Hi Laura, Looking at the code from that mail, the subSelection is just a string with the atom spec you want, but without the model number part. So for carbon alphas it would be "@CA". For the example you gave it would be ":3-55@CA". --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 4, 2021, at 8:07 AM, Laura Morris via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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 <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@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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