[Chimera-users] Regarding Hydrogen Bond

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 1 08:48:07 PDT 2012

Hi Amit,
You can check between any residues you want.  

With FindHBond, you can select one set of atoms and then choose the option "Only find H-bonds" with at least one end, exactly one end, or both ends selected, or between the selection and a second set of specified atoms.  See the manual:

With Find Clashes/Contacts, you can select one set of atoms, "designate" it, then look for contacts among those atoms, or between those atoms and all other atoms, or between those atoms and a second set of designated atoms.  See the manual:

Both those tools are in the menu under Tools... Structure Analysis. The commands findhbond and findclash have the same capabilities.

Here is information on how to "select" atoms in Chimera:
...and how to specify atoms in the command line:

For example, the following command would select residues 12 and 14-16 in chain A of model 0:

select #0:12.a,14-16.a

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

On Oct 31, 2012, at 11:13 PM, Amit Jaiswal wrote:

> Dear Elaine,
>                  I am stuck with a new problem and that is can I select multiple 
> residues from different chains and check their interaction. There are some results from  Haddock and I want to study the interaction residues from different chains. Is it also possible to know their bonding pattern? Please help me out.

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