[chimerax-users] Analysis of the protein-ligand docking results with the X-ray data

[Enrico Martinez]

Dear ChimeraX users!
First, I very much appreciate the support of the Chimera team related
to my questions!

I have another question regarding analysis of the protein ligand
interactions in the docking poses saved in multi-model format. I need
to find a possibility (e.g. via some script that could be executed in
the chimeraX) to compare each docking pose with the X-ray structure
(loaded as the separate model) in order to select automatically the
model (=
docking solution) which may fit better to the X-ray structure. The
problem is that the ligand used in the docking is not the same as in
the X-ray structure (although they are quite similar in the functional
groups).

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 docking ensemble) that has
the closest position of the ligand as in the X-ray structure?
Here is the example of the workflow:

open docking_ensemble.pdb
open xray.pdb
# fit X-ray structure to the first docking solution based on the protein atoms
match #2 to #1.1
# compare each docking pose (ligand with X-ray and determine which
model has the most similarity to it
# determine the model #1.X which would have closest similarity to the
X-ray structure
# close all the models, with the exemption of the model #1.X
close ~ #1.X

I would be grateful for any suggestions for possible algorithms!
With kind regards,
Enrico