[Chimera-users] command line clustering (how to select a subSection?)

[Laura Morris]

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 (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-May/005166.html) 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:


def main():
    import chimera
    modelList = chimera.openModels.list(modelTypes=[chimera.Molecule])
    subSelection = None # Change this to CAs or  heavy atoms
    clusterInfo = _cluster(modelList, subSelection)
    saveReps(clusterInfo, "reps.pdb") # Change file name if needed

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 at 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?

Any help is appreciated.

Regards,

Laura


-----

Laura C. Morris

Scientific Computing Professional

Edison & Prestegard Labs

Complex Carbohydrate Research Center

706-542-6286 (lab 1075)

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