<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Joern,<div>From that same page,</div><div><br></div><div>"The geometric criteria are based on a survey of small molecule
crystal structures, as described in<blockquote>
<a href="http://www.ncbi.nlm.nih.gov/pubmed/9007693" target="_blank">
Three-dimensional hydrogen-bond geometry and probability information
from a crystal survey.</a>
Mills JE, Dean PM.
<i>J Comput Aided Mol Des.</i> 1996 Dec;10(6):607-22.
</blockquote>
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. "</div><div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>I hope this helps,</div><div>Elaine</div><div><div>
<div><div>----------</div><div>Elaine C. Meng, Ph.D. </div><div>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</div><div>Department of Pharmaceutical Chemistry</div><div>University of California, San Francisco</div><div><br></div></div></div><div><div>On Oct 14, 2010, at 8:13 AM, Joern Lenz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div>I used the automated H-bond detection of Chimera to detect H-bonds between an target protein and its docked lignds.</div><div>On your webpages (<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html</a>) I found the following:</div><div><br></div><div><a name="tolerances"><b>"[...] Relax H-bond constraints</b></a> indicates that tolerances to
<b>Relax constraints by</b> should be applied to the precise
<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria">geometric criteria</a> [...];
empirically, tolerances of <b>0.4 angstroms</b> and <b>20.0 degrees</b>
work well for most macromolecular structures." </div><div><br></div><div>Can you lease tell me if there is a literature which discusses this relaxation in more detail and can be referenced</div><div>Many thanks for a reply.</div><div>Cheers</div><div>Joern</div></div></blockquote></div><br></div></div></body></html>