[Chimera-users] hydrogen bonds in Chimera

[Kenward Vaughan]

On Wed, 9 May 2012 07:47:19 -0500
"Beale, John" <John.Beale at stlcop.edu> wrote:

> 
> I have a model of a ligand docked in the active site of a receptor
> protein. I want to visualize only the hydrogen bonds between ligand
> and receptor- not for the entire protein. Is this possible in Chimera?
> 
> John
> 
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy

Hi John,

Exposing those interactions is pretty straightforward.  Select the
ligand itself, then go to Tools > Structure Analysis > FindHBonds. In
the dialog that opens up, you will want to check the box "Only find
H-bonds" and select from the dropdown menu "with exactly one end
selected."

You can adjust the parameters in the top area to suit your taste.  

Clicking on Apply or OK will then get the results!

You may want to consider narrowing down your field of view as well,
using the Select Zone tool to remove atoms/residues outside a certain
distance from the ligand itself.


Kenward
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