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<p class="MsoNormal">Hi Eric,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you very much! <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Ben <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Eric Pettersen <pett@cgl.ucsf.edu>
<br>
<b>Sent:</b> 06 August 2020 00:40<br>
<b>To:</b> benjamintam <benjamintam@um.edu.mo><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] Using python to run rotamer<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Ben,<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>It might be easier to just use the "swapaa" command than to use the useRotamer() or useBestRotamers() calls (there is no useRotamers() call). You can run any regular Chimera command from
Python by using the runCommand() function, <i>e.g.</i> to run "swapaa leu #0:248.a" you would:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>from chimera import runCommand<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>runCommand("swapaa leu #0:248.a")<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You should look at this simple example of a Chimera Python script that does some looping and writes out result files: <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cgl.ucsf.edu_chimera_docs_ProgrammersGuide_basicPrimer.html&d=DwMFaQ&c=KXXihdR8fRNGFkKiMQzstu-8MbOxd1NuZkcSBymGmgo&r=EElAJhvpEXZIOG4aO3Q_1Fg1wh-iIcDTLJ2t8QVMlxU&m=tAlvtvhqR4bZXsSVLxOtdy1Kr93uvTSSz3XaNbvvH6g&s=04iNgJ5i2fvGm9HvoCYkIPt82I1yvvcNDHgfhZab32o&e=">Very
Basic Chimera Programming Primer</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">--Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Eric Pettersen<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>UCSF Computer Graphics Lab<o:p></o:p></p>
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<p class="MsoNormal">On Aug 5, 2020, at 1:21 AM, <a href="mailto:mailman-bounces@cgl.ucsf.edu">
mailman-bounces@cgl.ucsf.edu</a> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Dear all,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I am trying to simplify tedious and repetitive work through using Chimera. My work has to substitute a list of residue on a protein. For each row of the list, after the substitution, I need to save it as a separate file.<o:p></o:p></p>
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<p class="MsoNormal">Since I am a beginner of python coding, I would like to ask the following question before I attempt to code:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">-From what I said, is it possible to do it in Chimera?<o:p></o:p></p>
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<p class="MsoNormal">-Do I just call the Rotamer program out by using “useRotamers()”? If it is using that, how do I provide the residue number and residue type into the program?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Thanks for your time and help.<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Ben<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
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https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><o:p></o:p></p>
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