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

[Elaine Meng]

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
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html>
e.g. like this user posted
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-February/002359.html>

Here is information on how to run Chimera commands and save Reply Log contents in a python script.
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

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 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,