<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Sep 12, 2012, at 11:16 AM, Chetanya Pandya wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello,<div><br></div><div>I want to superimpose multiple structure sets and get the corresponding multiple sequence alignments using Chimera. I've been using the Match->Align option from the Tools menu. Now, I want to automate the process using the Python interface.</div>
<div><br></div><div>Unfortunately, I'm unable to find a command line option which does this. Can you help me out with this?</div></blockquote><br></div><div>Hi Chetanya,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>It's a little ambiguous if you are asking about a command version of Match->Align, or how to call it from Python. The issue is moot though since there currently is no command version of Match->Align, so you have to call it from Python! I don't know how familiar you are with Python or programming with Python, but the Chimera Programmer's Guide has some info to help.</div><div><br></div><a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html</a><div><br></div><div>If you don't know Python at all, follow the link in the Guide to the Python Tutorial and work through that, or at least the first few sections of that. Then for some Chimera-specific info, look at some of the Examples and the "basic primer" linked on the page.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Assuming you've written a script that has gotten to the stage where the structures are already open and superimposed, here's the info you'll need to use the Match->Align API:</div><div><br></div><div>1) Getting the list of open molecules:</div><div><br></div><div><i>from chimera import openModels, Molecule</i></div><div><i>mols = openModels.list(modelTypes=[Molecule])</i></div><div><br></div><div>2) Getting the list of chains to use. This example code assumes they're chain A:</div><div><br></div><div><i>chains = [m.sequence('A') for m in mols]</i></div><div><br></div><div>3) Call Match->Align to create the alignment.</div><div><br></div><div><i>from StructSeqAlign import makeAlignment</i></div><div><i>mav = makeAlignment(chains)</i></div><div><br></div><div>Note that the <i>makeAlignment</i> call will only return the Multalign Viewer instance starting with tomorrow's daily build (<i>i.e.</i> I made that change today!). Also, the <i>makeAlignment</i> call has a lot of optional arguments to change the parameters used in computing the alignment (<i>e.g.</i> cutoff, iteration, reference chain). Look at <your Chimera>/share/StructSeqAlign/__init__.py to see what the options are if you need to change the default behavior. (On a Mac, "<your Chimera>" is Chimera.app/Contents/Resources).</div><div><br></div><div>4) Save the alignment to a FASTA format file (named "x.fa") and Quit the MAV instance:</div><div><br></div><div><i>f = open("x.fa", "w")</i></div><div><i>from MultAlignViewer.formatters.saveFASTA import save</i></div><div><i>save(f, mav, mav.seqs, mav.fileMarkups)</i></div><div><i>f.close()</i></div><div><i>mav.Quit()</i></div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I hope this helps. Since this is pretty Python-intensive, I set followups to go to the chimera-dev mailing list rather than chimera-users.</div><div><br></div><div>--Eric</div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span>
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