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@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