[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.
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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