Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-18 Thread Spencer Bliven
Thanks for the quick fix! I would love to get a hotfix if possible. The PDBe API is a nice solution. I think that detecting CA traces will fix 90% of the cases. There are still a few edge cases besides CA which don't have a cartoon mode (e.g. 1hzs, which has a polydeoxyribonucleotide polymer type

[PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread Spencer Bliven
We have a pipeline that uses pymol to create images using the headless command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at least) crash if you try to ray-trace an empty viewport. Example: pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray' This particular example only has CA

Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread John Berrisford
Dear Spencer It is possible to work this out using the PDBe API. for our interactive API see: http://www.ebi.ac.uk/pdbe/api/doc/ The molecules url will give you this information: http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q entity 1 has ca_p_only: true, which means cartoon will not

Re: [PyMOL] Pymol crash when raytracing empty graphics

2015-08-17 Thread Thomas Holder
Hi Spencer, Thank you for the bug report. We could reproduce and fix the crash, if you want I can send you a hotfix build. I will also push the fix to the open source SVN repository soon. I second John's suggestions to query the ca_p_only property from the PDBe API. Also, the next PyMOL