Re: [PyMOL] Analysis of docking results in multi-model format

[Joel T. <joe...@ot...>]

Hi Enrico,

Which docking protocol are you using as this may already have RMSD to a reference ligand and presentation of best poses (based on scoring)

Joel

-----Original Message-----
From: Enrico Martinez <jms...@gm...> 
Sent: Friday, 25 March 2022 2:11 AM
To: pymol-users <pym...@li...>
Subject: [PyMOL] Analysis of docking results in multi-model format

Dear Pymol Users!
I am dealing with the analysis of the results of protein-ligand docking poses representing the multi-model pdb.  I need to find a possibility (e.g. via some script that could be executed in the pymol) to compare each docking pose with the X-ray structure (loaded as the separate model in pymol) in order to find automatically the model (= docking solution) which may fit better to it (e.g. via estimating RMSD of some part of the ligand in each docking solution compared to the X-ray structure).

Assuming that the both pdbs ((docking poses, and X-ray structure)) have been superimposed (based on the protein atoms) how could I automatically switch to the model (in the ensemble) with the identical position of the ligand as in the X-ray structure?  I would be grateful for any suggestions With kind regards, Enrico


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