find clash/contacts for protein-ligand complexes
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
Hello, Of course you can change the overlap and/or distance criteria. There is an "overlapCutoff" command option, or if you just want to ignore overlap and use the center-center distance as your criterion instead, see the "distanceOnly" option instead. These are all described in the "contacts" command help. Use command "help contacts" or see the copy at our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html#options> Or, you can use cutoff values that find more contacts than you want, and then postprocess the results from the Log or in your saved files to extract only the rows that meet whatever criteria you have in mind at the moment. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 21, 2022, at 4:22 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Elaine Meng -
Enrico Martinez