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<p>That looks spot on thanks Eric.</p>
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<p>Does chimera specify anything other than "isHelix"/"isSheet"/"isTurn"?</p>
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<p>I can see these in chimera's object model (stole your image below!). Is disordered sequence treated differently or just as Turn in Chimera?</p>
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<p>I'll run this through the commandline with Jaime's pychimera (a real game changer for me!) so creating output files I'll probably just handle with piping STDOUT.</p>
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<p><img size="54566" contenttype="image/png" id="img262623" style="max-width: 99.9%; user-select: none;" aria-expanded="false" tabindex="0" src="cid:bae07725-f281-4ce3-a9f2-72666f911e0b"><br>
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<p>Thanks,</p>
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<p>Joe</p>
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Joe Healey<br style="font-size:10pt">
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons)</span><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> 10 October 2016 18:54:08<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> chimera List<br>
<b>Subject:</b> Re: [Chimera-users] Computing 'basic' structure characteristics</font>
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<div class="">On Oct 9, 2016, at 9:53 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
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<div class=""><span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">If
you just want to look at predominance of secondary structures, you would not use those integers which mean first strand, second strand, first helix, etc. Instead you could just see how many residues are already assigned as strand, helix, and coil. There
aren’t commands to do this directly, only some very cumbersome approaches that I imagine are vastly inferior to using Python (like “select strand” and then writing a list of all those residues with “writesel” etc.).</span><br 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; -webkit-text-stroke-width: 0px;" class="">
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<span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">I
can’t help with the Python side, this is just the perspective from the commands side. All the commands I mentioned are documented,</span><br 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; -webkit-text-stroke-width: 0px;" class="">
<span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""><</span><a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html" 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html</a><span 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; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">></span><br 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; -webkit-text-stroke-width: 0px;" class="">
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<div>To supplement this part of the answer, you can loop through a bunch of PDB files in Python as outlined here:</div>
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<a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" class="">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a>
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<div class="">You can determine the fraction of residues in helix and sheet with code like this:</div>
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<div class=""><i class="">from chimera import openModels, Molecule</i></div>
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<div class=""><i class=""><span class="Apple-tab-span" style="white-space:pre"></span>#… inside the loop…</i></div>
<div class=""><i class=""><span class="Apple-tab-span" style="white-space:pre"></span>for mol in openModels.list(modelTypes=[Molecule]):</i></div>
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<div class=""><i class=""><span class="Apple-tab-span" style="white-space: pre;"></span>sheet_fract = len([r for r in mol.residues if r.isSheet]) / len(mol.residues)</i></div>
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<div class=""><i class=""><span class="Apple-tab-span" style="white-space: pre;"></span>helix_fract = len([r for r in mol.residues if r.isHelix]) / len(mol.residues)</i></div>
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<div class=""><i class=""><span class="Apple-tab-span" style="white-space:pre"></span># write them to a file with “print>>f” or to the reply log with just “print”</i></div>
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<div class="">The above assumes you have a little bit of familiarity with Python. I can provide more explanation if you need it.</div>
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<div class="">—Eric</div>
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<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>
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