<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Dec 5, 2008, at 4:11 AM, Ahir Utsav Pushpanath wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello. I was wondering whether you could tell me whether there is a graphic/command line option enabling me to create "hydrogen bonds" between my specific residue+ligand only. Or, whether it is possibly to manually draw hydrogen bonds between atoms. In addition, using the FindHbonds tool, is it possible to find H bonds between only ligand + a specific type of residues, for example hydrophobic or valine etc.</div></blockquote><br></div><div>Hi Ahir,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>What I would do if I were you would be to select the residues you care about along with the ligand, then in the FindHBonds tool check the "Only find H-bonds with" box and change the menu to "both ends selected". This will find only H-bonds completely contained in your selection. This may find a few H-bonds you don't want: ones between the non-ligand selected residues, and ones within the ligand itself. You can select the ones you don't want, and bring up the Selection Inspector (by clicking on the green button at the lower right of the main Chimera window) and change "displayed:" to "off". [control-double clicking on an H-bond will also bring up the Selection Inspector for it]<br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Another alternative is to open a second copy of your structure. Select the residues you want in one model and the ligand in the other. Then do the "both ends selected" thing like in the above paragraph, but also change "Find these bonds:" (upper right of the FindHBonds dialog) to "inter-model". Then you will only get H-bonds between your selected residues and the ligand and no extra H-bonds.<br></div><div><br></div><div>--Eric</div><div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br class="Apple-interchange-newline"> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div></div></div><br><div></div></div></body></html>