Printing Proteins Quickstart

Eduardo da Veiga Beltrame veigabeltrame@gmail.com

First, you need the coordinate file of the molecule you want to print. The files containing the
atoms coordinates for a molecule are called .pdb files (for protein data bank). These structures
are determined using an array of techniques such as x-ray crystallography and nuclear
magnetic resonance, and when they are published they are also deposited in databases and
become freely available for download. The biggest such database is the Protein Data Bank, and
if you are interested it's worth a visit: http://www.rcsb.org/.
If youre looking for cool sturctures and some explanations, the molecule of the month PDB
articles are a good way to start browsing. They are written by David Goodsell, who is awesome.
If you can't find your molecule, if it's not on the PDB it's probably because nobody knows it's
structure yet. If what you want is some small molecule, you can try searching for the structure
online, or can draw it using Avogadro, a free and open source molecule editor you can get at
www.avogadro.cc and stop complaining, it's not hard to use. And I'm also not teaching you how.
Once you have your PDB file, you can render it on any molecular visualizer, the workflows is
virtually the same. Here Ill be using chimera.
This is the workflow for printing any protein, in this example I'm doing kinesin, a motor protein
with 2 feet that walks along microtubules in cells transporting vesicles with chemicals, such as
neurotransmitters in neurons. You can read more about it here:
http://www.rcsb.org/pdb/101/motm.do?momID=64.

So once I get my pdb file, the first step is to open it on a molecular viewer, such as VMD, PyMol
and Chimera. Here Ill be using Chimera. When trying to visualize molecules, it is important to
keep in mind there is no "right" image for them, we can represent atoms in a variety of manners
that best present the features we want to convey. I've attached 4 different representations that
are commonly used, ribbons, which depicts structural motifs (helices and sheets), lines which
show all the bonds between atoms, spheres which is the traditional representation most people
know, and the surface representation which is roughly the surface that an external molecule
would see. For FDM printing surface is the best suited one. Once I get the representation as I
want, I just export an stl file directly, most viewers have a straightforward option to export stl or
similar files.
Guide for Chimera representations:
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html

Ribbons: this molecule is too big to print as ribbons, you need to print them at 300% the standard
chimera output for them to print well on FDM.

Spheres: Don't ever export large molecules as STL of spheres on Chimera, each sphere has a humongous
number of polygons, the way around it that I found is to actually render the surface, but making the
probe radius small so they look like surface.

Wires: You can't export an STL of wires (they have no volume). You can however export the STL of
licorice, which are fat wires, but they only work well for small molecules, because you need to print
them at at least 300% the standard chimera output.

Surface: This is the best type of rendering for printing, printing at 100% the standard chimera output
works wonderfully. Just always remember to run your file trough Netfabb, and I suggest using
Meshmixer to orient it so as to minimize overhangs.

Always check your rendered STL file on Meshmixer os Meshlab or any STL viewer to ensure it
was rendered as you wanted.
Chimera standard STL rendering resolution is fine for most representations, but when printing
surface models in large scale (more than the standard output size), it's a good idea to bump up
the amount of vertices to obtain a smoother (standard is 2, good amount is 10, you can get
more but the file size starts becoming humongous).
The easiest way to do it is, once you select the surface representation: Presets > Interactive 3
(hydrophobicity surface) , just go and hit Presets > Publication (any of them, the sillhouetes and
shadows don't affect STL quality.
You can also do that following the first steps here: http://www.over-engineered.com/projects/3dprinted-protein/
Or you can adjust the surface "vertex density" using the command "setattr" (set attribute), for
example:
setattr s density 10.0
When you're happy with that you see, export the file by going to File > Export Scenre, then
select STL and click ok.
From there I just import into Simplify, I add the supports and check to see they are good, then I
slice the file. These are very large stl files, often greater than 50mb, they usually take some 30
seconds to slice on our powerful custom build computer, and the biggest ones may take 10 or
15 minutes. I then check the sliced to file to check it has done nothing funny (when that happens
it's because the file had not been processed on Netfabb), then I load the printer. My molecules
can take anything from 1 hour to 50 hours. They take so long because they have a lot of
perimeter and the speed is reduced to get a good finish, so even for a small volume the print
takes a while. Usually they take between 3 and 16 hours.

Adding supports on Simplify.

Adding supports on Simplify.

Its advisable to always print with a raft, in order to ensure all the supports will adhere and print
correctly.

When it's done, I usually spend some 10 minutes (depending on their size), removing the
supports, they snap off pretty easily, but there are so many of them in so many little places it
can take a while sometimes. Thats it.