<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><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><br></div><div>Cheers</div><div>Joern</div></body></html>