Rosetta 3.1 Release Manual

Cluster Application

This is a Clustering tool for PDBs and or silent files in structure predictions. This tool helps to identify the decocy with the most neighbors within a certain RMSD threshold by clustering bunch of protein structures.The cluster application is at rosetta_source/src/apps/public/. The name of the application is

Command Lines and Options

Result Interpretation

You can use -nooutput to skip generating pdb files. All the clustering information are recored in the log file. You can find the "Summary" section at the bottom of the log file. For Example:
---------- Summary ---------------------------------
Cluster:  0  N: 1   c.0.*.pdb
    1HOE_0001  1.44308 0

Cluster:  1  N: 1   c.1.*.pdb
    1QYS_0001  97.4857 0

  Clusters: 2
  Structures: 2
  Cluster: 0s
  Additional Clustering: 0s
  Total: 3

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