[Chimera-users] Automating H bond distance retrieval

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 1 16:11:02 PDT 2018

Hi Samuel,
The “hbonds” command has options to save information including the distances to text file and/or to the Reply Log (which you can show ifrom the Favorites menu).

If manually saving Reply Log (click its Save button) is not practical in your situation, like you are going through a lot of structures, see this explanation of how to script the processing of multiple structures.  Such a script could also be used to generate different hbond output filenames for each input structure, or if you just save all the results in one long Reply Log instead of output files, this page also explains how to save Reply Log contents with Python.  (There is no Chimera command to do it).

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

> On Nov 1, 2018, at 9:58 AM, Samuel FreemanFox <Samuel.FreemanFox at portonbiopharma.com> wrote:
> Hi, 
> I was wondering about the possibility of writing a setup.com file which is capable of opening a receptor.pdb and ligand.pdb file, locating the H-bonds between these two structures and then reporting back the lengths of the bonds?
> Currently I am able to open both files, execute addh, addcharge, and hbonds with my setup.com file. However I am unsure of how to proceed from there.
> Many thanks and I look forward to your response.
> Samuel Freeman-Fox

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