I used Calibur to cluster my structures produced by Rosetta. And I got RMSD ~13 Anstrong within each cluster, to me it is very high.
And I'm wondering what's the common range of the RMSD within each cluster, that is acceptable ? (either clustered by Rosetta itself or Calibur)
And what's the algorithm to calculate the distance in the Cluster application of Rosetta?
Does it compare the distance for each residue one by one, like residue 1 alpha carbon in structure 1 with residue 1 alpha carbon in structure 2, and then residue 2 's alpha carbon in these two structures, until every residue in the two structures are compared correspondingly?
Also, how to pick up a structure that best present each cluster?
The overall goal for me is to pick up a best structure among all simulated structures by Rosetta, that is closest to the native structure.
I appreciate your answers in advance!