<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=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 17, 2021, at 3:42 PM, Chemmama, Ilan <<a href="mailto:Ilan.Chemmama@ucsf.edu" class="">Ilan.Chemmama@ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Hi Eric,</span><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br class=""></div><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">Thank you for the reply. </div><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">I have a couple of follow up questions if I may. </div><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br class=""></div><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">(i) I have run the script you attached but I get a few errors:</div><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br class=""></div><blockquote class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; margin: 0px 0px 0px 40px; border: none; padding: 0px;"><div class="">rot_type=“GLU"</div><div class="">rots=get_rotamers(res, resType=rot_type)</div></blockquote><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br class=""><div class="">gives only two rotamers (`len(rots))`. When I run this on the GUI, I get 54 rotamers which is what I would expect.</div></div></div></blockquote><div><br class=""></div>Well, that's because there's a bug in the example code I sent. Doh. The second line should be:</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>bbdep, rots = get_rotamers(res, resType=rot_type)</div><div><br class=""><blockquote type="cite" class=""><div class=""><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div class=""><br class=""></div><div class="">(ii) I get a Chimera error:</div><div class=""><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;">File "/opt/chimera-1.14-1.fc31/share/chimera/triggerSet.py", line 83, in invoke</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;"> self._funcData, triggerData)</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;"> File "/opt/chimera-1.14-1.fc31/share/chimera/Sequence.py", line 401, in wrapper2</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;"> s._residueCB(a1, a2, a3)</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;"> File "/opt/chimera-1.14-1.fc31/share/chimera/Sequence.py", line 626, in _residueCB</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;"> if res3to1(res.type) != ungapped[pos]:</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;">IndexError: string index out of range</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75); min-height: 20px;"><span class="" style="font-variant-ligatures: no-common-ligatures;"></span><br class=""></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;">Error processing trigger "Residue":</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;">IndexError: string index out of range</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75); min-height: 20px;"><span class="" style="font-variant-ligatures: no-common-ligatures;"></span><br class=""></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;"> File "/opt/chimera-1.14-1.fc31/share/chimera/Sequence.py", line 626, in _residueCB</span></div><div class="" style="margin: 0px; font-stretch: normal; font-size: 18px; line-height: normal; font-family: "Courier New"; background-color: rgba(63, 63, 63, 0.75);"><span class="" style="font-variant-ligatures: no-common-ligatures;"> if res3to1(res.type) != ungapped[pos]:</span></div></div><div class=""><br class=""></div><div class="">I found a workaround in the mean time. </div><div class="">I managed to make Chimera saved all the rotamers in a single PDB file, and an extra character was added to RES_NAME entry in the PDB file to differentiate each rotamer. </div><div class="">Then I just did some file manipulations and split the PDB appropriately. </div></div></div></blockquote><div><br class=""></div>Glad you got something satisfactory to work. :-)</div><div><br class=""></div><div>--Eric</div><div><br class=""><blockquote type="cite" class=""><div class=""><div class="" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div class=""><br class=""></div><div class="">Thanks again ! </div><div class="">Ilan</div></div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 17, 2021, at 2:40 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Ilan,<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>I see that the Dunbrack 2010 rotamer library is now being released under a more permissive license than previously, so this kind of quasi-bulk dumping of library info is probably okay. Nonetheless, since you are using the library so extensively it would be nice of you to register as a library user here if you could:<span class="Apple-converted-space"> </span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__dunbrack.fccc.edu_bbdep2010_&d=DwIFAg&c=iORugZls2LlYyCAZRB3XLg&r=mKSDZidXHAmavIl-Ov-liBnCRR7Q81s96Ue3o_9uiv0&m=WhkU7bXdiTiHIgdIWawwnAeUYVvhC0LnZfTGG8GEpVY&s=S3jcExeF5rf7cB2J3ns5Mwa8Btp-FXWolMsa3v2ysno&e=" class="">https://urldefense.proofpoint.com/v2/url?u=http-3A__dunbrack.fccc.edu_bbdep2010_&d=DwIFAg&c=iORugZls2LlYyCAZRB3XLg&r=mKSDZidXHAmavIl-Ov-liBnCRR7Q81s96Ue3o_9uiv0&m=WhkU7bXdiTiHIgdIWawwnAeUYVvhC0LnZfTGG8GEpVY&s=S3jcExeF5rf7cB2J3ns5Mwa8Btp-FXWolMsa3v2ysno&e=</a><span class="Apple-converted-space"> </span> . And of course if any publication results from it, cite the paper shown in the Rotamers dialog.<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>Okay, that said, you are going to have to use a Python script to do what you want. Assuming you have somehow selected the residue involved, to get all rotamers of LYS for it, the heart of the script would be:<br class=""><br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>from chimera import runCommand as run<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>from Rotamers import getRotamers<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>from chimera import selection<br class=""><br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>rot_type = "LYS"<br class=""><br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>res = selection.currentResidues()[0]<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>rots = getRotamers(res, resType=rot_type)<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>for i in range(len(rots)):<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span><span class="Apple-tab-span" style="white-space: pre;"></span>run("swapaa %s sel criteria %d" % (rot_type, i+1))<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span><span class="Apple-tab-span" style="white-space: pre;"></span>run("write 0 /path/to/save/folder/struct%s%d.%d.pdb" % (rot_type, res.id.position, i+1))<br class=""><br class="">Let me know If you need more help than that.<br class=""><br class="">--Eric<br class=""><br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>Eric Pettersen<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span>UCSF Computer Graphics Lab<br class=""><span class="Apple-tab-span" style="white-space: pre;"></span><br class=""><br class=""><blockquote type="cite" class="">On Feb 16, 2021, at 7:24 PM, Chemmama, Ilan <<a href="mailto:Ilan.Chemmama@ucsf.edu" class="">Ilan.Chemmama@ucsf.edu</a>> wrote:<br class=""><br class="">Dear Developers,<span class="Apple-converted-space"> </span><br class=""><br class="">I am trying to write a PDB for each rotamer in Chimera.<span class="Apple-converted-space"> </span><br class="">I run the command:<span class="Apple-converted-space"> </span><br class="">`swapaa RES :RESNUM lib Dunbrack criteria manual`<br class=""><br class="">I get the enumeration for each rotamers from SCRWL library.<span class="Apple-converted-space"> </span><br class="">I was wondering if there was a way to write each of those rotamers into separate PDB file using a script.<span class="Apple-converted-space"> </span><br class="">Some residues have large number of possible rotamers and manually selecting the rotamer and saving the PDB file is not tractable.<span class="Apple-converted-space"> </span><br class=""><br class="">Thank you very much !<span class="Apple-converted-space"> </span><br class="">Ilan<br class="">_______________________________________________<br class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription:<span class="Apple-converted-space"> </span><a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></blockquote><br class=""></div></div></blockquote></div><br class="" style="caret-color: rgb(0, 0, 0); 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