[Chimera-users] Loop through hundreds of files and find HBonds

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 13 07:49:52 PDT 2022

Dear Samuel,
First figure out interactively (by typing in the commands) what set of commands you need for each one.  Take a look at "addh" for adding hydrogens and "findhbond" for finding H-bonds.  Of course, you may also need other commands, like "open" "close" "select" etc.  See the commands index and click the links to see the detailed information for each command.

Then here is some basic information on how to use python to loop through several input files, and how to save the log. 

The "findhbond" command also has an option to save information to a file if you wanted a separate output file for each docked ligand file.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 13, 2022, at 5:41 AM, Samuel Kyobe via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Dear Chimera (and ChimeraX) team
> I have run a large docking experiment using several ligands to determine the best binders for further analysis in Molecular Dynamics studies and possible wetlab evaluation.
> I need to find some python example or code snippet capable of looping over hundreds of files and find several .pdb poses from a docking run and find Hydrogen bonds in each one using one receptor. 
> In the process of finding the H bonds, I would like to add Hydrogens, and the protonation state is unspecified. Then at FindHBond, I want to find intermodal Hbonds and write the results to a file.
> Thanks
> Samuel

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