<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,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I don’t know how familiar you are with Chimera programming, but I’m going to assume you have a residue you want to add the rotamers to in a Python variable named <i class="">r</i>. If so, the code to add all its rotamers as altlocs is:</div><div class=""><br class=""></div><div class=""><i class="">from Rotamers import useRotamer, getRotamers</i></div><div class=""><i class="">useRotamer(r, getRotamers(r)[1], retain=[‘’])</i></div><div class=""><br class=""></div><div class="">The <i class="">retain=[‘’]</i> argument will cause the original sidechain position to be retained (assuming it itself is not an altloc). If you need help finding the residues you want to work on in Python, let me know.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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>
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<div><br class=""><blockquote type="cite" class=""><div class="">On Jun 27, 2018, at 10:42 AM, Ahir Pushpanath <<a href="mailto:ahir29@gmail.com" class="">ahir29@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear Chimera Team/Users,<div class=""> I wanted to write a python script within chimera that aims to essentially print out a contact map of a selected chunk of residues on an open structure. However, before doing so, I wondered if there is any programmatic way to generate the rotamer library at every position (i.e when you open up the rotamer tool, you get an option of 5-6 conformations you can pick for a residue), I wanted to generate that for every residue in the protein programmatically (and save every rotamer possibility) (as an altlocation?) in the crystal structure. Only after that do I want to calculate the contact map, in essence, I am trying to be as expansive as possible for each residue's "possible" contacts with any other, taking into account the full rotamer ensemble. Any tips on how to manage this programmatically?<br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class="">Dr. Ahir Pushpanath<b class=""> PhD.</b><br class="">Senior Biologist,<br class=""></div>Johnson Matthey.<br class=""><div class=""><div class=""><br class=""><br class=""></div></div></div></div>
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