<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jul 20, 2011, at 9:43 AM, Sierk, Michael wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>All -<br><br>I would like to write a command file that will automatically read in two structures and a corresponding alignment file, then perform the superposition (and coloring, etc.). I can read in the pdb and pir files using the command line, and I can do the superposition in the Multalign Viewer using Structure->Match, but I cannot figure out how to do the superposition based on the sequence using the command line. I think if there was a way to select the residues that are aligned in the sequence alignment I could use the "match" command, but I don't see a way to do that. Is there an attribute analogous to mavPercentConserved that corresponds to "aligned"? Or is there an automatically generated region based on the sequence alignment?</div></blockquote><br></div><div>There are no command equivalents to Multalign Viewer menu items unfortunately. However, using a Python script you can cheat your way around that by locating the Multalign Viewer Python object and invoking its match method. I've attached a script that will invoke match on the newest Multalign Viewer instance open in Chimera. If you want to employ iteration in the matching, change this line of the script:</div><div><br></div><div>mav.match(associatedStructures[0], associatedStructures[1:])</div><div><br></div><div>to:</div><div><br></div><div>mav.match(associatedStructures[0], associatedStructures[1:], iterate=True, iterateCutoff=2.0)</div><div><br></div><div>You can execute the Python script in the middle of your Chimera script by simply using the "open" command to open it, e.g. "open ~/mavMatch.py"</div><div><br></div><div>--Eric</div><br><div apple-content-edited="true"> <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; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><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"></div></span> </div></body></html>