Re: [PyMOL] Anaconda python-bundle package documentation or help

[Norbert S. <st...@bb...>]

Dear Csongor,


as far as I know it is not well documented how you can access the python 
objects and its methods or data structures created by the PyMOL API. For 
many tasks one usually finds some information, often PyMOL or python 
scripts. Concerning your example of the hydrogen bonds determined by the 
distance command, the following python script may provide hints:


https://pymolwiki.org/index.php/Get_raw_distances

and: 
https://pymol-users.narkive.com/zHPUseVG/pymol-is-there-a-way-to-count-hydrogen-bond-interactions

When working with the PyMOL distance command to determine hydrogen bonds 
please note that the algorithm is very generous concerning non-linearity 
of the D-H...A angles if you use the default parameters. In addition, it 
will miss some perfect hydrogen bonds.

See
https://research.uni-leipzig.de/straeter/pymol/pymol_hbond.html
and
https://github.com/schrodinger/pymol-open-source/pull/374

Best wishes,

Norbert

Am 22.01.2025 um 15:21 schrieb Csongor MATYAS via PyMOL-users:
> Hey everyone,
>
> I am trying to use pymol from python to have some repetitive tasks 
> done. I've managed to get some basic functions running but I'm running 
> into walls frequently. I couldn't find a tutorial or documentation 
> about this. Am I missing something? I know it's under development but 
> I would assume that some basic instructions would be available 
> somewhere, otherwise the conda package isn't very useful.
>
> I've managed to sort out the cmd.select() function for example but I 
> can't use the data, there is no object or output. All I can do is to 
> cmd.save() selection into a .pdb file. I've managed to select ligand, 
> and then residues around it, I've also been able to use 
> show_contacts() (from link below) between two selections, but I can't 
> access the pairs that suggest hydrogen bonding, it is only a visual 
> thing. Even from pymol, the software, if I do it manually, I don't 
> know how to save those (unless I save it as a pymol session file that 
> is not human readable).
>
> https://wiki.pymol.org/index.php/Show_contacts
>
> Please, if anyone has advice, anything is appreciated 😄
>
> Csongor
>
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