rna_cluster issue: Structures within same cluster have RMSD higher than cutoff

[mandar5335]

Hi,

I am using rna_cluster to cluster top 1% of structures after FARFAR2 run.

rna_cluster.mpi.linuxgccrelease -in:file:silent ../simple_cycle.out -out:file:silent clustered.out -nstruct 2000 -cluster:radius 5

After that structures from same cluster (confirmed with nclust id) were extracted from clustered.out with extract_pdbs command. However, their RMSD is higher than 5 Angstrom (~15 Angstrom).

This was confirmed with Pymol, Gromac's gmx rms command as well.

Is this bug or Is something missing in rna_cluster command line?

Best, Mandar