[chimerax-users] Analysis of Hydrogen bonds in multi-model pdb

[Elaine Meng]

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 at 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