<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Joe,<div class=""><span class="Apple-tab-span" style="white-space:pre">        </span>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 <i class="">a&nbsp;priori</i>&nbsp;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:</div><div class=""><br class=""></div><div class=""><div id="divtagdefaultwrapper" class="" style="background-color: rgb(255, 255, 255);"><div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; margin-top: 0px; margin-bottom: 0px;"><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options" class="OWAAutoLink" id="LPlnk564949">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html#options</a></div><div class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">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.</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">—Eric</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div></div><div><blockquote type="cite" class=""><div class="">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:</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; background-color: rgb(255, 255, 255); font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi again,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">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.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Is there are resource with more information on the commandline implementation of match anywhere other than the link below?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options" class="OWAAutoLink" id="LPlnk564949">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html#options</a><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I took a look at Eric's suggestion of the match.py script here:&nbsp;<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html" class="OWAAutoLink" id="LPlnk823849">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">But I can't quite unwrap the options specified in the command for my uses.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I've put the semi-complete script in pastebin here&nbsp;<a href="http://pastebin.com/6k9cew55" class="OWAAutoLink" id="LPlnk657343">http://pastebin.com/6k9cew55</a>&nbsp;incase it gives you some indication of what I'm attempting to do.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Many thanks</div><br class=""><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></div><hr tabindex="-1" style="font-family: Helvetica; font-size: 12px; 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; background-color: rgb(255, 255, 255); display: inline-block; width: 635.03125px;" class=""><span style="font-family: Helvetica; font-size: 12px; 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; background-color: rgb(255, 255, 255); float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="font-family: Helvetica; font-size: 12px; 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; background-color: rgb(255, 255, 255);" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space">&nbsp;</span>Greg Couch &lt;<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a>&gt;<br class=""><b class="">Sent:</b><span class="Apple-converted-space">&nbsp;</span>08 September 2016 22:43:55<br class=""><b class="">To:</b><span class="Apple-converted-space">&nbsp;</span>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>BB<br class=""><b class="">Subject:</b><span class="Apple-converted-space">&nbsp;</span>Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers</font><div class="">&nbsp;</div></div><div style="font-family: Helvetica; font-size: 12px; 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; background-color: rgb(255, 255, 255);" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">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.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">&nbsp;&nbsp;&nbsp; -- Greg<br class=""></div><br class=""><div class="moz-cite-prefix">On 09/08/2016 11:53 AM, Healey, Joe wrote:<br class=""></div><blockquote cite="mid:DB6PR0101MB2279F5E3A61251AB67027D9ED4FB0@DB6PR0101MB2279.eurprd01.prod.exchangelabs.com" type="cite" class=""><div id="divtagdefaultwrapper" style="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="">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.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either</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 class="moz-txt-link-abbreviated" href="mailto:J.R.J.Healey@warwick.ac.uk">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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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></div><hr tabindex="-1" style="display: inline-block; width: 625.234375px;" class=""><div id="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>Greg Couch<span class="Apple-converted-space">&nbsp;</span><a class="moz-txt-link-rfc2396E" href="mailto:gregc@cgl.ucsf.edu">&lt;gregc@cgl.ucsf.edu&gt;</a><br class=""><b class="">Sent:</b><span class="Apple-converted-space">&nbsp;</span>07 September 2016 19:49:19<br class=""><b class="">To:</b><span class="Apple-converted-space">&nbsp;</span>Healey, Joe;<span class="Apple-converted-space">&nbsp;</span><a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space">&nbsp;</span>BB<br class=""><b class="">Subject:</b><span class="Apple-converted-space">&nbsp;</span>Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers</font><div class="">&nbsp;</div></div><div class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Yes, Chimera's Python code is only "warrantied" to work with its own Python.&nbsp; See question 3b of the Chimera Programming FAQ,<a moz-do-not-send="true" 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>, for how to install other software into Chimera.&nbsp; Other parts of the FAQ may help you too.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">That said, Jaime Rodríguez-Guerra took my previous comments on this subject,<span class="Apple-converted-space">&nbsp;</span><a moz-do-not-send="true" 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>, and came up with pychimera,<span class="Apple-converted-space">&nbsp;</span><a moz-do-not-send="true" href="https://pypi.python.org/pypi/pychimera" class="">https://pypi.python.org/pypi/pychimera</a>.&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.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">&nbsp;&nbsp;&nbsp; HTH,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">&nbsp;&nbsp;&nbsp; Greg<br class=""></div><br class=""><div class="moz-cite-prefix">On 09/07/2016 07:36 AM, Healey, Joe wrote:<br class=""></div><blockquote cite="mid:DB6PR0101MB2279542470892F3506BCAF62D4F80@DB6PR0101MB2279.eurprd01.prod.exchangelabs.com" type="cite" 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="">Hi Eric,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">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?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">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!).</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">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'.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script.</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Do you have any advice about how best to proceed?</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Many thanks,</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 moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:J.R.J.Healey@warwick.ac.uk">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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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 moz-do-not-send="true" 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=""><hr tabindex="-1" style="display: inline-block; width: 615.4375px;" class=""><div id="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>Eric Pettersen<span class="Apple-converted-space">&nbsp;</span><a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:pett@cgl.ucsf.edu">&lt;pett@cgl.ucsf.edu&gt;</a><br class=""><b class="">Sent:</b><span class="Apple-converted-space">&nbsp;</span>31 August 2016 18:23<br class=""><b class="">To:</b><span class="Apple-converted-space">&nbsp;</span>Healey, Joe<br class=""><b class="">Cc:</b><span class="Apple-converted-space">&nbsp;</span><a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br class=""><b class="">Subject:</b><span class="Apple-converted-space">&nbsp;</span>Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers</font><div class="">&nbsp;</div></div><div class="">Hi Joe,<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>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…</div><div class=""><br class=""></div><div class=""><a moz-do-not-send="true" 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></div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class=""><div class="" style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; word-wrap: break-word;"><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 class=""><br class=""></div></div></div><div class=""><blockquote type="cite" class=""><div class="">On Aug 31, 2016, at 3:02 AM, Healey, Joe &lt;<a moz-do-not-send="true" 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" class="" style="font-style: 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; font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><div class="" style="margin-top: 0px; margin-bottom: 0px;">Hi,</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">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.</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">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.</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">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?</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div class="" style="margin-top: 0px; margin-bottom: 0px;">Thanks</div><div class="" style="margin-top: 0px; margin-bottom: 0px;"><br class=""></div><div id="Signature" class=""><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;">Joe Healey<br class="" style="font-size: 10pt;"></div><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><br class=""></div><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><span class="" style="text-decoration: underline;">&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" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><span class="" style="font-size: 10pt;">M.Sc. B.Sc. (Hons)</span><br class=""></div><div id="divtagdefaultwrapper" class="" style="font-size: 12pt; background-color: rgb(255, 255, 255); font-family: Calibri, Arial, Helvetica, sans-serif;"><span class="" style="font-size: 10pt;"></span><div class=""><span class="" style="font-size: 10pt;">PhD Student</span></div><div class=""><span class="" style="font-size: 10pt;">MOAC CDT, Senate House</span></div><div class=""><span class="" style="font-size: 10pt;">University of Warwick<br class=""></span></div><div class=""><span class="" style="font-size: 10pt;">Coventry<br class=""></span></div><div class=""><span class="" style="font-size: 10pt;">CV47AL<br class="">Mob: +44 (0) 7536 042620 &nbsp;| &nbsp;</span><span class="" style="font-size: 10pt;">Email:<span class="Apple-converted-space">&nbsp;</span><a moz-do-not-send="true" href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a></span></div><div class=""><span class="" style="font-size: 10pt;"><br class=""></span></div><div class=""><span class="" style="font-size: 10pt;">Jointly working in:<br class=""></span></div><div class=""><span class="" style="font-size: 10pt;"><a moz-do-not-send="true" 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 class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">WMS&nbsp;</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">Microbiology and Infecti</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">on Un</span><span class="" style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 13.3333330154419px; background-color: rgb(255, 255, 255);">it)</span></span></div><div class=""><span class="" style="font-size: 10pt;">and the&nbsp;<a moz-do-not-send="true" 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 class="" style="font-size: 10pt;"><br class=""></span></div><div class=""><span class="" style="font-size: 10pt;">Twitter:<span class="Apple-converted-space">&nbsp;</span><a moz-do-not-send="true" href="https://twitter.com/JRJHealey" id="LPNoLP" class="">@JRJHealey</a>&nbsp; |&nbsp;&nbsp;</span><span class="" style="font-size: 10pt;">Website:<span class="Apple-converted-space">&nbsp;</span></span><a moz-do-not-send="true" href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" id="LPNoLP" class="" style="font-size: 10pt;">MOAC Page</a></div></div></div></div><span class="" style="font-family: Helvetica; font-size: 12px; font-style: 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; float: none; display: inline !important;">_______________________________________________</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: 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;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: 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; float: none; display: inline !important;">Chimera-users mailing list:<span class="Apple-converted-space">&nbsp;</span></span><a moz-do-not-send="true" href="mailto:Chimera-users@cgl.ucsf.edu" class="" style="font-family: Helvetica; font-size: 12px; font-style: 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;">Chimera-users@cgl.ucsf.edu</a><br class="" style="font-family: Helvetica; font-size: 12px; font-style: 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;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: 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; float: none; display: inline !important;">Manage subscription:<span class="Apple-converted-space">&nbsp;</span></span><a moz-do-not-send="true" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="" style="font-family: Helvetica; font-size: 12px; font-style: 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;">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></div></div></div><br class=""><fieldset class="mimeAttachmentHeader"></fieldset><br class=""><pre wrap="" class="">_______________________________________________
Chimera-users mailing list: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a>
Manage subscription: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>
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