[Chimera-users] hydrogen bonds in Chimera

Kenward Vaughan kay_jay at earthlink.net
Wed May 9 08:58:44 PDT 2012

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

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.

In a completely rational society, the best of us would aspire to be 
_teachers_ and the rest of us would have to settle for something less, 
because passing civilization along from one generation to the next 
ought to be the highest honor and the highest responsibility anyone 
could have.     - Lee Iacocca

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