<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="">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 style="font-style: normal;" class="">, </span><i class="">rotamers</i><span style="font-style: normal;" class="">) where </span><i class="">rotamers</i><span style="font-style: normal;" class=""> 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="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 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="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="">Hi,<span class="Apple-converted-space"> </span><br class=""></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 class="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="Apple-converted-space"> </span><br class=""></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 class="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="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);">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="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></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 class="elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><pre class="FluidPluginCopy ContentPasted0"><span class="ContentPasted1 elementToProof" 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="ContentPasted1 elementToProof" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><div class=""><div id="Signature" class=""><div class=""><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Noé Robert,</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Fifth-year student in bioengineering, minor in Bioinformatics and Modelling, at engineering school Polytech Nice Sophia, France</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class="">Phone : +33 7 81 00 52 02</div><div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;" class=""><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="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=""><br class=""></span></div><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><br 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; 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