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<p>chimera --nogui can't access graphics. Headless chimera has
software OpenGL rendering, so it can be used to create images.
Make sure to use the windowsize command to set the size of the
framebuffer. Don't know if pychimera cares.</p>
<p><br>
</p>
<p> -- 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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charset=windows-1252">
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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>
<div id="Signature">
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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: +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>
</div>
<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"><gregc@cgl.ucsf.edu></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> </div>
</div>
<div>
<p>Yes, Chimera's Python code is only "warrantied" to work
with its own Python. 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. 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>.
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">
<div id="divtagdefaultwrapper"
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;
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Joe Healey<br style="font-size:10pt">
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<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
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 </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 moz-do-not-send="true"
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 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> </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>
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display:inline!important">Manage
subscription:<span
class="Apple-converted-space"> </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>
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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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