<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Gustavo,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>When defining hydrogen bonds, there are atoms that are clearly good donors or acceptors, and then there are others that could be considered very weak donors or acceptors (<i class="">e.g.</i> some forms of carbon as a donor). Neutral <i class="">sp3</i> sulfur as an acceptor is also such as case. As per <b class="">Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins</b> (<a href="https://doi.org/10.1002/prot.22327" class="">https://doi.org/10.1002/prot.22327</a>):</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>"<i class="">It is revealed that sulfur atom is a very poor H‐bond acceptor, but a moderately good H‐bond donor</i>.”</div><div class=""><br class=""></div><div class="">We have chosen not to include very weak donors and acceptors in Chimera’s detection of hydrogen bonds. Nonetheless, if you wish to have Chimera treat neutral <i class="">sp3</i> sulfur as an acceptor, this can be accomplished with a fairly simple edit of Chimera’s code. Namely edit the file <i class=""><your Chimera></i>/share/FindHBond/base.py and find the lines that look like this (should be lines 404 and 405):</div><div class=""><br class=""></div><div class=""> genericAccInfo['Sar'] = genericAccInfo['S3-'] = (accGeneric,<br class=""> _processArgTuple([3.83, 85], distSlop, angleSlop))</div><div class=""><br class=""></div><div class="">Below them, add two more lines for the neutral <i class="">sp3</i> sulfur acceptor:</div><div class=""><br class=""></div><div class=""> genericAccInfo['S3'] = (accGeneric,<br class=""> _processArgTuple([3.83, 89], distSlop, angleSlop))</div><div class=""><br class=""></div><div class="">Maintain the indentation level; indentation is significant in the Python language. If you are using a Mac, then <i class=""><your Chimera></i> is Chimera.app/Contents/Resources. With those two lines added, Chimera finds two hydrogen bonds involving the sulfur.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 11, 2018, at 2:30 PM, Gustavo Seabra <<a href="mailto:gustavo.seabra@ufpe.br" class="">gustavo.seabra@ufpe.br</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi there,<br class=""><br class="">I’m trying to use the findHBond tool to count Hbonds in a system. However, I noticed ti does not find any HB involving sulfur atoms in my system.<br class=""><br class="">I’ve put together a simple example system here to show what I mean. After opening the files, I do:<br class=""><br class="">1. Select the ligand (Select > Residue > LIG)<br class="">2. Tools > Surface/Binding Analysis > FindHBonds<br class="">3. Find These Bonds: Both<br class="">4. Relax H-bond constraints: (I tried even relaxing to 1A and 30deg, with no change)<br class="">5. Select “Only find H-bonds with at least one end selected”<br class="">6. Hit Apply.<br class=""><br class="">Chimera does find some HBonds involving nitrogen and oxygen, but no HBond is found involving the sulfur atom on the ligand, even though there is a serine (Ser525) close enough to make a HBond to the ligand S atom.<br class=""><br class="">So, I wonder what I am doing wrong here? Am I skipping any steps? I have checked in a different program (PoseView) and it can find the bond with no problem.<br class=""><br class="">Thank you very much,<br class=""><br class="">--<br class="">Gustavo Seabra<br class=""><span id="cid:25D8EAFC-BCB5-47AA-BE40-A54C3DA28453@gateway.sonic.net"><6MMPr_1.mol2></span><span id="cid:0047E60E-8513-45A8-9D05-B4DC5E459496@gateway.sonic.net"><receptor.pdb></span><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>