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

[Tamas H. <bio...@gm...>]

Dear Csongor,
cmd select creates a named selection. if you do not use a name, the 
default name "sele" will be used. You see this if you use the gui 
version. Plus: https://pymol.org/dokuwiki/doku.php?id=api:cmd:select 
cmd.select("resi 150-160")

cmd.color("red", "sele")

cmd.select("myselection", "resi 150-160")

cmd.color("red", "myselection")

Bests,

Tamas

On 1/22/25 15:21, Csongor MATYAS via PyMOL-users wrote:
> 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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