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Recently I've been clustering in Chimera but running into memory limitations on my system. I'd like to do the clustering on a computer with more RAM, but I need to be able to do this using only the command line. I found an old post (<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html" id="LPlnk325162">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html</a>)
that includes an example script to do the clustering, but I don't know how to change the subSection to the residues and atoms I want. Here's the portion of relevant code:</div>
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<div><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">def main():
<div> import chimera</div>
<div> modelList = chimera.openModels.list(modelTypes=[chimera.Molecule])</div>
<div> subSelection = None # Change this to CAs or heavy atoms</div>
<div> clusterInfo = _cluster(modelList, subSelection)</div>
<div> saveReps(clusterInfo, "reps.pdb") # Change file name if needed</div>
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The "Change this to CAs or heavy atoms" is exactly what I want to do, but I have no idea how to do it. If this were command line in Chimera, I'd use something like "select #0:3-55@CA". I know there's a "runCommand" function that can be included (using "from
chimera import runCommand"). Is this used in some way to set subSelection, and if so, how?<br>
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Any help is appreciated.</div>
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Regards,</div>
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Laura<br>
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