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. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> Then here is some basic information on how to use python to loop through several input files, and how to save the log. <https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> 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 ----- 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@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