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choderalab / msm-pipeline

A pipeline for MSMs.
GNU Lesser General Public License v3.0
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Align macrostate PDBs #35

Closed maxentile closed 7 years ago

maxentile commented 7 years ago
jchodera commented 7 years ago

Aligns all structures to a single configuration sampled from the minimum free energy macrostate and saves PDBs

I think we had discussed a two-stage procedure here:

  1. Align the cluster generator onto a single structure (e.g. the minimum free energy macrostate)
  2. Align cluster members onto their cluster generator
maxentile commented 7 years ago

Ahh, right, sorry I had misinterpreted the specification, fixing now.

Note that we don't actually have structures for the cluster generators (the "generators" are points in the tICA projection that don't necessarily correspond to a structure), so I'll just say the "generator" is the configuration with the minimum mean RMSD to all other samples drawn from that macrostate?

jchodera commented 7 years ago

Note that we don't actually have structures for the cluster generators (the "generators" are points in the tICA projection that don't necessarily correspond to a structure), so I'll just say the "generator" is the configuration with the minimum mean RMSD to all other samples drawn from that macrostate?

Oh, right---I keep forgetting we're using k-means and not k-medoids (which we used in the 2007 paper for exactly this reason).

Yes, this sounds like a fine approach.

maxentile commented 7 years ago

I think this should be ready to review and merge: @sonyahanson , @jchodera ?

jchodera commented 7 years ago

Looks great!