[Chimera-users] Listing hydrogen bond geometries
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
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).
> 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:
>> 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?
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