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

[Jared S. <jar...@co...>]

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 (tho...@sc...) wrote:

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,  
Thomas  


> On Mar 29, 2018, at 9:54 PM, Gary Oberbrunner <ga...@da...> wrote:  
>  
> Thanks for the idea Jared, but no, still nothing but atoms.  
>  
> On Thu, Mar 29, 2018 at 3:31 PM, Jared Sampson <jar...@co...> wrote:  
> 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 (ga...@da...) wrote:  
>  
>> 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 graphics objects as well if that's possible. Any hints?  
>>  
>>  
>> --  
>> Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.  

--  
Thomas Holder  
PyMOL Principal Developer  
Schrödinger, Inc.