[Chimera-users] Total number of atoms in all submodels

Cruz, Phil (NIH/NIAID) [C] phil.cruz at nih.gov
Thu Mar 19 13:16:32 PDT 2015


Dear Chimera users,

When I fetch a biological unit into Chimera from PDB, the symmetry related units are placed into separate submodels.  I would like to find the total number of atoms in all submodels that make up the biological unit within a python script.

Constructs (and variations that I've tried) such as the following only give the number of atoms in each sub model:

numAtoms = len(openModels.list(modelTypes=[Molecule])[0].atoms)

Is there some way to get the grand total of atoms?

Alternatively, if the script could find the total number (or list) of the submodels, I could probably still handle it.

My example is the virus capsid 1ej6.

Thanks for any suggestions.


--
Phillip Cruz, Ph.D.
Contractor, Medical Science & Computing

Computational Structural Biologist
Computational Biology Section
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Dr., Room 3B62
Bethesda, MD 20892-0485
Office:  301-451-1089
http://bioinformatics.niaid.nih.gov<http://bioinformatics.niaid.nih.gov/> (Within NIH)
http://exon.niaid.nih.gov<http://exon.niaid.nih.gov/> (Public)

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