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

Laura Morris lcmorris at uga.edu
Fri Jun 4 08:07:00 PDT 2021

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.




Laura C. Morris

Scientific Computing Professional

Edison & Prestegard Labs

Complex Carbohydrate Research Center

706-542-6286 (lab 1075)

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