Re: [PyMOL] how to get session to include CGO graphics objs?

Ah, thanks for the correction, Thomas.  I didn't realize the behavior was different between the command and Python function.  I guess I should have looked into it further and not just emailed from my phone! Cheers, Jared On March 29, 2018 at 6:58:41 PM, Thomas Holder

Re: [PyMOL] how to get session to include CGO graphics objs?

Hi Gary & Jared, PyMOL session files do not contain any graphics geometry. Export as COLLADA or VRML are the best options. The cmd.fetch() function is not asynchronous by default, only the fetch command is. This is controlled by the quiet=0 argument which is passed to all commands. Cheers,

Re: [PyMOL] how to get session to include CGO graphics objs?

Thanks for the idea Jared, but no, still nothing but atoms. On Thu, Mar 29, 2018 at 3:31 PM, Jared Sampson wrote: > Hi Gary - > > `cmd.fetch()` runs asynchronously by default, meaning `cmd.show()` might > execute before the structure is actually loaded. Try amending

Re: [PyMOL] how to get session to include CGO graphics objs?

Hi Gary -  `cmd.fetch()` runs asynchronously by default, meaning `cmd.show()` might execute before the structure is actually loaded.  Try amending to: cmd.fetch(mol_id, async=0) Does that make a difference? Cheers, Jared On March 29, 2018 at 2:18:29 PM, Gary Oberbrunner

[PyMOL] how to get session to include CGO graphics objs?

I'm running pymol "headless" in a script. After initializing pymol and calling finish_loading(), I do this: cmd.fetch(mol_id) cmd.show('spheres','all') session = cmd.get_session() ... but my session object only includes one object, the cObjectMolecule. I'm looking for it to include the