[Chimera-users] Export Pov-Ray file with a python script.

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 23 13:02:18 PDT 2014


Hi Javier,
I don't have an answer for your specific issue, but while others look at that, a few thoughts...

You might also want to hide any atoms/bonds that are displayed (e.g. command: ~disp #0 ).  Personally, I have better success making nice images directly in Chimera than via its export to raytracing option.  If the main reason you're doing it is to get shadows and/or smoother-looking objects, you might try commands something like:

set shadows
setattr s density 8
set subdivision 10

However, I understand you may have other reasons for wanting povray files.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 23, 2014, at 12:48 PM, jiserte at unq.edu.ar wrote:

> I'm writing a small python script to generate Pov-Ray with chimera. The script loads a pdb file containing a protein and a ligand, modifies the protein view to ribbon and the ligand to surface. Then exports the .pov file. However the image created by Pov-Ray shows only the surface of ligand.
> 
> The image is shown correctly in the chimera GUI. If I run the commands one by one in the chimera command line, the .pov file generated is ok.
> 
> The script is:
> -----------------------------------------
> import chimera
> from chimera import runCommand
> runCommand('windowsize 800 600')
> runCommand('open ../../kinase.domain.2/A.4K9Y.pdb')
> runCommand('ribbon #0')
> runCommand('surf ligand')
> runCommand('export test.pov')
> ------------------------------------------
> 
> After running the script the ReplyLog contains:
> 
> -----------------------------------------
> A.4K9Y.pdb opened
> /opt/UCSF/Chimera64-1.7/bin/mscalc 1.400000 2.000000 1
> MSMSLIB 1.3 started on hamal
> Copyright M.F. Sanner (March 2000)
> Compilation flags
> 
> Surface A.4K9Y.pdb, category ligand, probe radius 1.4, vertex density 2
>  1 connected surface components
>  Total solvent excluded surface area = 436.845
>  Total solvent accessible surface area = 772.871
> -----------------------------------------
> 
> Javier Iserte




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