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tubiana / TTClust

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)
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Clustering with rmsd calculated for heavy (noh) atoms #15

Closed MuhammadIIsmail closed 4 years ago

MuhammadIIsmail commented 4 years ago

Can you provide the possible arguments for -sr? as I want to change it from the (default=backbone) to heavy atoms of both backbone and side chains.

Thank you.

MuhammadIIsmail commented 4 years ago

I mean by -sr the "selection syntax for RMSD"

tubiana commented 4 years ago

Hi!

The link to the selection syntax description on the readme is indeed broken, here's another link: http://mdtraj.org/1.9.3/atom_selection.html. I use the MDTRAJ selection syntax since I use this package for parsing and calculate the distance matrix :-)

To select the heavy atoms of backbone and side-chain I would just select "protein and not type H" which will select all atoms (backbone and sidechain) excluding hydrogens Best regard, Thibault Tubiana.