<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Feb 2, 2011, at 11:03 AM, Angelica Nakagawa Lima wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi<br><br>I can get the rotamers if I use the graphical version (when I click in tools -> Structure Editing -> rotamers). But I would like to do same thing with the comands. <br>I used the comand swapaa (swapaa ile :10.a) and I write the pdb with the ile's rotamer (the most probable), however I would like to write the pdb file with the second most probable rotamer too.<br> How do I do this?</blockquote><br></div><div>Hi Angelica,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I've implemented an enhancement that will be available in tomorrow's 1.6 daily build that may or may not solve your problem. The change is that if in the swapaa command you specify an integer N as the "criteria" value then the Nth most probable rotamer will be used. So a criteria of 2 will use the second most probable rotamer, 1 will use the most probable (same as 'p'), 14 the 14th most probable, etc. You cannot mix integer criteria with the letter criteria.</div><span class="Apple-tab-span" style="white-space:pre"> </span>So I think this addresses your problem if you wanted to write one file with the most-probable rotamer, and another file with the second-most-probable one. If you wanted to write one file with <i>both</i> rotamers (using alt locs) then this change doesn't help but there may or may not be something I can do about that. -- let me know if that's the case.<div><br></div><div>--Eric</div><br><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br></body></html>