Re: [PyMOL] How to delete/hide unwanted poses in Pymol?

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

Hi Luigi,

that depends on how the data are read into PyMOL and how the coordinate 
files are structured.

For example, if you read in a pdb file ligand1.pdb, which contains this 
ligand with different poses having different residue numbers and next 
you read in a second pdb file for the second ligand, it may work as follows:

load ligand1.pdb
load ligand2.pdb
# delete the unwanted poses
remove not ((ligand1 and resid 3) or (ligand2 and resid 8))
show sticks

or

load ligand1.pdb
load ligand2.pdb
hide everything
# show only the desired poses
show sticks, (ligand1 and resid 3) or (ligand2 and resid 8)

If you need to do this repeatedly with many poses, a convenient way 
would be to write a script that generates objects for each ligand/pose 
and you can toogle them visible via the menu on the right side of the 
PyMOL interface (commands enable and disable).

If you coordinate files are structured in a different way or if all data 
are in one coordinate file, modifications may be necessary. Perhaps you 
need to distinguish the ligands and poses based on residue names (resn) 
and numbers (resi). Google for "pymol selection algebra" and commands 
show, hide, remove, enable, disable.

With more sophisticated script programming, one may automatically 
generate different objects for each pose read from a pdb file.

Best,

Norbert

Am 09.11.2023 um 11:41 schrieb Luigi Marongiu, PhD via PyMOL-users:
> Hello,
> I have several poses from a docking to a protein and I have different 
> ligands to compare.
> I can load on PyMol the different ligands on a same protein file, and 
> I can look at each pose for the different ligands but only, let's say, 
> in sync: pose 1 of ligand 1 together with pose 1 of ligand 2; pose 2 
> of ligand 1 together with pose 2 of ligand 2; and so forth.
> Let's say that I am interested in comparing pose 3 of ligand 1 and 
> pose 8 of ligand 2.
> How can I hide or delete the unwanted poses?
> Thank you.
>
>
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