Analysis of Hydrogen bonds in multi-model pdb
Dear ChimeraX users! Another question related to the analysis of the multi-model pdb obtained from protein-ligand docking calculations. I am using ChimeraX to visualise protein-ligand interactions between each pose predicted by docking and protein in my script: # calculate H-bond in first 10 frames of the multi-model pdb hbonds #1.1-10&protein restrict #1.1-${hb_poses}&ligand coordsets false interModel false makePseudobonds false log true intraRes false saveFile output.log Is it possible to print (or save somewhere?) the number of the state that has 1) the maximal number of the hydrogen bonds? 2) has a particular hydrogen bond of my interest? Cheers, Enrico
Hello, ChimeraX doesn't have options for those specific tasks -- instead you would need to write your own script(s) to post-process the output log file. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:49 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users! Another question related to the analysis of the multi-model pdb obtained from protein-ligand docking calculations. I am using ChimeraX to visualise protein-ligand interactions between each pose predicted by docking and protein in my script:
# calculate H-bond in first 10 frames of the multi-model pdb hbonds #1.1-10&protein restrict #1.1-${hb_poses}&ligand coordsets false interModel false makePseudobonds false log true intraRes false saveFile output.log
Is it possible to print (or save somewhere?) the number of the state that has 1) the maximal number of the hydrogen bonds? 2) has a particular hydrogen bond of my interest? Cheers, Enrico
Right, thank you very much Elaine! Cheers, Enrico чт, 31 мар. 2022 г. в 18:29, Elaine Meng <meng@cgl.ucsf.edu>:
Hello, ChimeraX doesn't have options for those specific tasks -- instead you would need to write your own script(s) to post-process the output log file. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 31, 2022, at 2:49 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users! Another question related to the analysis of the multi-model pdb obtained from protein-ligand docking calculations. I am using ChimeraX to visualise protein-ligand interactions between each pose predicted by docking and protein in my script:
# calculate H-bond in first 10 frames of the multi-model pdb hbonds #1.1-10&protein restrict #1.1-${hb_poses}&ligand coordsets false interModel false makePseudobonds false log true intraRes false saveFile output.log
Is it possible to print (or save somewhere?) the number of the state that has 1) the maximal number of the hydrogen bonds? 2) has a particular hydrogen bond of my interest? Cheers, Enrico
participants (2)
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Elaine Meng -
Enrico Martinez