<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 2, 2009, at 1:47 PM, Karan Uppal wrote:</div><div><blockquote type="cite"><div>Hello,<br><br>I am trying to write a Python script to extract the header information <br>from the MultAlign Viewer tool. Are there any command-line commands to <br>interface with this tool and save the header information without <br>manually using the toolbar.<br></div></blockquote><br></div><div>On Mar 3, 2009, at 9:49 AM, Karan Uppal wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br><br>I want to simplify the question I asked yesterday. Is there any way to <br>store the output of Match Maker, specifically the RMSD values for every <br>residue and the list of residues in the alignment regions in an <br>external file from command line?</div></blockquote><br></div><div>Hi Karan,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>There is an underlying function in MatchMaker (MatchMaker.match) that can be called from Python to perform the same work as MatchMaker and retrieve the matching information. I've attached a script that uses the function to match chain A of two open models (the script assumes exactly two structures are open) and print the RMSD, residue pairs, and their CA-CA distances to the reply log. You should look over the script and the definition of the match function (in chimera/share/MatchMaker/__init__.py) and modify it to suit your needs. I assume you know enough Python to convert the plain print statements into the equivalents needed to output to a file.<br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Let me know if you have questions.<br></div><div><br></div><div>--Eric</div><div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br class="Apple-interchange-newline"> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div></div></div><div><br class="webkit-block-placeholder"></div><div><br></div></div></body></html>