-in:file:fullatom #Read as fullatom input structure -out:file:silent cluster.out #Output silent structures instead of PDBs -run:shuffle #Use shuffle mode -cluster:radius -1 #Cluster radius in A for RMS clustering or in inverse GDT_TS for Global Distance Test score clustering. Use "-1" to trigger automatic radius detection #-cluster:input_score_filter 0 #Ignore structures above certain energy (this seems to be not necessary) #-cluster:exclude_res [ ..] #Exclude residue numbers from structural comparisons