[Chimera-users] Listing hydrogen bond geometries

Eric Pettersen pett at cgl.ucsf.edu
Thu Jul 14 17:34:22 PDT 2011

Did he reply to you as to whether he just wanted D-H-A angles or the  
whole tamale?


On Jul 13, 2011, at 4:51 PM, Elaine Meng wrote:

> Hi Greg,
> You can measure angles with the angle command or Angles/Torsions  
> (under Tools... Structure Analysis).
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#angles 
> >
> 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
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria 
> >
> 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.
> Best,
> Elaine
> ----------
> 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
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