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

jiserte at unq.edu.ar jiserte at unq.edu.ar
Wed Apr 23 12:48:02 PDT 2014

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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