigma-Aldrich MSDS.
The Merck Index and other scientific databases provide information about chemicals, their properties, and reactions.
Professional Services includes custom development, system deployment, educational training, and technical support for
pharmaceutical, biotechnology, and chemical customers, including government and academia, by experienced staff.

Web www.cambridgesoft.com Email info@cambridgesoft.com

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ChemBioOffice.Com
CS Chem3D

for Windows Quick Reference

SCREEN ELEMENTS
Model Display Demo
Toolbar Toolbar

Computation
Tools Palette Toolbar
Model
Explorer

ChemDraw
Model Window
Window

Spectrum
Viewer

Dihedral
Driver

TOOLBARS

Building Toolbar Demo Toolbar

Single Triple Build
Translate Zoom Bond Bond From Text Rock Speed Stop

Select Spin

Rotate Move Double Dummy Eraser Select Amplitude

Objects Bond Bond Axis

Model Display Toolbar Calculation Toolbar

Background Depth View Serial Full Screen
Effect Stereo Fading Axes Numbers Display Start Stop

Display
Mode

Background RedBlue Perspective Model Atom Residue Run MM2

Color Axes Label Labels Minimization
WORKING WITH SELECTIONS
If you want to Heres how
Select an atom or bond Click an atom in the Model Explorer. SHIFT+CLICK the adjacent atom

add atoms and bonds to the selects Use SHIFT+CLICK or CTRL+CLICK in the Model Explorer

remove atoms and bonds from the selection SHIFT+CLICK or CTRL+CLICK selected atoms

select several atoms and bonds Drag in the Model Explorer next to the atoms

deselect all atoms and bonds Click in an empty space in the Model Explorer

BUILDING TECHNIQUES
Change a bond type Drag over the bond using a different bond tool

Change an atom type using the Replacement Text box With Text Tool, click atom, type atom type (e.g. H Enol), press ENTER

Change an element using the Replacement Text box With Text Tool, click atom, type an element (e.g. N), press ENTER

Reserialize atoms using the Replacement Text box With Text Tool, click atom, type a starting number, press ENTER

Add a substructure using the Replacement Text box With Text Tool, click atom, type a substructure (e.g. OEt), press ENTER

Create a dummy atom using a bond tool Click and drag using the Uncoordinated Bond Tool

Move an atom Drag the atom with the Move tool

Move the model in the window Drag the model with the Transform tool

Pull atoms toward you Drag the atom with the Move tool

Push atoms away from you Drag the atom with the Move tool

Convert a ChemDraw structure to a model Draw structure in ChemDraw window

Place a picture of a model in ChemDraw Select the entire model (CTRL+A) then Copy As from Edit Menu

Convert a model into a ChemDraw structure Select the entire model(CTRL+A) then Copy As from Edit Menu

ROTATING TECHNIQUES
Open the rotation dial Click the arrow on the right of the rotation icon

Rotate a specified amount Select axis to be rotated; drag rotation dial hand to desired position

Rotate selected fragments Select a dihedral rotation on the rotation dial; drag rotation dial hand

Rotate all fragments, regardless of selection Drag a rotation bar

Save rotation frames as a movie Select a Spin... command from the Movie menu

Stop recording frames Click the stop button on Movie menu or Computation toolbar

Replay recorded frames Click the start button on the Movie menu(or toolbar)

Create a rotating demo Use the Demo toolbar

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CS ChemFinder

for Windows Quick Reference

SCREEN ELEMENTS
Title Bar Record Toolbar

Menu Bar
Search Toolbar
Main Toolbar
Text Toolbar
Main Form
Form Toolbar Framed Data Box

Structure Window
Subform

Explorer Window

Favorites Tab
Table Header
Queries Tab

New Record
Indicator

Status Bar Total DB Size

Data Read-only Query Current Current List Size

Table Indicator Indicator Record

TOOLBARS
New Save BIOVIZ
Form Form Paste Redo Print Print

Database
Wizard
Open Cut Copy Undo Layout Switch to
Form Mode Table

Enter Retrieve Previous Restore

Query All Query List
Right-click in the plot,
and choose Properties
Find to modify the plot
List
Find Find Save Restore Over
Selection
Current List Previous Current
Tool Frame Text Button Subform
Molecule List List

Previous Next Add Commit

Grid
Omit Data Picture Boolean
First Framed
Record Box Box
Go To Last Undo Delete
QUICK START
The following instructions are intended to give you a quick start using CS ChemFinder. For more detailed instructions, see the
CS ChemFinder Users Guide.

Creating a Database Searching

1. Create an empty form by selecting New from the File
menu.
2. Right-click in the form and choose Data Source.
3. Click Create Database.
4. Name your database (.MDB file), and click OK, then click
OK in the Form Properties dialog box.
Four fields are created automatically: MolID, Structure,
Formula, and MolWeight.
To create other fields, see Creating New Fields below.
Creating New Fields
1. Right-click in the form and choose Properties.
2. On the Field tab of the Form Properties dialog box, click
Create Field.
3. Type a field name, type, and width. Click OK.
4. To assign the new field: right-click on the appropriate data
box and choose the field.
1. On the Search toolbar, click the Enter Query button. The
form is cleared.
2. To enter a structural query, double-click in the Structure
Data Box. If the Structure Data Box is set to ChemFinder
style, ChemDraw will open. Create a structure in
ChemDraw and use Ctrl+W to return to ChemFinder. If
the Structure Data Box is set to ChemDraw style, a
ChemDraw toolbar will appear. Create a structure directly
in the Structure Data Box, then click outside the box to
continue.
3. To enter an alphanumeric query: click the data box you
want to search and type the query in the data box.
4. Choose the type of search you want from the Search menu.
5. Click the Search button on the Search toolbar.
6. Click the Retrieve All button on the Search toolbar to
browse the full database.
7. Use the Queries panel in the Explorer window to manage
your searches.

Importing Data from SDFiles

Creating a Form
1. Double-click a field in the Database panel of the Explorer
window. The field is added to the form.
2. Use the selection tool to select and drag the field boxes to
where you want them in the form.
3. Choose Save from the File menu to save your form as a
CFW file.
1. Open an existing or blank form.
2. Point to Import on the File menu, and choose SDFile.
3. Choose your .SDF file. Click OK.
4. Select your import options (Overwrite, Append, or Merge).
5. To edit a field, double-click its name in the left pane.
6. Click OK.

Adding Records and Entering Data

Using Your Form with an Existing Database
1. On the Record toolbar, click the Add Record button. The
form is cleared. 1. Right-click in a field box, and choose Data Source.

2. To enter structures: double-click in the Structure Box acti- 2. Choose Open Database in the Box Properties dialog box.
vate the ChemDraw toolbar. Click outside the Structure 3. Choose a database (.MDB file) and click Open.
Box when you have completed drawing your structure.
4. In the left pane of the Database tab, click the field you
3. To enter alphanumeric data: click in the data box and type want to assign to the data box you selected in Step 1.
the new data.
5. Click OK.
4. When you are finished, click Commit Changes or Undo
6. To assign fields to other data boxes: right-click on a data
Changes. If you have more than two records, you can
box and choose a field.
Commit Changes by moving to another record using the
Record tools.
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CS E-Notebook
for Windows Quick Reference
SCREEN ELEMENTS

Title Bar Menu Bar Navigation Toolbar Search Button

Close Page Help Button

New Page
Section
Collection Tree Tabs
Save Button

New Section
Button
Next Step
Button Pages in
Reaction
Tab

History
Pane

COLLECTION MENU

Browsing Options
SECTION MENU
Import XML File
Export XML File Open annotation
dialog Copy & Paste
Section
Paste a Copy Move
Paste a of Original Section
Shortcut
Duplicate
Delete
Rename
Alter Location Export
in Collection Tree Print
Refresh

View Previous
Versions
View Properties
such as Creation
Date
QUICK START

Creating an Electronic Notebook

1. From the Start menu select ChemOffice and then click on E-Notebook
2. Enter your username and password if prompted.
3. To create a Notebook, right-click your user at the top of the collection tree on the left. Select New,
then Notebook.

Closing and Printing Notebook Entries

1. To close a Page so that it can no longer be modified, right-click the Page and the tree, and select
Close from the menu.
2. To Print, right-click the Page, and select Print from the menu. Then follow the print dialog box.

Using a Reaction Section

1. Make sure that the reaction tab is selected. (Click the reaction tab to select it).
2. To draw a reaction, click in the reaction box and use the ChemDraw tools.
3. The stoichiometry table is updated as you draw the reaction. To edit the table, type new values into
the cells, and the table will update automatically.
4. To add a reaction property, right-click the table and select Add Property.
5. Right-click in the procedure text to access the AutoText menu.

Creating new Pages and Sections

1. To create a new Page, right-click the Notebook in the collection tree and select New, then Page.
2. To add a new section to a Page, click the Page in the collection tree. Then click the New Section but-
ton, and select the type of section you wish to add.

Using a Spectra Section

1. Make sure that the Spectra tab is selected.
2. Click the New Section button to add a new subtab for a Spectrum
3. Click the Import/Export button, and follow the dialog to select the spectrum to import.

Searching Notebook Entries

1. To perform a search, click the Search button at the top of the screen.
2. From the Search for list, select the type of search you wish to perform.
3. Enter your search criteria, and click Search Now.

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 CS Software Problem Report
For faster response and accuracy, use the Web:
www.cambridgesoft.com/services/mail
USER INFORMATION (Please Print Legibly) Submit this form via
Name WWW www.cambridgesoft.com/services/mail
Title EMAIL support@cambridgesoft.com
Firm FAX 1 617 5889360
Street MAIL CambridgeSoft, 100 CambridgePark Dr.
City State Zip Cambridge, MA 02140 USA
Country
Tel Fax
Email

DETAILS OF THE PROBLEM

SYSTEM CONFIGURATION
SOFTWARE
Application Name
Please cut here or photocopy page.

Version Number
Serial Number

SYSTEM
Windows (version)
MacOs (version)
Web Browser(s) (version)
!

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 CS ChemOffice

Desktop to Enterprise Solutions

ChemOffice Ultra, desktop

edition, includes it all, with
ChemDraw Ultra, Chem3D Ultra,
BioOffice Ultra, Inventory Ultra,
E-Notebook Ultra and ChemInfo Ultra for
a seamlessly integrated suite. Draw reaction
mechanisms for publication and visualize
3D molecular surfaces, orbitals and
molecular properties. Features include
The Merck Index, ChemACX Database,
CombiChem/Excel, ChemDraw/Excel, and BioViz.
Bring your work to the web or query online
databases with the ChemDraw ActiveX/Plugin.
C h e m O f f i c e E n t e r p r i s e is a comprehensive
knowledge management and informatics solution,
covering elextronic notebooks, biological screening,
chemical registration and more over your intranet.
Enterprise Ultra includes E-Notebook for record
keeping, BioAssay for low and high-throughput
screening, integrated plate inventory, Inventory for
reagents, BioSAR for SAR reports , Registration
system and ChemACX Database of available chemicals.
Technologies include ChemDraw ActiveX and Oracle Cartridge.

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