<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Deepak,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Well, as long as you have the GUI running the script is pretty simple. Assuming you have the structures open you want, the script would be:</div><div class=""><br class=""></div><div class="">from MultAlignViewer.MAVIewer import MAViewer</div><div class="">mav = MAViewer(“full-path-to-fasta-file”)</div><div class="">mav.match(mav.seqs[0].matchMaps.keys()[0], mav.seqs[1].matchMaps.keys())</div><div class="">mav.Quit()</div><div class=""><br class=""></div><div class="">This will match the model that auto-associated with the second alignment sequence onto the model that auto-associated with the first sequence, and then exit the MultAlign Viewer instance.</div><div class=""><br class=""></div><div class="">Some notes:</div><div class=""><br class=""></div><div class="">(1) There’s probably a 99.9% chance the structures auto-associate with the correct sequences, but in case you want to be 100% sure, you would provide “autoAssociate=False” to the MAViewer constructor and then call mav.associate(model-to-associate, seq=seq-to-associate-with) to associate each model with the proper sequence.</div><div class=""><br class=""></div><div class="">(2) The matching occurs with default settings. If you want to use other settings (e.g. iteration/pruning), look at the doc string for the match method in <your Chimera installation>/share/MultAlignViewer/MAViewer.py. On a Mac, “<your Chimera installation>” is Chimera.app/Contents/Resources.</div><div class=""><br class=""></div><div class="">(3) Presumably you want to do this in a loop. Look at <a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" class="">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a> for the basics of how to do that.</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><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Nov 25, 2016, at 9:41 AM, Deepak Kumar <<a href="mailto:deepakk1@andrew.cmu.edu" class="">deepakk1@andrew.cmu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Dr. Meng & All Chimera Users,<br class=""><br class="">Regarding the question, yes, I am looking for a script that could superimpose two pdb structures based on a fasta alignment. Please let me know how this could be done.<br class=""><br class="">Thanks much!<br class=""><br class="">Deepak<br class="">________________________________________<br class="">From: Elaine Meng [<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>]<br class="">Sent: Friday, November 25, 2016 7:32 PM<br class="">To: Deepak Kumar<br class="">Cc: chimera List<br class="">Subject: using Chimera to superimpose structures using sequence alignments<br class=""><br class="">Hi Deepak,<br class="">You would still have to show the Chimera GUI (it cannot be done running Chimera with no GUI), but if you mean using a script instead of interactively choosing menu items, it may be possible. However, there is no Chimera command to do this. It would require a Python script.<br class=""><br class="">For future reference, we recommend sending Chimera questions to the <a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> list (which I CC’d here, so you do not need to re-send this question). Since today is a holiday, and I do not know Python, somebody may be able to help you with this question next week.<br class="">Best,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D.<br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class="">On Nov 24, 2016, at 3:08 PM, Deepak Kumar <<a href="mailto:deepakk1@andrew.cmu.edu" class="">deepakk1@andrew.cmu.edu</a>> wrote:<br class=""><br class=""><blockquote type="cite" class="">Dear Dr. Meng,<br class="">I am a Bioinformatician at the Computational Biology Department of Carnegie Mellon University. I have been using Chimera for visualization purposes and for many other of its features. I got to learn about your expertise from here:<br class=""><br class=""><a href="http://www.cgl.ucsf.edu/home/meng/index.html" class="">http://www.cgl.ucsf.edu/home/meng/index.html</a><br class=""><br class="">May I please request you to give your suggestions on this problem mentioned below:<br class=""><br class="">I know of one feature "multialign viewer" which uses a fasta alignment file to superimpose two pdb structures in Chimera. However, I have been using this feature through the GUI of Chimera. I am in need of using this feature standalone i.e superimpose two pdb structures based on a fasta alignment file. May I please request you to let me know, how can I perform this step standalone and not through Chimera GUI.<br class=""><br class="">Thank you so much for your time and consideration.<br class="">Yours Sincerely,<br class="">Deepak<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>