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<p>Yes, Chimera's Python code is only "warrantied" to work with its
own Python. See question 3b of the Chimera Programming FAQ, <a
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. 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
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
href="https://pypi.python.org/pypi/pychimera">https://pypi.python.org/pypi/pychimera</a>.
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> HTH,</p>
<p><br>
</p>
<p> 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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style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<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>
<div id="Signature">
<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">
</div>
<div id="divtagdefaultwrapper" style="font-size:12pt;
color:#000000; background-color:#FFFFFF;
font-family:Calibri,Arial,Helvetica,sans-serif">
<br>
</div>
<div id="divtagdefaultwrapper" style="font-size:12pt;
color:#000000; background-color:#FFFFFF;
font-family:Calibri,Arial,Helvetica,sans-serif">
<span style="text-decoration:underline">
</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">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: +44 (0) 7536 042620 | </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 </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 <a
moz-do-not-send="true"
href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/"
id="LPNoLP">Gibson Lab</a> (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> | </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>
</div>
</div>
<br>
<br>
<div style="color: rgb(0, 0, 0);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
Eric Pettersen <a class="moz-txt-link-rfc2396E" href="mailto:pett@cgl.ucsf.edu"><pett@cgl.ucsf.edu></a><br>
<b>Sent:</b> 31 August 2016 18:23<br>
<b>To:</b> Healey, Joe<br>
<b>Cc:</b> <a 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> </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. The
mailing list gives the attachment a “.bin” extension but
it’s really a .py file. Just change the extension if you
need to. 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="color:rgb(0,0,0);
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>
<blockquote type="cite" class="">
<div class="">On Aug 31, 2016, at 3:02 AM, Healey, Joe
<<a moz-do-not-send="true"
href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>>
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">
</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 | </span><span
class="" style="font-size:10pt">Email:<span
class="Apple-converted-space"> </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"> </span>(<span
class=""
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:13.3333330154419px;
background-color:rgb(255,255,255)">WMS </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 <a
moz-do-not-send="true"
href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/"
id="LPNoLP" class="">Gibson Lab</a> (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"> </span><a
moz-do-not-send="true"
href="https://twitter.com/JRJHealey"
id="LPNoLP" class="">@JRJHealey</a> | </span><span
class="" style="font-size:10pt">Website:<span
class="Apple-converted-space"> </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;
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orphans:auto; text-align:start; text-indent:0px;
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<span class="" style="font-family:Helvetica;
font-size:12px; font-style:normal;
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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"> </span></span><a
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href="mailto:Chimera-users@cgl.ucsf.edu" class=""
style="font-family:Helvetica; font-size:12px;
font-style:normal; font-weight:normal;
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text-align:start; text-indent:0px;
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widows:auto; word-spacing:0px">Chimera-users@cgl.ucsf.edu</a><br
class="" style="font-family:Helvetica;
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font-size:12px; font-style:normal;
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</blockquote>
</div>
<br class="">
</div>
</div>
</div>
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<pre wrap="">_______________________________________________
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