I'm using Rosetta ~10,000 PDB output and using cluster software Calibur to cluster it.
And question occurs to me, is that, are the alpha carbon RMSD for each clusters, were calculated after all the PDBs are superimposed? or were RMSD calculate before they are superimposed, to represent the most popular states in space? (either answer about Calibur or Rosetta's own cluster application will be very helpful!)
Because my RMSD for each cluster is very large ~10 Angstrom, which should ideally < 2 angstrom to get a close to native structure, right?
Thanks for your help!