[Chimera-users] hydrogen bond in proteins

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 27 09:34:05 PDT 2010

Hi Atila,
Of course the hydrogen bonds are always to the hydrogen atom  -- the difference is only how the lines are drawn.  Many structures do not include the hydrogens, so it makes sense to draw the line from the donor heavy atom to the acceptor heavy atom.  However, we recently made a change that if your structure does include hydrogens, the lines will be drawn to the hydrogens instead.

This is only in the newest versions, not the 1.4.1 production release.  You would need to get a "daily build" download, Chimera version 1.5, to see this change.

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 Sep 27, 2010, at 7:32 AM, atila petrosian wrote:

> Hi chimera users
> I used (find Hydrogen bonds) option for my pdb file (containing 2 strands of amino acids), but chimera show HBs that being between O and N atoms, while I want to chimera show HBs that being between O and H atoms (usually, in proteins, HB is formed between O atom of C=O group and H atom of N-H group, consequently; C=O…H-N).
> Please guide me.
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