[Chimera-users] question regarding UCSF Chimera FindHBond feature

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 25 08:43:55 PST 2021

Hello Aditi Laddha,
There is not one specific distance or angle, instead several different ones depending on the atom types of the acceptor and donor atoms.  This is explained in the help page:


"The geometric criteria are based on a survey of small-molecule crystal structures, as described in

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.

There are many different sets of geometric criteria, corresponding to the many different donor-acceptor combinations (see Tables 5-8 in the reference)."

Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 24, 2021, at 11:59 PM, Aditi Laddha via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I have been using the FindHBond feature of Chimera for finding hydrogen bonds between water molecules and the polypeptide chains. I need to use some specific distance and angle criteria to find H-bonds, so I wanted to ask what is the default distance (D....A) and angle criteria (D-H....A) used in the software to find out the H-bonds, 

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