[Chimera-users] FindHBond

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 14 17:17:07 PST 2009

Hi Greg,
There are many different distance and angle criteria depending on the  
different donor and acceptor atom types.  These cutoffs are in tables  
5-8 of the reference cited in the page you were viewing:

Three-dimensional hydrogen-bond geometry and probability information  
from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996  


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 Dec 14, 2009, at 4:32 PM, Greg Friedland wrote:

> Also, I'm curious what cutoffs are used. I looked at http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria 
>  but I was hoping for more details. I.e what numbers from the paper  
> are used for the proton-acceptor distances, donor-proton-acceptor  
> angle and the corresponding dihedral angle.

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