<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Dec 29, 2009, at 1:01 PM, Ravinder Abrol wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="font-family: monospace; ">We have Chimera installed and I hadn't thought of using<span class="Apple-converted-space"> </span><br>it to add hydrogens. I just tried it and it worked.<br>We have many pdbs that we need to run this on, so I found a --nogui mode in<span class="Apple-converted-space"> </span><br>chimera. I tried using this to load a pdb and added hydrogens to waters<span class="Apple-converted-space"> </span><br>using:<br>addh hbond true spec :hoh<br>but this command adds hydrogens to many of my Histidines also, which I don't<span class="Apple-converted-space"> </span><br>want. Seems like spec option is not working? Do you know a way around this?</span></span></blockquote><br></div><div>Hi Ravi,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>The "spec" argument to addh only specifies models. addh will always add hydrogens to the entire model(s) specified. To protonate water and yet preserve current histidine protonation you will have to get tricky. Namely, change the name of delta-protonated histidines to HID, epsilon-protonated to HIE, and doubly-protonated to HIP, then use "useHisName true" in the addh command. You can script this as:</div><div><br></div><div>setattr r type HID :HIS@hd1,dd1,td1 #handle deuterium/tritium as well</div><div>setattr r type HIP :HID@he2,de2,te2</div><div>setattr r type HIE :HIS</div><div>addh useHisName true [+ any other args you want]</div><div>setattr r type HIS :HIE:HIP:HID # set residue name back to HIS</div><div>write [your args]</div><div><br></div><div>--Eric</div><div><br></div><div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><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; "> 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><br class="Apple-interchange-newline"></div></span></div><br><div></div></div></body></html>