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

Eric Pettersen pett at cgl.ucsf.edu
Fri Jun 4 08:36:06 PDT 2021

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 at CA".


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jun 4, 2021, at 8:07 AM, Laura Morris via Chimera-users <chimera-users at 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 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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