[Chimera-users] H-bond angle criteria (cut-off)

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 2 16:27:07 PDT 2015

Hi Felipe,
We don’t show the specific angle and distance cutoff values because there are very many different values depending on the donor and acceptor atom types.  As mentioned in the FindHBond documentation (click Help button on dialog or see the copy on our website):


"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). There is an upper bound on distance and one or more angular range criteria for each category of H-bond. It is generally useful to relax the criteria since most structures are not as high-resolution as those used in the survey. User-specified tolerances are added to each criterion's upper bound and/or subtracted from its lower bound (depending on the particular criterion).
When there are no explicit hydrogens on a potential donor atom, FindHBond will use the donor atom type to infer their presence. For functional groups where the hydrogen positions are well-determined by the positions of the nonhydrogen atoms, the H-bonds detected in the presence and absence of explicit hydrogen atoms should be virtually identical. For functional groups where the hydrogen position is not well-determined (such as rotatable hydroxyls), the presence of an explicit hydrogen atom will limit the detected H-bonds to those appropriate for the observed position, instead of all of its possible positions.”

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 Jun 1, 2015, at 1:29 PM, Felipe Vasquez <anfelvas at gmail.com> wrote:

> Hi,
> I am using the H-bond function in UCSF Chimera and I noted that the relaxed parameter for angle criteria is 20 by default. However, since that I have no hydrogen atoms in the pdb structure, I assume that the angle theta (donor-hydrogen-acceptor) cannot be used by Chimera as an angle criteria, and so the psi or phi angles might be used instead. Which angle is actually used in the relaxed parameters? And most important, what is the default value of that angle (angle minus relaxing value)?
> Thanks in advance for your help.
> Best regards,
> Andrés Felipe Vásquez J., BSc, MSc.
> Grupo de Fisiología Molecular
> Subdirección de Investigación Científica y Tecnológica
> Dirección de Investigación en Salud Pública
> Instituto Nacional de Salud
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> +57 (1) 2207700 ext. 1419
> Bogotá, D.C., Colombia 
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