[chimerax-users] find clash/contacts for protein-ligand complexes

[Enrico Martinez]

Dear ChimeraX users!
I would like to use the "find clash/contacts" command to find if the
position of the ligand (predicted by docking) is in the proximity to
the two residues located in the binding pocket. I have already tried

#check contacts in first 10 docking poses
contacts #1.1-10&protein& :41,49 restrict #1.1-10&ligand interModel
false makePseudobonds false log true intraRes false saveFile
contactsALL_rep$.log

This gives me the output about 84 detected contacts:
 #1.14/? MET 49 CE    #1.14/A UNL 1 C   0.191    3.449
 #1.4/? MET 49 CG     #1.4/A UNL 1 C    0.147    3.613
 #1.7/? HIS 41 NE2    #1.7/A UNL 1 C    0.131    3.389
 #1.10/? MET 49 CE    #1.10/A UNL 1 C   0.120    3.520
 #1.3/? HIS 41 CD2    #1.3/A UNL 1 C    0.095    3.425
 #1.3/? MET 49 CG     #1.3/A UNL 1 C    0.089    3.551
 #1.8/? MET 49 CG     #1.8/A UNL 1 C    0.070    3.510
 #1.5/? MET 49 CG     #1.5/A UNL 1 C    0.023    3.617
 #1.4/? MET 49 CE     #1.4/A UNL 1 C    0.006    3.754
...
 #1.10/? HIS 41 CG    #1.10/A UNL 1 C   -0.377    3.837
 #1.1/? HIS 41 O      #1.1/A UNL 1 C    -0.378    3.618
 #1.14/? HIS 41 CD2   #1.14/A UNL 1 S   -0.382    3.924

may I further limit the number of the detected contacts (e.g. via
modifying geometrical criteria) in order to be able to draw a
conclusion about the proximity of the ligand to the selected residues,
which may be done according to the values in the Overlap  column?
Many thanks in advance!
Enrico