[Chimera-users] Listing hydrogen bond geometries

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 13 16:51:07 PDT 2011

Hi Greg,
You can measure angles with the angle command or Angles/Torsions (under Tools... Structure Analysis).

However, as for automatically extruding the relevant angles for hydrogen bonds...
It can become quite hairy because several different angles are examined per possible H-bond depending on the donor and acceptor types, as detailed in the figures and tables of 

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


Maybe you meant only the D-H-A angle if your structure has hydrogens, which would be a more tractable data dump.  Is that what you wanted?  Let us know, someone may be able to provide the needed python or tips toward writing that code.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 13, 2011, at 3:32 PM, Greg Friedland wrote:

> Hello,
> I would like to list the hydrogen bond geometries between two models. I have found the feature to do this in the FindHBond panel but it only lists the distances not the angles. This information appears to be used in identifying the hydrogen bonds however, so is it possible to extract this information as well? If not, can you suggest another tool that could do this?
> Thanks,
> Greg

More information about the Chimera-users mailing list