findClusters

This script clusters structures by their positional RMSD, using the given atom selection.

Usage: findClusters [option] <pdb files>

where options are zero or more of:

-psf=<psf file>
-selection=<atoms to consider for clustering [name CA]>
-fitSelection=<atoms to use for fitting [defauts to -selection]>
-noFit
-tolerance=<distance tol used to exit algorithm [1.000000]>

If -noFit is specified, then the structures are not fit before being clustered.

Initially, each structure is in a separate cluster. The algorithm to combine these clusters is as follows:

  1. find closest two clusters, combine these
  2. generate a new distance matrix, where now distance between clusters is the shortest structure-structure distance of the clusters
  3. repeat until the shortest distance is larger than the tolerance

The result is printed to stdout.

If the -psf option is not given, PSF information is automatically generated from the input PDB. All input structures must have the same PSF.

Additional common options