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

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 9 09:01:25 PDT 2018

Hi Gustavo,
There is a “findhbond” command (or “hbonds”, same thing) that has all the same options as the FindHBond graphical interface.  Use command “help findhbond” to show the manual page for the command and its keywords, or see the same thing on our website here:


Exactly how to give the command depends on all the options you want to use, and just like the dialog there are many possible options.  If you enter just “findhbond” without any options, it will use defaults and all atoms.  Another common use is to select some atoms and then use the command with the “selRestrict” option to find only the hbonds of  those atoms.  The following example includes display options to show all residues that have hbonds and make the lines thicker and color them orange.

findhbond color orange linewidth 3 reveal true

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 1:47 AM, Gustavo Seabra <gustavo.seabra at ufpe.br> wrote:
> Hi all,
> Is there a way to run the Chimera's hydrogen bond counting tool (FindHBond) using the command line only? Could someone post me to the best way?

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