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<p>Hi Chimera Team,</p>
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<p>I've been following this great tutorial:</p>
<p><a href="https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html#case1" class="OWAAutoLink" id="LPlnk280133" previewremoved="true">https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html#case1</a></p>
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<p>To render a structure by conservation. I'd like to run this non-interactively for a number of proteins though. Could you tell me what the python or 'chimera code' equivalents would be?</p>
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<p>For instance, I would provide a structure (or structures in a session) and MSA in fasta format already, so without interactive menus I'd like to:</p>
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<li><span style="font-size: 12pt;">Open the structure(s) and MSA</span></li><li><span style="font-size: 12pt;"></span><span style="font-size: 12pt;">get the conservation from MultAlign (the actual conservation metric doesn't particularly matter to me at the moment)</span></li><li><span style="font-size: 12pt;">Render any open models by conservation, say using the cyan-maroon colour scale</span></li><li><span style="font-size: 12pt;">Additionall depict as smooth worms with defined min and max radii</span></li></ol>
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If this is possible!</p>
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<p>Thanks!</p>
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<p>Joe</p>
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Joe Healey<br style="font-size:10pt">
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<span style="text-decoration:underline"> </span><br>
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<span style="font-size:10pt">M.Sc. B.Sc. (Hons) MSRB</span><br>
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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: +44 (0) 7536 042620 | </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 </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 href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/" id="LPNoLP">Gibson Lab</a> (Warwick Chemistry)<br style="">
</span></div>
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</span></div>
<div><span style="font-size:10pt">Twitter: <a href="https://twitter.com/JRJHealey" id="LPNoLP">
@JRJHealey</a> | </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> | ORCID: <span id="ms-rterangepaste-start"></span><span>orcid.org/0000-0002-9569-6738</span><span id="ms-rterangepaste-end"></span></div>
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