Question
Asked 4th Feb, 2014

Protocol on how to 3D print protein structures?

We have bought a Makerbot 3D printer and would greatly appreciate it if someone send me a protocol on how to print 3D protein structures (e.g. from Molecular Modeling Database/Structure, Protein Databank, etc.)
Thanks!

Most recent answer

10th Aug, 2016
Oliver A H Jones
RMIT University
You can also use the NIH 3D print exchange (http://3dprint.nih.gov/) it works really well. You just load upload the .pdb file and it will convert it for you and give you a the files you need. See See https://www.youtube.com/watch?v=RvQ6R_op128
3 Recommendations

Popular Answers (1)

30th Jul, 2014
Aaron J Oakley
University of Wollongong
I routinely print molecules on my Makerbot using the following protocol:
1. Load molecule into VMD ( http://www.ks.uiuc.edu/Research/vmd/ )
2a. If rendering as a cartoon, thicken the model so as to convey structural rigidity onto the final print. Choose an aspect ratio of about 2, thickness of about 1.
2b. If rendering van der Waals surfaces, set the atomic radii to be about 1.4.
3. Turn off the XYZ Axes, otherwise they will be rendered too.
4. Render as an STL file.
5. Use a program such as netfabb to repair the stl (the ones from VMD are often not manifold or orientable).
6. Load into Makerware.
7. When printing, I recommend using rafts. Supports are compulsory as there are invariably overhangs.
I have produced a number of protein models available on the thingiverse:
Good luck!
12 Recommendations

All Answers (13)

6th Feb, 2014
Rolando Garcia-Milian
Yale University
Thank you Tobias, I will look at those.
20th Feb, 2014
Denis Hudrisier
French National Centre for Scientific Research
I recently did this (please watch https://www.youtube.com/watch?v=yPOYMP_-4kM).
Here is the step-by-step procedure I used:
1. search for the molecule of interest in Protein Data Bank then export in pdb format
2. Open using the Chimera freeware
3. Prepare the molecule as you wish to see it printed (I use ribbons only but you could try solid structure, that's no problem)
4. Directly export in .stl format (most 3D printers recognize this format)
5. Open the stl file in your 3D-printer software: it is often necessary to "repair" the molecule. There if you want me to be more specific I can only do it for the "UP" and "MakerBot" printers.
6. Print: it takes hours and it's a nightmare to remove the support material but once it's done the result is beautiful!
I hope it helps! Don't hésitate to ask me for more details!
Here is a link to a tutorial I prepared:
9 Recommendations
26th Feb, 2014
Graham T Johnson
University of California, San Francisco
MakerBot is not ideal for printing protein models unless they are very simple, so I'll recommend using coarse molecular surfaces and then finding an orientation that minimizes the number of concavities/overhangs along the vertical axis.
For more general printing advice, I've pasted some discussion we recently had on the Chimera group list serve at the bottom (not specific to maker bot).
First a very general recommendation about 3D printing for people without a printer:
If you want to do full color models, you can hire a service to do it for you, e.g., the lab where I got my PhD: http://models.scripps.edu (they will take care of all of the support and struts etc.) or you can export a VRML file (I've not tried Chimera's VRML files, but I'm sure it would work fine), and upload that to an online service to print in a huge variety of materials, including metal, such as http://www.shapeways.com. The website will give you instant feedback about the printability of your model, followed a couple days later by some human input.
NIH plans to support 3D printing very soon. Here is a placeholder for their future website (nothing clickable for the public yet, but the movie will inspire) and you can request to join the beta testers group to gain full access to the website: http://3dprint.nih.gov
FROM A CHIMERA GROUP LISTSERVE DISCUSSION- a Discussion about this topic:
Here's a link to the 3-D models we make using Chimera and our uPrint
...
Just a few more details from the Chimera end. You can use File... Export Scene and choose the STL format.
There are some things to consider, such as structural integrity and whether the exported triangles are well-behaved. The link Tom sent has some discussion of these issues. Also, there is a relatively new "struts" command (not in 1.8, you need a daily build) to add reinforcing bars to a structure for 3D printing:
2 Recommendations
28th Feb, 2014
Denis Hudrisier
French National Centre for Scientific Research
Very interesting comment Graham and thanks for the links!
Regarding the printing of complex molecular models, I love the idea of using water soluble support material (http://www.3dppvd.org/wp/2013/02/soluble-support-material/). Can be done by using two extruders on a Makerbot and use HIPS as material for support.
The most amazing models in my view: http://www.prsnlz.me/vids/kawakami-model-demo/
1 Recommendation
27th Jun, 2014
Darrell Hurt
National Institutes of Health
Check out the new NIH 3D Print Exchange. We do a lot of the compute for you so that all you have to do is send the file to the printer.
1 Recommendation
30th Jul, 2014
Aaron J Oakley
University of Wollongong
I routinely print molecules on my Makerbot using the following protocol:
1. Load molecule into VMD ( http://www.ks.uiuc.edu/Research/vmd/ )
2a. If rendering as a cartoon, thicken the model so as to convey structural rigidity onto the final print. Choose an aspect ratio of about 2, thickness of about 1.
2b. If rendering van der Waals surfaces, set the atomic radii to be about 1.4.
3. Turn off the XYZ Axes, otherwise they will be rendered too.
4. Render as an STL file.
5. Use a program such as netfabb to repair the stl (the ones from VMD are often not manifold or orientable).
6. Load into Makerware.
7. When printing, I recommend using rafts. Supports are compulsory as there are invariably overhangs.
I have produced a number of protein models available on the thingiverse:
Good luck!
12 Recommendations
1st Dec, 2015
Denis Hudrisier
French National Centre for Scientific Research
For your interest, please find a list of protein models printed by some of my students.
1 Recommendation
17th May, 2016
Eduardo Beltrame
Federal University of Santa Catarina
 I have written a detailed guide explaining every step for rending and printing molecular models: http://munfred.com/proteins.html
4 Recommendations

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