<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="">As you’ve noticed, the back end of your script pretty much has the exact code you need, just commented out. &nbsp;The function called in that code. MatchMaker.match(), is the function that the mmaker command ultimately calls (there’s an intermediate “cmdMatch” function that does some argument parsing). &nbsp;You already do the correct imports at the top of your script (“from MatchMaker import match, …”). &nbsp;I think you just need to adapt the commented-out code into the script’s workflow.<div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 20, 2016, at 3:16 PM, Healey, Joe &lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>&gt; wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" style="font-style: normal; font-variant-caps: normal; font-weight: normal; 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; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Ah yes now I see. mmaker is what I want. I've figured out the appropriate syntax for the command I'd want to execute in chimera syntax I think.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">In the code snippet below, it seems to me I have 2 options? I can synthesise a string and iterate the mmaker function in chimera syntax with something like:</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div class="">&nbsp; &nbsp; chimera.openModels.open(top_hit, type="PDB")<br class="">&nbsp;<br class="">&nbsp; &nbsp;&nbsp;# Open model structures<br class="">&nbsp; &nbsp;&nbsp;for&nbsp;model_path&nbsp;in&nbsp;model_list:<br class="">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;chimera.openModels.open(model_path,type="PDB")<br class="">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;print("Opened: "&nbsp;+ model_path)<br class="">&nbsp;<br class="">&nbsp; &nbsp; rmsd_file&nbsp;=&nbsp;'{0}.tsv'.format(rmsd)<br class="">&nbsp; &nbsp;&nbsp;with&nbsp;open(rmsd_file,&nbsp;"a")&nbsp;as&nbsp;rmsd_output_file:<br class="">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;for&nbsp;j&nbsp;in&nbsp;len(model_list):</div><div class="">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;match_cmd = 'mmaker #0 #{0} alg nw iter false'.format(j)<br class="">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;runCommand(match_cmd)</div><div class=""><br class=""></div><div class=""># &lt;somewhere in here retrieve the rmsd and append to a result file&gt;</div><div class=""><br class=""></div><div class="">or the other option would be to do the above but avoiding the string synthesis step with something like:</div><div class="">chimera.module.mmaker()</div><div class=""><br class=""></div><div class="">If the module can be accessed directly? If so which module is the mmaker function within?</div><div class=""><br class=""></div><div class=""><br class=""></div>Though I still don't know how to access the RMSD value from the mmaker function in either of these manners. Would executing mmaker in either such way&nbsp;return a tuple or list where the RMSD is a particular index?</div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class="">Looking at your Match script the rmsd was the 3rd value of the tuple in the line:&nbsp;<div class="">atoms1, atoms2, rmsd = match(CP_SPECIFIC_SPECIFIC, [(c1, c2)], defaults[MATRIX],"nw", defaults[GAP_OPEN], defaults[GAP_EXTEND],iterate=defaults[ITER_CUTOFF])[0]</div><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Would the same be true for mmaker?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">(Sorry to ask so many questions in one go. I don't know what your policy is on whether all related questions should be in the same issue, or whether I should be raising separate ones)</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Thanks again for all your help</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class="">Joe Healey<br style="font-size: 10pt;" class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="text-decoration: underline;" class="">&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;</span><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-size: 10pt;" class="">M.Sc. B.Sc. (Hons)</span><br class=""></div><div id="divtagdefaultwrapper" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><span style="font-size: 10pt;" class=""></span><div class=""><span style="font-size: 10pt;" class="">PhD Student</span></div><div class=""><span style="font-size: 10pt;" class="">MOAC CDT, Senate House</span></div><div class=""><span style="font-size: 10pt;" class="">University of Warwick<br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">Coventry<br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">CV47AL<br class="">Mob: +44 (0) 7536 042620 &nbsp;| &nbsp;</span><span style="font-size: 10pt;" class="">Email:<span class="Apple-converted-space">&nbsp;</span><a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a></span></div><div class=""><span style="font-size: 10pt;" class=""><br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">Jointly working in:<br class=""></span></div><div class=""><span style="font-size: 10pt;" class=""><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP" class="">Waterfield Lab</a><span class="Apple-converted-space">&nbsp;</span>(<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);" class="">WMS&nbsp;</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);" class="">Microbiology and Infecti</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);" class="">on Un</span><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);" class="">it)</span></span></div><div class=""><span style="font-size: 10pt;" class="">and the&nbsp;<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP" class="">Gibson Lab</a>&nbsp;(Warwick Chemistry)<br class=""></span></div><div class=""><span style="font-size: 10pt;" class=""><br class=""></span></div><div class=""><span style="font-size: 10pt;" class="">Twitter:<span class="Apple-converted-space">&nbsp;</span><a href="https://twitter.com/JRJHealey" id="LPNoLP" class="">@JRJHealey</a>&nbsp; |&nbsp;&nbsp;</span><span style="font-size: 10pt;" class="">Website:<span class="Apple-converted-space">&nbsp;</span></span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" id="LPNoLP" style="font-size: 10pt;" class="">MOAC Page</a></div></div></div><br class=""><br class=""><div style="" class=""><div class=""><hr tabindex="-1" style="display: inline-block; width: 660.515625px;" class=""><div id="x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users-bounces@cgl.ucsf.edu" class="">chimera-users-bounces@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:chimera-users-bounces@cgl.ucsf.edu" class="">chimera-users-bounces@cgl.ucsf.edu</a>&gt; on behalf of<span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users-request@cgl.ucsf.edu" class="">chimera-users-request@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:chimera-users-request@cgl.ucsf.edu" class="">chimera-users-request@cgl.ucsf.edu</a>&gt;<br class=""><b class="">Sent:</b><span class="Apple-converted-space">&nbsp;</span>20 September 2016 19:30<br class=""><b class="">To:</b><span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space">&nbsp;</span>Chimera-users Digest, Vol 161, Issue 19</font><div class="">&nbsp;</div></div></div><font size="2" class=""><span style="font-size: 10pt;" class=""><div class="PlainText">Send Chimera-users mailing list submissions to<br class="">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><br class=""><br class="">To subscribe or unsubscribe via the World Wide Web, visit<br class="">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class="">or, via email, send a message with subject or body 'help' to<br class="">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users-request@cgl.ucsf.edu" class="">chimera-users-request@cgl.ucsf.edu</a><br class=""><br class="">You can reach the person managing the list at<br class="">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users-owner@cgl.ucsf.edu" class="">chimera-users-owner@cgl.ucsf.edu</a><br class=""><br class="">When replying, please edit your Subject line so it is more specific<br class="">than "Re: Contents of Chimera-users digest..."<br class=""><br class=""><br class="">Today's Topics:<br class=""><br class="">&nbsp;&nbsp; 1. Re: Recursive structure matching and acquisition of<br class="">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; descriptive numbers (Eric Pettersen)<br class=""><br class=""><br class="">----------------------------------------------------------------------<br class=""><br class="">Message: 1<br class="">Date: Tue, 20 Sep 2016 11:30:38 -0700<br class="">From: Eric Pettersen &lt;<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>&gt;<br class="">To: "Healey, Joe" &lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>&gt;<br class="">Cc: "<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>BB" &lt;<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>&gt;<br class="">Subject: Re: [Chimera-users] Recursive structure matching and<br class="">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; acquisition of&nbsp; descriptive numbers<br class="">Message-ID: &lt;<a href="mailto:30002D29-1B25-4596-8868-EB3370B72E42@cgl.ucsf.edu" class="">30002D29-1B25-4596-8868-EB3370B72E42@cgl.ucsf.edu</a>&gt;<br class="">Content-Type: text/plain; charset="windows-1252"<br class=""><br class="">Hi Joe,<br class="">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I guess the first thing is that the command equivalent for MatchMaker is ?matchmaker? or ?mmaker?, not ?match?.&nbsp; The ?match? command is for when you know a priori the exact set of atoms you want matched in the two structures.&nbsp; ?matchmaker? is for when you let Chimera figure out the set of atoms to use based on the sequences and secondary structure.&nbsp; The documentation for the matchmaker command is here:<br class=""><br class=""><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options</a>&lt;<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options</a>&gt;<br class=""><br class="">I looked at your script and didn?t see anything obviously wrong.&nbsp; What exactly isn?t working?&nbsp; And unfortunately the answer is no, you can?t run a GUI&nbsp; operation and easily find the command equivalent.&nbsp; ChimeraX will have that capability though.<br class=""><br class="">?Eric<br class=""><br class=""><br class="">&gt; On Sep 20, 2016, at 5:07 AM, Healey, Joe &lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>&gt; wrote:<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; Hi again,<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; I'm making decent headway with the problem I mentioned before with Jaime's help and the use of pychimera. I'm down to the nitty-gritty of doing the actual RMSD/Match function alignment though and could use a bit more information.<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; Is there are resource with more information on the commandline implementation of match anywhere other than the link below?<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options</a>&lt;<a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options</a>&gt;<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; I took a look at Eric's suggestion of the match.py script here:<span class="Apple-converted-space">&nbsp;</span><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a>&gt;<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; But I can't quite unwrap the options specified in the command for my uses.<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed?<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; I've put the semi-complete script in pastebin here<span class="Apple-converted-space">&nbsp;</span><a href="http://pastebin.com/6k9cew55" class="">http://pastebin.com/6k9cew55</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="http://pastebin.com/6k9cew55" class="">http://pastebin.com/6k9cew55</a>&gt; incase it gives you some indication of what I'm attempting to do.<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; Many thanks<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; Joe Healey<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; M.Sc. B.Sc. (Hons)<br class="">&gt; PhD Student<br class="">&gt; MOAC CDT, Senate House<br class="">&gt; University of Warwick<br class="">&gt; Coventry<br class="">&gt; CV47AL<br class="">&gt; Mob: +44 (0) 7536 042620&nbsp; |&nbsp; Email:<span class="Apple-converted-space">&nbsp;</span><a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>&gt;<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; Jointly working in:<br class="">&gt; Waterfield Lab &lt;<a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" class="">http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/</a>&gt; (WMS Microbiology and Infection Unit)<br class="">&gt; and the Gibson Lab &lt;<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" class="">http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/</a>&gt; (Warwick Chemistry)<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; Twitter: @JRJHealey &lt;<a href="https://twitter.com/JRJHealey" class="">https://twitter.com/JRJHealey</a>&gt;&nbsp; |&nbsp; Website: MOAC Page &lt;<a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" class="">http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey</a>&gt;<br class="">&gt; From: Greg Couch &lt;<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:gregc@cgl.ucsf.edu" class="">mailto:gregc@cgl.ucsf.edu</a>&gt;&gt;<br class="">&gt; Sent: 08 September 2016 22:43:55<br class="">&gt; To: Healey, Joe;<span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:chimera-users@cgl.ucsf.edu" class="">mailto:chimera-users@cgl.ucsf.edu</a>&gt; BB<br class="">&gt; Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers<br class="">&gt;&nbsp;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; chimera --nogui can't access graphics.&nbsp; Headless chimera has software OpenGL rendering, so it can be used to create images.&nbsp; Make sure to use the windowsize command to set the size of the framebuffer.&nbsp; Don't know if pychimera cares.<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&nbsp;&nbsp;&nbsp;&nbsp; -- Greg<br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt; On 09/08/2016 11:53 AM, Healey, Joe wrote:<br class="">&gt;&gt; Brilliant, that sounds like the most likely option. I had stumbled across pychimera a couple of days ago while trying to find out if chimera could simply be imported as a module. I initially steered away from it as I don't have sudo rights for the server where I'm trying to set all this up (couldnt run pip), but I've since sorted it with our sysadmin.<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt; On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt; Joe Healey<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt; M.Sc. B.Sc. (Hons)<br class="">&gt;&gt; PhD Student<br class="">&gt;&gt; MOAC CDT, Senate House<br class="">&gt;&gt; University of Warwick<br class="">&gt;&gt; Coventry<br class="">&gt;&gt; CV47AL<br class="">&gt;&gt; Mob: +44 (0) 7536 042620&nbsp; |&nbsp; Email:<span class="Apple-converted-space">&nbsp;</span><a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>&gt;<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt; Jointly working in:<br class="">&gt;&gt; Waterfield Lab &lt;<a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" class="">http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/</a>&gt; (WMS Microbiology and Infection Unit)<br class="">&gt;&gt; and the Gibson Lab &lt;<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" class="">http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/</a>&gt; (Warwick Chemistry)<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt; Twitter: @JRJHealey &lt;<a href="https://twitter.com/JRJHealey" class="">https://twitter.com/JRJHealey</a>&gt;&nbsp; |&nbsp; Website: MOAC Page &lt;<a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" class="">http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey</a>&gt;<br class="">&gt;&gt; From: Greg Couch &lt;<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a>&gt; &lt;<a href="mailto:gregc@cgl.ucsf.edu" class="">mailto:gregc@cgl.ucsf.edu</a>&gt;<br class="">&gt;&gt; Sent: 07 September 2016 19:49:19<br class="">&gt;&gt; To: Healey, Joe;<span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:chimera-users@cgl.ucsf.edu" class="">mailto:chimera-users@cgl.ucsf.edu</a>&gt; BB<br class="">&gt;&gt; Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers<br class="">&gt;&gt;&nbsp;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt; Yes, Chimera's Python code is only "warrantied" to work with its own Python.&nbsp; See question 3b of the Chimera Programming FAQ,<a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b" class="">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b</a>&lt;<a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b" class="">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b</a>&gt;, for how to install other software into Chimera.&nbsp; Other parts of the FAQ may help you too.<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt; That said, Jaime Rodr?guez-Guerra took my previous comments on this subject,<span class="Apple-converted-space">&nbsp;</span><a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html" class="">http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html" class="">http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html</a>&gt;, and came up with pychimera,<span class="Apple-converted-space">&nbsp;</span><a href="https://pypi.python.org/pypi/pychimera" class="">https://pypi.python.org/pypi/pychimera</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="https://pypi.python.org/pypi/pychimera" class="">https://pypi.python.org/pypi/pychimera</a>&gt;.&nbsp; I haven't checked to see how it handles all of my caveats, and it can't completely without using a modified Python, but I suspect that it would be good enough for you.<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp; HTH,<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp; Greg<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt; On 09/07/2016 07:36 AM, Healey, Joe wrote:<br class="">&gt;&gt;&gt; Hi Eric,<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however.<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Am I right in thinking that chimera can't be imported in to python inside a normal bash shell, and rather it must be done the other way round? So file manipulation and such must be done by calls to the system from within the chimera python shell, rather than a python interpreter calling chimera modules in?<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; It certainly makes the chimera steps I plan to do much easier, but I was going to include it in a pipeline with some other programs and it makes that a little more taxing (though not insurmountable!).<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Additionally, I plan to invoke this inside a script on a headless linux box (hence why running it through a python script was ideal), so whatever solution I use will need to be 'command line friendly'.<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script.<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Do you have any advice about how best to proceed?<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Many thanks,<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Joe Healey<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; M.Sc. B.Sc. (Hons)<br class="">&gt;&gt;&gt; PhD Student<br class="">&gt;&gt;&gt; MOAC CDT, Senate House<br class="">&gt;&gt;&gt; University of Warwick<br class="">&gt;&gt;&gt; Coventry<br class="">&gt;&gt;&gt; CV47AL<br class="">&gt;&gt;&gt; Mob: +44 (0) 7536 042620&nbsp; |&nbsp; Email:<span class="Apple-converted-space">&nbsp;</span><a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>&gt;<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Jointly working in:<br class="">&gt;&gt;&gt; Waterfield Lab &lt;<a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" class="">http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/</a>&gt; (WMS Microbiology and Infection Unit)<br class="">&gt;&gt;&gt; and the Gibson Lab &lt;<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" class="">http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/</a>&gt; (Warwick Chemistry)<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Twitter: @JRJHealey &lt;<a href="https://twitter.com/JRJHealey" class="">https://twitter.com/JRJHealey</a>&gt;&nbsp; |&nbsp; Website: MOAC Page &lt;<a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" class="">http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey</a>&gt;<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; From: Eric Pettersen &lt;<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>&gt; &lt;<a href="mailto:pett@cgl.ucsf.edu" class="">mailto:pett@cgl.ucsf.edu</a>&gt;<br class="">&gt;&gt;&gt; Sent: 31 August 2016 18:23<br class="">&gt;&gt;&gt; To: Healey, Joe<br class="">&gt;&gt;&gt; Cc:<span class="Apple-converted-space">&nbsp;</span><a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:chimera-users@cgl.ucsf.edu" class="">mailto:chimera-users@cgl.ucsf.edu</a>&gt;<br class="">&gt;&gt;&gt; Subject: Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers<br class="">&gt;&gt;&gt;&nbsp;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Hi Joe,<br class="">&gt;&gt;&gt; This old chimera-users post has a Python script attachment that demonstrates how to call the underlying MatchMaker function to get the RMSD value programmatically.&nbsp; The mailing list gives the attachment a ?.bin? extension but it?s really a .py file.&nbsp; Just change the extension if you need to.&nbsp; Let me know if you have any questions about how to adapt the script to your needs?<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a>&gt;<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; ?Eric<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; Eric Pettersen<br class="">&gt;&gt;&gt; UCSF Computer Graphics Lab<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; On Aug 31, 2016, at 3:02 AM, Healey, Joe &lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>&gt;&gt; wrote:<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; Hi,<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; I have several hundred structure simulations that were performed on our HPC resource. Each simulation has approximately 5 models associated with it. I also have HMM model homologies for each of these proteins.<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; I would like to use chimera's matchmaker function to compare the simulated structured to their nearest 'real' counterpart with a resolved structure. In order to do this I plan to script chimera to pull in the simulated models as well as the near homolog and then run the matchmaker algorithm.<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; My question is: can the RMSD value that is returned in the reply log be 'accessed directly' such that for each match that is performed, I can obtain the RMSD and thus a ranking for the best fitting structures - or will it require parsing the reply log?<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; Thanks<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; Joe Healey<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; M.Sc. B.Sc. (Hons)<br class="">&gt;&gt;&gt;&gt; PhD Student<br class="">&gt;&gt;&gt;&gt; MOAC CDT, Senate House<br class="">&gt;&gt;&gt;&gt; University of Warwick<br class="">&gt;&gt;&gt;&gt; Coventry<br class="">&gt;&gt;&gt;&gt; CV47AL<br class="">&gt;&gt;&gt;&gt; Mob: +44 (0) 7536 042620&nbsp; |&nbsp; Email:<span class="Apple-converted-space">&nbsp;</span><a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:J.R.J.Healey@warwick.ac.uk" class="">mailto:J.R.J.Healey@warwick.ac.uk</a>&gt;<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; Jointly working in:<br class="">&gt;&gt;&gt;&gt; Waterfield Lab &lt;<a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" class="">http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/</a>&gt; (WMS Microbiology and Infection Unit)<br class="">&gt;&gt;&gt;&gt; and the Gibson Lab &lt;<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" class="">http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/</a>&gt; (Warwick Chemistry)<br class="">&gt;&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;&gt; Twitter: @JRJHealey &lt;<a href="https://twitter.com/JRJHealey" class="">https://twitter.com/JRJHealey</a>&gt;&nbsp; |&nbsp; Website: MOAC Page &lt;<a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" class="">http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey</a>&gt;_______________________________________________<br class="">&gt;&gt;&gt;&gt; Chimera-users mailing list:<span class="Apple-converted-space">&nbsp;</span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:Chimera-users@cgl.ucsf.edu" class="">mailto:Chimera-users@cgl.ucsf.edu</a>&gt;<br class="">&gt;&gt;&gt;&gt; Manage subscription:<span class="Apple-converted-space">&nbsp;</span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>&lt;<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>&gt;<br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;&gt;&gt; _______________________________________________<br class="">&gt;&gt;&gt; Chimera-users mailing list:<span class="Apple-converted-space">&nbsp;</span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>&lt;<a href="mailto:Chimera-users@cgl.ucsf.edu" class="">mailto:Chimera-users@cgl.ucsf.edu</a>&gt;<br class="">&gt;&gt;&gt; Manage subscription:<span class="Apple-converted-space">&nbsp;</span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>&lt;<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>&gt;<br class="">&gt;&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class="">&gt;<span class="Apple-converted-space">&nbsp;</span><br class=""><br class="">-------------- next part --------------<br class="">An HTML attachment was scrubbed...<br class="">URL: &lt;<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160920/d01fa12e/attachment.html" class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160920/d01fa12e/attachment.html</a>&gt;<br class=""><br class="">------------------------------<br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list<br class=""><a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class=""><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=""><br class="">End of Chimera-users Digest, Vol 161, Issue 19<br class="">**********************************************</div></span></font></div></div></div></div></blockquote></div><br class=""></div></body></html>