can i use Pychimera for clustering NAMD MDS results from the dcd and psf file ?

insilichem / pychimera

Use UCSF Chimera Python API in a standard interpreter

http://pychimera.readthedocs.io

GNU Lesser General Public License v3.0

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Open hima111997 opened 4 years ago

hima111997 commented 4 years ago

is there a way to use PyChimera for clustering molecular dynamics simulation using dcd and psf files generated from NAMD?

jaimergp commented 4 years ago

It's technically possible, but I am not sure the Python API is that exposed outside the GUI. There are some scripts here: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts

That said, you might be better off with libraries like MDAnalysis or PyTraj.