README

======
Contents
--------
1. New features in HyperChem Release 4.5.
Ab-initio calculations
Isotope effects
Interface to ChemDraw
Copy orbital and spectral images from quantum mechanical calculations
Change chirality of amino acids
String arguments in script messages
New script messages
2. Corrections to the documentation.
New Features Manual
Reference Manual
3. Creating a new basis set.
4. Hints on particular aspects of the use of HyperChem.
Joining the HyperChem e-mail users group
HyperChem World Wide Web
Saving vibrational and UV-visible spectra
Recursive scripts
Speeding up DDE Executes to HyperChem
Altering chem.ini settings
5. Controlling the amount of logging information produced during calculations
6. Notes on running ab initio calculations
Running ab initio calculations on your local PC
Running ab initio calculations on remote UNIX systems
7. Notes on specific printers and display devices
Changes for an IBM 8514/a display adapter or compatible display card
Printing to the Apple Laser Writer IINTX:

1. New features in HyperChem Release 4.5.

============================================
Ab-initio calculations
----------------------
The most significant change between versions 4 and 4.5 of HyperChem
is the addition of ab-initio functionality.
Using any basis set of s, p or d orbitals, ab-initio calculations of
the following kinds can be performed:
SCF calculations of single point energies
geometry optimizations
molecular dynamics
vibrational analysis
optical spectroscopy
A large number of basis sets are supplied, and users are also
able to define their own basis sets. HyperChem uses a simple
text format to describe basis sets, making users' modifications
easy. Considerable flexibility in the choice of a basis set is
available, including the ability to simply select a set of atoms
with the mouse and assign a basis set to those atoms only. This
makes it possible to have different basis sets assigned to
different atoms, or even to select an atom and interactively
assign a primitive s, p, sp, d or spd shell to that atom with the
user specifying an exponent for the shell. It is even possible
to interactively select a set of atoms and have their nuclei
treated as "ghost nuclei" * HyperChem uses the basis functions
but neglects the nuclear interactions. Single-point correlation
energy calculations at the MP2 level can also be performed. The
ab initio calculations are completely integrated into HyperChem's
usual graphical support, allowing users to visualize orbital energy
plots, electron densities, IR and UV spectra, etc. Chemical
reactions can be explored by performing molecular dynamics with
forces computed by ab initio methods.
Isotope effects
---------------
The user can now specify a mass to any atom displayed in
HyperChem. This can be used to explore isotope effects in
vibrational analysis.
Note that this user-assigned mass is only valid for semi-
empirical and ab initio methods. To change the mass of
an atom in molecular mechanics, one must change the mass
of its type (in the file ___typ.txt).
Interface to ChemDraw
---------------------
HyperChem can now read ChemDraw files. Since ChemDraw is a drawing
program and not a modelling program, it handles some structural
elements in ways that must be corrected manually in order that they
be read properly by HyperChem.
When an "aromatic" ring is drawn in ChemDraw, the result is a
circle -- a picture element -- attached to a structure with single
bonds. When a ChemDraw file (type .CHM) is read by HyperChem, it
ignores the picture elements and processes only the chemical
structures, so an "aromatic" ring shows up with single bonds.
To have the ring brought into HyperChem drawn with aromatic bonds,
you must change the bond type for the ring bonds to "aromatic" in
ChemDraw by selecting the ring and using the Object/Bond
Properties menu item. Alternately, you can change the bonding
to aromatic after the structure is imported to HyperChem by
double-clicking on a bond.
Copy orbital and spectral images
--------------------------------
Users now can copy images of the molecular orbital energy level
diagram and electronic and vibrational spectra, for semi-empirical
or ab initio quantum mechanical calculations, to either the Windows'
Clipboard or to a file. These images can then be imported into other
Windows' applications, such as Microsoft Word, to produce hard copy.
HyperChem can store images of the molecular orbital energy level
diagram in either of two types of files - a bitmapped (BMP) or
Windows metafile (WMF) - depending on the image setting of the Setup
Image dialog box invoked from the menu item, Edit/Setup Image.
These are standard Windows' file types that many other
programs use. The color of the orbital energy level diagram image
placed in the clipboard or file can be controlled from the
Preferences dialog box via the menu item, File/Preferences. For
details on setting up the file format and images, please see the
HyperChem Release 4.0 Reference Manual.
Change chirality of amino acids
-------------------------------
Users now can now change the chirality of an amino acid when
using the Mutate dialog, by choosing either the L or D isomer
buttons. A residue can be changed to another residue of different
chirality, or the chirality can be changed by itself.
String arguments in script messages
-----------------------------------
A deficiency was noted in release 4.0 with regards to string arguments.
Embedded escape characters within string arguments were ignored. This has
been corrected in Release 4.5. Strings which are not quoted are treated
literally. Strings which are quoted are treated as C-strings with escape
characters defined by a preceding '\' character.
The following strings are equivalent string argument assignments:
abinitio-integral-path c:\hyper\integral
abinitio-integral-path "c:\\hyper\\integral"
The '\\' string is the quoted escape string for '\'. The '\n' string is the
quoted escape string for a new line.
New script messages
-------------------
The following HyperChem messages have been added:
assign-basisset
abinitio-mo-initial-guess
abinitio-cutoff
abinitio-buffer-size
abinitio-integral-format
abinitio-integral-path
abinitio-direct-scf
abinitio-use-ghost-atoms
abinitio-scf-convergence
abinitio-d-orbitals
abinitio-calculate-gradient
abinitio-mp2-correlation-energy
abinitio-mp2-frozen-core
backend-communications
backend-host-name
backend-user-id
backend-user-password
backend-process-count
atom-mass
atom-basisset
atom-extra-basisset
mp2-energy
compile-script-file
declare-integer
declare-string
delete-file
execute-hyperchem-client
execute-string
factory-settings
file-diff-message
no-source-refs-in-errors
omsgs-not-to-file
pop-no-value
pop-value
print-variable-list
push
read-binary-script
source-refs-in-errors
toggle
unconstrain-bond-angle
unconstrain-bond-length
unconstrain-bond-torsion
orbital-count
atom-info
cancel-menu
global-inhibit-redisplay
hide-errors
hide-messages
info-access
info-enum-id-of
info-enum-list
info-factory-setting
info-id-of
info-type-of
info-type-of-element
info-variable-target
mechanics-data
mechanics-info
notify-with-text
omsg-file
one-line-arrays
path
residue-count
residue-label-text
script-menu-caption
script-menu-checked
script-menu-command
script-menu-enabled
script-menu-help-file
script-menu-help-id
script-menu-in-use
script-menu-message
script-refs-in-errors
view-in-hin-file
keep-atom-charges
See on-line help or the HyperChem Release 4.5 for Windows New
Features manual for descriptions of these messages. See the
Corrections to the documentation section below for descriptions
of the keep-atom-charges HyperChem message that is missing from
the New Features manual.
2. Corrections to the documentation
======================================
New Features Manual
-------------------
The following HyperChem messages do not appear in Chapter 6 of
the New Features manual (but is included in the on-line help for
Scripts & DDE):
Script Variable: keep-atom-charges
Type: Boolean
Read/Write Status: R, W
Use: Whether or not to keep the atom charges
when switching the molecular mechanical
calculation method from one to another.
Reference Manual
----------------
On page 291, the menu-file-print file menu activator should have
Print as the dialog box.
On page 331, the description for serial-number should appear
instead of the duplicate description of version.
3. Creating a new basis set.
================================
HyperChem supports the commonly used basis sets with its distribution
disks. Uses can also create their own basis sets by following the
format of HyperChem basis set definition.
To create a new basis set:
--------------------------
1). Create a file with an extension of .BAS (say my.bas) in the
HyperChem directory (say c:\hyper).
2). Edit this file, my.bas, and type in the information of basis
set, such as, element symbols, number of shells for each
element, shell types, number of primitives, scaling factors,
and exponents and coefficients for each primitive.
For more detailed information of HyperChem basis set file,
please see, pages 157 - 159 of the HyperChem for Windows
Release 4.5 New Features Manual.
3). Add an entry of "my=my.bas" into the section [basisset] in
the CHEM.INI file that locates in your HyperChem directory.
After you restart HyperChem, you can use this new basis set.
To use this new basis set:
--------------------------
1). Create or read in a molecular system.
2). Open the Ab Initio Method dialog box via the Setup menu.
3). Choose the Other to active the Assign Other Basis Set button
in the Ab Initio Method dialog box.
4). L-click on the Assign Other Basis Set button to bring up
the Assign Other Basis Set dialog box.
5). Choose "my" from the Assign Other Basis Set dialog box and
then L-click on OK.
6). L-click on the Apply Basis Set button in the Ab Initio
Method dialog box or just L-click on OK.
HyperChem applies this new basis set, "my" basis set to
the selected atoms, if any, or to all the atoms.
HyperChem will use the basis set information from your new basis
set file, "my.bas", when you run ab initio calculations for this
given molecular system.

4. Hints on using specific aspects of HyperChem.

===================================================
Joining the HyperChem Internet e-mail users' group
--------------------------------------------------
The HyperChem Internet e-mail users' group is designed to encourage
users to share their experiences and ideas to improve their use of
HyperChem. Information on scientific and technical issues, such
as Visual Basic tools, HyperChem structures, and product support
questions, can be posted to this group. To become a subscriber,
send an e-mail message to:
hyperchem-request@hyper.com
with the line:
subscribe hyperchem
as the message body. You will automatically be subscribed and
sent instructions on use of the e-mail group.
HyperChem World Wide Web
------------------------
Hypercube now maintains a World Wide Web (www) site at
http:/www.hyper.com.
If you have access to the www, you are invited to visit our site
regularly to keep informed of new developments in the world of
HyperChemistry. In particular there may be new releases and new
products you may wish to know about or auxiliary materials you may
wish to download via ftp.
Saving vibrational and electronic spectra
-----------------------------------------
The HyperChem sample files include script files for saving HyperChem
vibrational and electronic spectra results so that you can read them
back into HyperChem for later use. These scripts cause HyperChem to
create new script files that can be opened later to restore the results.
The sample files are called SAVEIR.SCR and
SAVEUV.SCR (for vibrational and electronic results respectively). See
the comments within these files for further details.
Recursive scripts
-----------------
From a script that you write with a text editor, you can call another
script (called recursive scripting). The recursion depth depends on
finite system resources, however, and will thus vary depending on the
scripts and available resources.
Speeding up DDE Executes to HyperChem
-------------------------------------
The speed of DDE Execute commands that alter properties of molecules
in HyperChem can be sped up by using the "inhibit-redisplay" script
command. Turning redisplay off (inhibit-redisplay Yes) before sending
a set of Execute commands to HyperChem, and then turning redisplay on
(inhibit-redisplay No) after they are complete speeds up the execution.
You should be aware that if inhibit-redisplay is left in the "Yes"
state the HyperChem workspace will not be updated at all until the
inhibition is removed by executing an "inhibit-redisplay No" command.
LogAltering chem.ini settings
-----------------------------
If you wish to alter chem.ini settings that are not accessible through
the user interface, such as Networking, you can follow one of the
following two procedures.
Edit chem.ini
-------------
a. Close all copies of HyperChem you may have running, as
HyperChem writes over chem.ini on exit.
b. Edit the file chem.ini with a text editor, such as Notepad,
and alter the settings you wish to change.
c. Start HyperChem; the new values of chem.ini settings will
be read in and used.
Reset from a script
-------------------
This method has the advantage that you do not have to exit HyperChem
to change the settings.
a. Write a script containing a command that resets the desired
setting.
b. Run this script from the Script menu. The desired setting
is altered immediately.

5. Controlling the amount of logging information produced during calculations

===============================================================================
A last-minute addition to the File/Log dialog box now allows users to change
the values of MechanicsPrintLevel and QuantumPrintLevel from within HyperChem.

6. Notes on running ab initio calculations

=============================================
Running ab initio calculations on your local PC
-----------------------------------------------
HyperChem allows the user to specify, via CHEM.INI or the script
command "abinitio-integral-path", the disk drive used to store the
ab initio two-electron integrals. The two-electron integral files
with an extension of .TMP may still remain in the directory specified
by the CHEM.INI file, if your PC is rebooted or your PC's power
supply is disconnected during ab initio calculations. So in this
case, you may wish to free up the disk space by deleting these .TMP
files.
Running ab initio calculations on remote UNIX systems
-----------------------------------------------------
HyperChem writes the two-electron integrals into files with prefix
HCGAU in your root directory or /usr/tmp or /tmp directory
(whatever is writable) on the remote UNIX systems when you run
remote ab initio calculations. The two-electron integrals may
also remain in this directory if your PC is rebooted, your PC's
power supply is disconnected, or you hit the Cancel menu from
HyperChem during ab initio calculations. So in this case, you
may wish to free up the disk space by deleting these files with
prefix HCGAU.

7. Notes on specific printers and display devices

====================================================
Changes for an IBM 8514/a display adapter or compatible display card
--------------------------------------------------------------------
If you are using an IBM 8514/A display adapter or compatible such as
the ATI Ultra Display video card, you may notice a number of random
scan lines at the bottom of your HyperChem window. To remedy this
situation, exit HyperChem and open the chem.ini file with a text
editor such as Write or Notepad (don't convert to Write format).
Under the heading [HyperChem], type the following: SlowErase=Yes.
The next time you initiate HyperChem, the chem.ini file with it's
new addition will be read. SlowErase will clean up your display,
but you will experience a 50% decrease in painting speed. If speed
is more important to you than noise, you can delete the SlowErase
entry from chem.ini, or set SlowErase=No.
Printing to the Apple Laser Writer IINTX:
-----------------------------------------
If you experience problems with default settings when you send large
batch jobs to the postscript printer, try using the following
settings:
In the Connect Dialog Box:
Transmission Retry 500
Fast Printing Direct to Port = deselect
In the Settings Dialog Box:
Baud rate = 9600
Data bits = 8
Parity = None
Stop Bits = 1
Flow Control = Hardware
In the Setup/Options Dialog Box:
Send Header with Each Job = deselect
In the Advanced Options Dialog Box:
Use Printer Fonts for all True Type Fonts = deselect
Virtual Memory (KB) (Tested at 2048KB) = max. avail (print
testps.txt to check value).
Compress Bitmaps = deselect
Conform to Adobe Document Structuring Convention = deselect
Return to the Options Dialog Box:
Send Header = select
Send Header with Each Job = deselect .