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
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
Hi again, Joe -
Try saving in COLLADAhttp://www.pymolwiki.org/index.php/COLLADA format with
`save myfile.dae` (in PyMOL v1.7.3.2 or later).
If you're using Blender, you'll need to `set collada_geometry_mode, 1`, because
Blender only supports polylists for COLLADA import, and not the more
Hi Joe -
The coordinate system in the .obj file is in camera space, where (0,0,0) is the
center of the viewport, positive x to the right, positive y up, and positive z
out of the screen toward the viewer. If you want to correlate them, you would
need to transform the model coordinates using
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
