[Chimera-users] Relax H-bond constraints

Joern Lenz lenz.joern at googlemail.com
Fri Oct 15 01:54:38 PDT 2010

Dear Elaine,

many thanks for the quick answer.


Am 14.10.2010 um 17:44 schrieb Elaine Meng:

> Hi Joern,
> From that same 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). 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. "
> The "relaxation" or more accurately, addition of tolerance values to the strict values, is purely empirical and based on our own observations of structures from the PDB.  For example, if a structure has a beta-sheet assignment, you would expect to see the regular pattern of H-bonds connecting the strands.  Also, one would expect needing looser tolerances for the PDB because it contains many structures at lower resolution than the small molecules from the Cambridge database used by Mills & Dean.
> There is no publication describing the investigation of tolerance values.   However, we made it user-controlled so that you can use whatever tolerances you want, including zero.
> I hope this helps,
> 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 Oct 14, 2010, at 8:13 AM, Joern Lenz wrote:
>> Hi,
>> I used the automated H-bond detection of Chimera to detect H-bonds between an target protein and its docked lignds.
>> On your webpages (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html) I found the following:
>> "[...] Relax H-bond constraints indicates that tolerances to Relax constraints by should be applied to the precise geometric criteria [...]; empirically, tolerances of 0.4 angstroms and 20.0 degrees work well for most macromolecular structures."  
>> Can you lease tell me if there is a literature which discusses this relaxation in more detail and can be referenced
>> Many thanks for a reply.
>> Cheers
>> Joern

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