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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">That will work. So the question now is how to assign the Multialign Viewer to a variable when opening a file with pre-aligned sequences. Eg after running
the following command<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">runCommand('open myseqalignment.fas')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">the multialign window opens and the sequence-structure associations are made. How can I access this Multialign viewer instance? Is there something equivalent
to <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">mav = the_multialign_viewer_created_when_opening_a_file<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks again<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hernando<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Eric Pettersen [mailto:pett@cgl.ucsf.edu]
<br>
<b>Sent:</b> Tuesday, May 07, 2019 1:04 PM<br>
<b>To:</b> Hernando J Sosa<br>
<b>Cc:</b> Chimera<br>
<b>Subject:</b> Re: [Chimera-users] Association info<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Ah, in that case if your Multalign Viewer instance is in a variable named ‘mav', call:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">mav.saveAssocInfo(“save-file-path”)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">—Eric<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On May 7, 2019, at 8:00 AM, Hernando J Sosa <<a href="mailto:hernando.sosa@einstein.yu.edu">hernando.sosa@einstein.yu.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Eric, </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I need that but also the residue number at each alignment position for the associated structures . All this info is in the 'association file' that is produced
from the Multialign Viewer menu (MultiAlignViewer->File->Sava Association Info...). I would like to be able to produce this file or retrieve the relevant info within a python script as I want to do this with many structures/alignments. So far the only way
to produce this 'association file' that i know of is through the GUI menus. My plan was to produce this file(s) and then read and parse the info in my python script.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Here is sample of an association file produced by the Multialign viewer</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">struct1 associates with seq1 chain K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 1 - GLU 390.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 2 - ASN 391.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 3 - SER 392.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 4 - GLN 393.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 5 - VAL 394.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">..</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">..</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">..</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">struct2 associates with seq2 chain K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 1 - ALA 5.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 2 - GLU 6.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 3 - SER 7.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 4 - ASN 8.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 5 - ILE 9.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 6 - LYS 10.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 7 - VAL 11.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 8 - MET 12.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 9 - CYS 13.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> 10 - ARG 14.K</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">..</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">..</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">..</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The file tells me which sequence is associated with which structure and also the corresponding residues according to the alignment. e.g S7 in struct 2 corresponds
with S392 in struct1). This is the info I need.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hernando</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span class="apple-converted-space"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span></span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Eric
Pettersen [<a href="mailto:pett@cgl.ucsf.edu">mailto:pett@cgl.ucsf.edu</a>]<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Monday, May 06, 2019 5:39 PM<br>
<b>To:</b><span class="apple-converted-space"> </span>Hernando J Sosa<br>
<b>Cc:</b><span class="apple-converted-space"> </span>Chimera<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [Chimera-users] Association info</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal">Hi Hernando,<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>If all you need to know is what structure associated with which sequence, the Multalign Viewer instance has an ‘associations’ attribute that is a
dictionary of Molecule objects to Sequence objects. Both of those objects have ’name’ attributes which could be printed out. You don’t really describe what precise ‘association info’ you want to save, so I’m not sure if this meets your needs or not. If
not, let me know exactly what you want to save.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">—Eric<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""><br>
<span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>Eric Pettersen</span><o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""> </span></span><span class="apple-converted-space"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""> </span></span><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">UCSF
Computer Graphics Lab</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On May 6, 2019, at 11:43 AM, Hernando J Sosa <<a href="mailto:hernando.sosa@einstein.yu.edu"><span style="color:purple">hernando.sosa@einstein.yu.edu</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Dear Chimera,<br>
<br>
How can I save the Multialign viewer 'association info' to a file from a python script (I saw a script to save the sequence alignment in different formats but haven't seen how to save the association info).<br>
<br>
Thanks<br>
<br>
Hernando<br>
<br>
<br>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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