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<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);">Hi,
<br>
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<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0">I would like to come back to this answer from M. Pettersen :<br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0"><i>"To answer the Python side of this, chimera.Rotamers.getRotamers(<span class="FluidPluginCopy ContentPasted0">residue</span>)
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.</i>"<br>
</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0">As I'm not used to this scale of Chimera use, I don't know how to
run getRotamers on the specific residue I want and I'm having quite a hard time exploring python scripts refering to getRotamers. I would just need to run this function to get the
<span style="font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0 FluidPluginCopy">
<i class="ContentPasted1">'rotamerProb' </i><span class="ContentPasted1">attribute</span></span> of each rotamer, the rest would be performed using commands.
<br>
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<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0">So I would like to know what would be the code line to have getRotamers
returning "mols" on a specific residue, for instance ":3.a"</span></div>
<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="ContentPasted0">Thank you a lot and have a great weekend !<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Envoyé :</b> mardi 3 janvier 2023 18:26<br>
<b>À :</b> Noe Robert <noe.robert@etu.univ-cotedazur.fr><br>
<b>Cc :</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Objet :</b> Re: [Chimera-users] Question concerning rotamer choosing</font>
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<div class="" style="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><i class="">rotamers</i><span class="" style="font-style:normal">) where </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>
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<div class="">--Eric</div>
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<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>
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<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>
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<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="">
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<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="">
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<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="">
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<pre class="x_FluidPluginCopy x_ContentPasted0"><span class="x_ContentPasted1 x_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="x_ContentPasted1 x_elementToProof" 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>
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<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; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; 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">
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