[Chimera-users] 3D Printing our protein

R.J. Swett rswett at chem.wayne.edu
Mon May 20 06:02:40 PDT 2013

You might want to try saving the two domains as separate PDB's if there 
are export issues with hidden domains. If you hide a domain and then go 
to save pdb and select "save displayed only"  you'll be able to save 
each domain in it's own file. As far as file formats go, have you tried 
VRML? I know that's pretty universal for 3D printers and might help with 
studying the structure as you'd be able to color the atoms by their atom 
types. Is your 3D printer capable of color? Another thing you might want 
to try is displaying the protein backbone as ribbon and the sidechain 
as  wire and setting the wire thickness to a higher number. That might 
give you the internal detail you want without saving the data for every 
single atom. Also, displaying as Ball and Stick might work too. Those 
controls are in the Actions > Atoms/bonds menu. Also, are you wanting to 
include the solvent or are you deleting it?

R.J. Swett
Wayne State University
357 Chemistry
Detroit, MI 48201

Lab Phone 313-577-0552
Cell Phone 906-235-0768

On 5/19/2013 9:23 PM, Bart Janssen wrote:
> Hi
> My apologies for what are likely to be stupid questions. We are plant 
> developmental biologists and we just obtained our first X-ray crystal 
> structure for a new hormone receptor in plants. We'd really like to 
> make a 3D model of the protein using one of the 3D printers at our 
> institute.
> I've been trying to use and understand Chimera for the last week and 
> I'm a bit out of my depth :). I can import our protein 4DNP.pdb and 
> display it using solid surface or using the sphere representations of 
> atoms. I can also display it with the "lid" domain hidden and vice versa.
> My problem has been getting files that our 3D printer can read. The 
> solid surface model of the whole protein can be exported as a scene in 
> .stl format and that can be printed just fine. Although I can't figure 
> out how to adjust resolution or the smoothness of the exported file.
> But I'd really like to print the two domains of the protein 
> separately. If I use Solid surface model with the lid hidden what I 
> get is an eggshell like model which has no internal detail. If I use 
> atoms shown as spheres instead I get the internal detail I want BUT 
> when I try and export the scene I get a 2 Gb+ file that is unreadable 
> by the printer. If I export .obj format instead the colleague who runs 
> the printer says the file won't load and appears to have errors.
> I have a horrible feeling I am going about this entirely the wrong way 
> but I can't find a tutorial that describes what I'm trying to achieve. 
> I do realise chimera is not really written for the somewhat trivial 
> use that I am attempting but it really would be helpful if we had a 
> physical model of the protein to look at.
> Is there a tutorial I should follow or another part of Chimera (or 
> another program) that I should be using instead? Any advice would be 
> much appreciated.
> Cheers
> Bart
> Bart Janssen
> Scientist
> Plant Development team
> Breeding and genomics
> Plant and Food Research
> Private Bag 92169
> Auckland 1142
> New Zealand
> Ph +64 09 9257179
> bart.janssen at plantandfood.co.nz
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