<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Clarisse,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>While it is theoretically possible to add methyl groups as donors in Chimera, it is by no means easy. Firstly, you’d have to come up with geometric criteria as per the source Chimera uses:<div class=""><br class=""></div><div class=""><a href="http://www.ncbi.nlm.nih.gov/pubmed/9007693" target="_blank" style="font-family: -webkit-standard;" class="">Three-dimensional hydrogen-bond geometry and probability information from a crystal survey.</a><span style="font-family: -webkit-standard; font-size: medium;" class=""> Mills JE, Dean PM. </span><i style="font-family: -webkit-standard;" class="">J Comput Aided Mol Des.</i><span style="font-family: -webkit-standard; font-size: medium;" class=""> 1996 Dec;10(6):607-22.</span></div><div class=""><span style="font-family: -webkit-standard; font-size: medium;" class=""><br class=""></span></div><div class="">Then you would have to modify the FindHBond module to add methyl donors and their geometry criteria. The learning curve would be steep.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Since you have explicit hydrogens on your structures, a simpler alternative that may be good enough is to use the Find Clashes/Contacts tool to find “contacts” between methyl hydrogens and hydroxyl oxygens. Just run the tool, select methyl hydrogens (e.g. “sel methyl & H”), designate them as a set to check, select the hydroxyl oxygens (“sel hydroxyl & O”), designate them as the second set, set checking to be between the two sets, then perhaps check contacts using the default parameters, or whatever parameters you felt were appropriate.</div></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>BTW, you have to get tomorrow’s build to have the “methyl & H” thing work, because there was a bug where “methyl” only selected the methyl carbon.</div><div class=""><br class=""></div><div class="">—Eric</div><br class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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=""><br class=""></div></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
</div>
<br class=""></body></html>