<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="">Hi Noé,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The numeric criteria cannot be mixed with any of the other criteria and simply picks the Nth most probable rotamer (based on its prevalence in all proteins). It cannot be used to pick the 3rd-least clashes, etc. If you really want to do that you would have to resort to using Python.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The rotamers you get from chimera.Rotamers.getRotamers() only have their probability attribute (rotamerProb) assigned, since the clashes and H-bonds take time to compute and may not be needed, depending on what the user requested. To assign clash score and number-of-H-bonds attributes (clashScore and numHbonds respectively) you would need to call chimera.Rotamers.processClashes()/processHbonds(). You should look at the part of the chimera.Rotamers.useBestRotamers() function that calls those routines to see what you need to do.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 3, 2023, at 10:08 AM, Noe Robert via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="elementToProof" 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;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Thank you for answering this side of my question, I now have a small deviation to tak</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">e in my approach thanks to<span class="Apple-converted-space"> </span></span><span class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><font class="FluidPluginCopy" size="2"><span class="ContentPasted0" style="font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif; background-color: rgb(255, 255, 255);">Elaine C. Meng</span></font><span class="Apple-converted-space"> </span>who clarified to me the value on the probability parameter.<span class="Apple-converted-space"> </span><br class="">Have a great day,</span></div><div class="elementToProof" 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;"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);" class="">Robert Noé<br class=""></span></div><div id="appendonsend" 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=""></div><hr tabindex="-1" 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; display: inline-block; width: 483.125px;" 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=""></span><div id="divRplyFwdMsg" dir="ltr" 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=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">De :</b><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Envoyé :</b><span class="Apple-converted-space"> </span>mardi 3 janvier 2023 18:26<br class=""><b class="">À :</b><span class="Apple-converted-space"> </span>Noe Robert <<a href="mailto:noe.robert@etu.univ-cotedazur.fr" class="">noe.robert@etu.univ-cotedazur.fr</a>><br class=""><b class="">Cc :</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Objet :</b><span class="Apple-converted-space"> </span>Re: [Chimera-users] Question concerning rotamer choosing</font><div class=""> </div></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; word-wrap: break-word; line-break: after-white-space;">To answer the Python side of this, chimera.Rotamers.getRotamers(<i class="">residue</i>) gets a list of rotamers (really Molecule instances) for that residue (Dunbrack library by default). Each of those Molecule instances has a 'rotamerProb' attribute, which is the value you see in the graphical user interface. You apply the rotamer you want by calling chimera.Rotamers.useRotamer(<i class="">residue</i><span class="" style="font-style: normal;">,<span class="Apple-converted-space"> </span></span><i class="">rotamers</i><span class="" style="font-style: normal;">) where<span class="Apple-converted-space"> </span></span><i class="">rotamers</i><span class="" style="font-style: normal;"> is a list of rotamers to apply, probably just one (at a time) in your case because if you supply multiple rotamers then they will all be used by putting each one in a different alternate location.</span><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>Eric Pettersen</div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jan 2, 2023, at 6:26 AM, Noe Robert via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="x_Apple-interchange-newline"><div class=""><div class="x_elementToProof" style="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; text-decoration: none;"><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">Hi,<span class="x_Apple-converted-space"> </span><br class=""></span></div><div class="x_elementToProof" style="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; text-decoration: none;"><span class="x_elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">I'm currently trying to write a python script which automatizes mutageneses on Chimera 1.16, and calculates clashes inducted by the change of amino acid through a local minimization (which explains why I'm using Chimera instead of ChimeraX).<span class="x_Apple-converted-space"> </span><br class=""></span></div><div class="x_elementToProof" style="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; text-decoration: none;"><span class="x_elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">I would like to choose which rotamer to use depending on their probability from the rotamer library Dunbrack (for instance, when probability is >0.1), which<span class="x_Apple-converted-space"> </span></span><span class="x_elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">is visible on the "Rotamers graphical user interface". Is there a way to extract these probability values using a script, in order to run it on a certain number of rotamers ? That way it would be quite automated.</span><span class="x_elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></span></div><div class="x_elementToProof" style="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; text-decoration: none;"><span class="x_elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><pre class="x_FluidPluginCopy x_ContentPasted0"><span class="x_elementToProof x_ContentPasted1" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">On Jul 1, 2015, Eric Pettersen advised to modify the "Python script that uses the functions in the Rotamers module" (<a href="https://www.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011193.html" title="https://www.cgl.ucsf.edu/pipermail/chimera-users/2015-July/011193.html" data-loopstyle="link" id="LPlnk716302" class="">here</a>), but I don't which one it is.<br class=""><br class="">Thank you,<br class=""><br class=""></span><span class="x_elementToProof x_ContentPasted1" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><div class=""><div id="x_Signature" class=""><div class=""><div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Noé Robert,</div><div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France</div><div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Phone : +33 7 81 00 52 02</div><div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;"><i class="">"let's limit the use of our resources and lighten our mails"</i><br class=""></div></div></div></div></span></pre><br class=""></span></div><div class="x_elementToProof" style="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; text-decoration: none;"><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></span></div><span class="" style="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; text-decoration: none; float: none; display: inline !important;">_______________________________________________</span><br class="" style="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; text-decoration: none;"><span class="" style="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; text-decoration: none; float: none; display: inline !important;">Chimera-users mailing list:<span class="x_Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="" style="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;">Chimera-users@cgl.ucsf.edu</a><br class="" style="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; text-decoration: none;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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