[Chimera-users] Chimera's hydrogen bond counting tool (FindHBond) from command-line?

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 9 10:05:31 PDT 2018

Hi Gustavo,
Ah yes, my answer was for the Chimera command line.  For the system command line, you can run Chimera in nogui mode with input python or chimera-command scripts. You could run findhbond with a chimera-command script, but you probably want to use a python script instead to also save the contents of the Reply Log to a file.

To run in nogui mode you use the “nogui” startup option
e.g. like this user posted

Here is information on how to run Chimera commands and save Reply Log contents in a python script.

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

> On Apr 9, 2018, at 9:50 AM, Gustavo Seabra <gustavo.seabra at ufpe.br> wrote:
> Hi Elaine,
> Thank you very much. However, it seems to me that the example you sent is supposed to be used in Chimera's command line, right?
> I was actually looking for a command I could issue from a shell command line, e.g. from bash, to create the list of hbonds without the need to start the GUI.
> Is there a way to do that?
> (More precisely, I want to use this command in a pipeline, using KNIME command line node to call it, and then treat the output in sequence.)
> Thanks,

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