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<p>Hi again,</p>
<p><br>
</p>
<p>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.</p>
<p><br>
</p>
<p>Is there are resource with more information on the commandline implementation of match anywhere other than the link below?</p>
<p><br>
</p>
<p><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>
</p>
<p><br>
</p>
<p>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></p>
<p><br>
</p>
<p>But I can't quite unwrap the options specified in the command for my uses.</p>
<p><br>
</p>
<p>Perhaps another way to ask this is, can I run a command in GUI chimera, and find the EXACT command that was executed?</p>
<p><br>
</p>
<p>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.</p>
<p><br>
</p>
<p>Many thanks</p>
<br>
<p><br>
</p>
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<div id="divtagdefaultwrapper" style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif">
Joe Healey<br style="font-size:10pt">
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons)</span><br>
</div>
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<span style="font-size:10pt"></span>
<div><span style="font-size:10pt">PhD Student</span></div>
<div><span style="font-size:10pt">MOAC CDT, Senate House</span></div>
<div><span style="font-size:10pt">University of Warwick<br style="">
</span></div>
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Mob: &#43;44 (0) 7536 042620 &nbsp;| &nbsp;</span><span style="font-size:10pt">Email: J.R.J.Healey@warwick.ac.uk</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Jointly working in:<br style="">
</span></div>
<div><span style="font-size:10pt"><a href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/" id="LPNoLP">Waterfield Lab</a> (<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">WMS&nbsp;</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Microbiology
 and Infecti</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">on Un</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">it)</span></span></div>
<div><span style="font-size:10pt">and the&nbsp;<a href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP">Gibson Lab</a>&nbsp;(Warwick Chemistry)<br style="">
</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Twitter: <a href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a>&nbsp; |&nbsp;&nbsp;</span><span style="font-size:10pt">Website: </span><a href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="font-size:10pt" id="LPNoLP">MOAC Page</a></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Greg Couch &lt;gregc@cgl.ucsf.edu&gt;<br>
<b>Sent:</b> 08 September 2016 22:43:55<br>
<b>To:</b> Healey, Joe; chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers</font>
<div>&nbsp;</div>
</div>
<div>
<p>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.</p>
<p><br>
</p>
<p>&nbsp;&nbsp;&nbsp; -- Greg<br>
</p>
<br>
<div class="moz-cite-prefix">On 09/08/2016 11:53 AM, Healey, Joe wrote:<br>
</div>
<blockquote cite="mid:DB6PR0101MB2279F5E3A61251AB67027D9ED4FB0@DB6PR0101MB2279.eurprd01.prod.exchangelabs.com" type="cite">
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<p>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.</p>
<p><br>
</p>
<p>On a related point, is running chimera with --nogui equivalent to running headless chimera? I'm just wondering if pychimera is happy with either</p>
<p><br>
</p>
<p><br>
</p>
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Joe Healey<br style="font-size:10pt">
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons)</span><br>
</div>
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              color:#000000; background-color:#FFFFFF;
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<span style="font-size:10pt"></span>
<div><span style="font-size:10pt">PhD Student</span></div>
<div><span style="font-size:10pt">MOAC CDT, Senate House</span></div>
<div><span style="font-size:10pt">University of Warwick<br style="">
</span></div>
<div><span style="font-size:10pt">Coventry<br style="">
</span></div>
<div><span style="font-size:10pt">CV47AL<br style="">
Mob: &#43;44 (0) 7536 042620 &nbsp;| &nbsp;</span><span style="font-size:10pt">Email: <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><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Jointly working in:<br style="">
</span></div>
<div><span 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">Waterfield Lab</a> (<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
                    font-size:13.3333330154419px;
                    background-color:rgb(255,255,255)">WMS&nbsp;</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;
                    font-size:13.3333330154419px;
                    background-color:rgb(255,255,255)">Microbiology
 and Infecti</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;
                    font-size:13.3333330154419px;
                    background-color:rgb(255,255,255)">on Un</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;
                    font-size:13.3333330154419px;
                    background-color:rgb(255,255,255)">it)</span></span></div>
<div><span 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">Gibson Lab</a>&nbsp;(Warwick Chemistry)<br style="">
</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Twitter: <a moz-do-not-send="true" href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a>&nbsp; |&nbsp;&nbsp;</span><span style="font-size:10pt">Website: </span><a moz-do-not-send="true" href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="font-size:10pt" id="LPNoLP">MOAC Page</a></div>
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<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Greg Couch
<a class="moz-txt-link-rfc2396E" href="mailto:gregc@cgl.ucsf.edu">&lt;gregc@cgl.ucsf.edu&gt;</a><br>
<b>Sent:</b> 07 September 2016 19:49:19<br>
<b>To:</b> Healey, Joe; <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">
chimera-users@cgl.ucsf.edu</a> BB<br>
<b>Subject:</b> Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers</font>
<div>&nbsp;</div>
</div>
<div>
<p>Yes, Chimera's Python code is only &quot;warrantied&quot; 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">
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.</p>
<p><br>
</p>
<p>That said, Jaime Rodríguez-Guerra took my previous comments on this subject, <a moz-do-not-send="true" href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html">
http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html</a>, and came up with pychimera,
<a moz-do-not-send="true" href="https://pypi.python.org/pypi/pychimera">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.</p>
<p><br>
</p>
<p>&nbsp;&nbsp;&nbsp; HTH,</p>
<p><br>
</p>
<p>&nbsp;&nbsp;&nbsp; Greg<br>
</p>
<br>
<div class="moz-cite-prefix">On 09/07/2016 07:36 AM, Healey, Joe wrote:<br>
</div>
<blockquote cite="mid:DB6PR0101MB2279542470892F3506BCAF62D4F80@DB6PR0101MB2279.eurprd01.prod.exchangelabs.com" type="cite">
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<p>Hi Eric,</p>
<p><br>
</p>
<p>That looks good thank you. I think I'm going about this slightly the wrong way after some investigation however.</p>
<p><br>
</p>
<p>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?</p>
<p><br>
</p>
<p>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!).</p>
<p><br>
</p>
<p>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'.</p>
<p><br>
</p>
<p>In effect all I need is the actual algorithm for the matching process to be accessed somehow from a python script.</p>
<p><br>
</p>
<p>Do you have any advice about how best to proceed?</p>
<p><br>
</p>
<p>Many thanks,</p>
<p><br>
</p>
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Joe Healey<br style="font-size:10pt">
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons)</span><br>
</div>
<div id="divtagdefaultwrapper" style="font-size:12pt;
                  color:#000000; background-color:#FFFFFF;
                  font-family:Calibri,Arial,Helvetica,sans-serif">
<span style="font-size:10pt"></span>
<div><span style="font-size:10pt">PhD Student</span></div>
<div><span style="font-size:10pt">MOAC CDT, Senate House</span></div>
<div><span style="font-size:10pt">University of Warwick<br style="">
</span></div>
<div><span style="font-size:10pt">Coventry<br style="">
</span></div>
<div><span style="font-size:10pt">CV47AL<br style="">
Mob: &#43;44 (0) 7536 042620 &nbsp;| &nbsp;</span><span style="font-size:10pt">Email: <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><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Jointly working in:<br style="">
</span></div>
<div><span 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">Waterfield Lab</a> (<span style="font-family:Calibri,Arial,Helvetica,sans-serif;
                        font-size:13.3333330154419px;
                        background-color:rgb(255,255,255)">WMS&nbsp;</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;
                        font-size:13.3333330154419px;
                        background-color:rgb(255,255,255)">Microbiology
 and Infecti</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;
                        font-size:13.3333330154419px;
                        background-color:rgb(255,255,255)">on Un</span><span style="font-family:Calibri,Arial,Helvetica,sans-serif;
                        font-size:13.3333330154419px;
                        background-color:rgb(255,255,255)">it)</span></span></div>
<div><span 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">Gibson Lab</a>&nbsp;(Warwick Chemistry)<br style="">
</span></div>
<div><span style="font-size:10pt"><br style="">
</span></div>
<div><span style="font-size:10pt">Twitter: <a moz-do-not-send="true" href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a>&nbsp; |&nbsp;&nbsp;</span><span style="font-size:10pt">Website: </span><a moz-do-not-send="true" href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey" style="font-size:10pt" id="LPNoLP">MOAC Page</a></div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Eric Pettersen
<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>
<b>Sent:</b> 31 August 2016 18:23<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> <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>
<b>Subject:</b> Re: [Chimera-users] Recursive structure matching and acquisition of descriptive numbers</font>
<div>&nbsp;</div>
</div>
<div>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>
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<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>
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<div class="">—Eric</div>
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<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>
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<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>
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Hi,</div>
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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>
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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>
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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>
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Thanks</div>
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Joe Healey<br class="" style="font-size:10pt">
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<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="">
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<span class="" style="font-size:10pt">M.Sc. B.Sc. (Hons)</span><br class="">
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<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="">
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<div class=""><span class="" style="font-size:10pt">Coventry<br class="">
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<div class=""><span class="" style="font-size:10pt">CV47AL<br class="">
Mob: &#43;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>
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<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;
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                                      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;
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                                      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>
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</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>
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                            display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica;
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<span class="" style="font-family:Helvetica;
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                            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;
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                            word-spacing:0px">Chimera-users@cgl.ucsf.edu</a><br class="" style="font-family:Helvetica;
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                            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;
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                            word-spacing:0px">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div>
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<pre wrap="">_______________________________________________
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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