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

Greg Couch gregc at cgl.ucsf.edu
Wed Apr 23 13:27:49 PDT 2014


So the trick is to do insert:

     runCommand('wait 1')

before doing the export.  That causes chimera to display the image 
before doing the export.  And that is needed because the ribbon is not 
generated until it is displayed.

     HTH,

     Greg

P.S.  The POV-Ray output in the 1.9 candidate release (and the daily 
builds) has been modified to work with the new parallel POV-Ray 3.7.  So 
if you are using POV-Ray, I would recommend installing the 3.7 version 
and then change the POV-Ray executable in the POV-Ray Options preference 
to use your installed POV-Ray instead of Chimera's built-in version.

On 04/23/2014 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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