[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:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

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:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

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:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html>
...and how to specify atoms in the command line:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

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
-----
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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