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<p>I might be able to offer a bit of help here, the Chimera team and Jaime helped me with basically this exact problem.</p>
<p><br>
</p>
<p>I have a script here <a href="https://github.com/jrjhealey/bioinfo-tools/blob/master/strucfit.py" class="OWAAutoLink" id="LPlnk253829" previewremoved="true">https://github.com/jrjhealey/bioinfo-tools/blob/master/strucfit.py</a> that you could take from.
You'll probably want to look specifically at lines 216-240. (Note - you'll also need to look at the relevant module imports for match and pychimera etc.</p>
<p><br>
</p>
<p>The script will need Jaime's implementation of pychimera too (he's super helpful!)</p>
<p><a href="https://github.com/insilichem/pychimera" class="OWAAutoLink" id="LPlnk869723" previewremoved="true">https://github.com/insilichem/pychimera</a><br>
<br>
</p>
The script gives output as below, a<span style="font-size: 12pt;">s the script automatically finds the best matching PDB file (that's what the first 150 lines or so
</span>is<span style="font-size: 12pt;"> looking for), there is additional information there.</span></div>
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<span style="font-size: 12pt;"><br>
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<span style="font-size: 12pt;">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">
Best Model I'm</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">
Hit Comparing RMSD Assorted homology metrics<br class="Apple-interchange-newline">
2k4r<span class="Apple-tab-span" style="white-space: pre;"> </span>PAK_01796_model5.pdb<span class="Apple-tab-span" style="white-space: pre;">
</span>2.81843275676<span class="Apple-tab-span" style="white-space: pre;"> </span>
37.5<span class="Apple-tab-span" style="white-space: pre;"> </span>13<span class="Apple-tab-span" style="white-space: pre;">
</span>0.00035<span class="Apple-tab-span" style="white-space: pre;"> </span>21.5</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">
2k4r<span class="Apple-tab-span" style="white-space: pre;"> </span>PAK_01796_model4.pdb<span class="Apple-tab-span" style="white-space: pre;">
</span>12.6869844869<span class="Apple-tab-span" style="white-space: pre;"> </span>
37.5<span class="Apple-tab-span" style="white-space: pre;"> </span>13<span class="Apple-tab-span" style="white-space: pre;">
</span>0.00035<span class="Apple-tab-span" style="white-space: pre;"> </span>21.5</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">
2k4r<span class="Apple-tab-span" style="white-space: pre;"> </span>PAK_01796_model3.pdb<span class="Apple-tab-span" style="white-space: pre;">
</span>14.4133021316<span class="Apple-tab-span" style="white-space: pre;"> </span>
37.5<span class="Apple-tab-span" style="white-space: pre;"> </span>13<span class="Apple-tab-span" style="white-space: pre;">
</span>0.00035<span class="Apple-tab-span" style="white-space: pre;"> </span>21.5</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">
2k4r<span class="Apple-tab-span" style="white-space: pre;"> </span>PAK_01796_model1.pdb<span class="Apple-tab-span" style="white-space: pre;">
</span>0.459177533295<span class="Apple-tab-span" style="white-space: pre;"> </span>
37.5<span class="Apple-tab-span" style="white-space: pre;"> </span>13<span class="Apple-tab-span" style="white-space: pre;">
</span>0.00035<span class="Apple-tab-span" style="white-space: pre;"> </span>21.5</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">
2k4r<span class="Apple-tab-span" style="white-space: pre;"> </span>PAK_01796_model2.pdb<span class="Apple-tab-span" style="white-space: pre;">
</span>15.1861411912<span class="Apple-tab-span" style="white-space: pre;"> </span>
37.5<span class="Apple-tab-span" style="white-space: pre;"> </span>13<span class="Apple-tab-span" style="white-space: pre;">
</span>0.00035<span class="Apple-tab-span" style="white-space: pre;"> </span>21.5</div>
</span></div>
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<p><br>
</p>
<p>Hope that's useful! Happy to offer more help (though I'm sure the chimera team have it covered!)</p>
<p><br>
</p>
<p><br>
</p>
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<div id="divtagdefaultwrapper" style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif">
Joe<br style="font-size:10pt">
</div>
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<div id="divtagdefaultwrapper" style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif">
<span style="font-size:10pt">M.Sc. B.Sc. (Hons) MSRB</span><br>
</div>
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<span style="font-size:10pt"></span>
<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="">
</span></div>
<div><span style="font-size:10pt">Coventry<br style="">
</span></div>
<div><span style="font-size:10pt">CV47AL<br style="">
Mob: +44 (0) 7536 042620 | </span><span style="font-size:10pt">Email: J.R.J.Healey@warwick.ac.uk</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Jointly working in:<br style="">
</span></div>
<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 </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 <a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP">Gibson Lab</a> (Warwick Chemistry)<br style="">
</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Twitter: <a href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a> | </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> | ORCID: <span>orcid.org/0000-0002-9569-6738</span></div>
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<b>Sent:</b> 22 December 2016 20:00<br>
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<b>Subject:</b> Chimera-users Digest, Vol 164, Issue 26</font>
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Today's Topics:<br>
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1. Saving Output From Match Align (Muk, Sanychen)<br>
<br>
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----------------------------------------------------------------------<br>
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Message: 1<br>
Date: Thu, 22 Dec 2016 16:11:00 +0000<br>
From: "Muk, Sanychen" <smuk@coh.org><br>
To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu><br>
Subject: [Chimera-users] Saving Output From Match Align<br>
Message-ID:<br>
<A69D81CB04F0734E96302AA9E36F9B233E521BEE@ppwexch2kx03.coh.org><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hello,<br>
<br>
I'm working on a script to superimpose pdb structures onto one another and then run the match -> align tool to align them to get the RMSD between residues of the pdb structures. I know that from the multialign interviewer window, I can then go to structure
acess match and then save the attributes as a text file that will contain the residue number and RMSD. Is there a command that I can use to output this attributes file automatically? Thank you, and happy holidays.<br>
<br>
Best,<br>
Sanychen Muk<br>
<br>
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