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<p>That looks spot on thanks Eric.</p>
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<p>Does chimera specify anything other than &quot;isHelix&quot;/&quot;isSheet&quot;/&quot;isTurn&quot;?</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&nbsp;(a real game changer for me!) so creating output files I'll probably just handle with piping STDOUT.</p>
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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="text-decoration:underline">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; </span>
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons)</span><br>
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<div><span style="font-size:10pt">PhD Student</span></div>
<div><span style="font-size:10pt">MOAC CDT, Senate House</span></div>
<div><span style="font-size:10pt">University of Warwick<br style="">
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<div><span style="font-size:10pt">Coventry<br style="">
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<div><span style="font-size:10pt">CV47AL<br style="">
Mob: &#43;44 (0) 7536 042620 &nbsp;| &nbsp;</span><span style="font-size:10pt">Email: J.R.J.Healey@warwick.ac.uk</span></div>
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<div><span style="font-size:10pt">Jointly working in:<br style="">
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<div><span style="font-size:10pt"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP">Waterfield Lab</a> (<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">WMS&nbsp;</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Microbiology
 and Infecti</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">on Un</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">it)</span></span></div>
<div><span style="font-size:10pt">and the&nbsp;<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP">Gibson Lab</a>&nbsp;(Warwick Chemistry)<br style="">
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<div><span style="font-size:10pt">Twitter: <a href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a>&nbsp; |&nbsp;&nbsp;</span><span style="font-size:10pt">Website: </span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="font-size:10pt" id="LPNoLP">MOAC Page</a></div>
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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 &lt;pett@cgl.ucsf.edu&gt;<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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<blockquote type="cite" class="">
<div class="">On Oct 9, 2016, at 9:53 AM, Elaine Meng &lt;<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>&gt; wrote:</div>
<br class="Apple-interchange-newline">
<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. &nbsp;Instead you could just see how many residues are already assigned as strand, helix, and coil. &nbsp;There
 aren&#8217;t commands to do this directly, only some very cumbersome approaches that I imagine are vastly inferior to using Python (like &#8220;select strand&#8221; and then writing a list of all those residues with &#8220;writesel&#8221; 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="">
<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="">I
 can&#8217;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="">&lt;</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="">&gt;</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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</i></div>
<div class=""><i class=""><span class="Apple-tab-span" style="white-space:pre"></span>#&#8230; inside the loop&#8230;</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 &#8220;print&gt;&gt;f&#8221; or to the reply log with just &#8220;print&#8221;</i></div>
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<div class="">The above assumes you have a little bit of familiarity with Python. &nbsp;I can provide more explanation if you need it.</div>
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<div class="">&#8212;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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