-in:file:s==Input pdb file(s)  
-in:file:silent==Input silent file
-in:file:fullatom==Read as fullatom input structure
-out:file:silent==Output silent structures instead of PDBs 
-score:weights==Supply a different weights file (default is score12)
-score:patch==Supply a different patch file (default is score12)
-run:shuffle==Use shuffle mode
-nstruct==Make how many decoys per input structure ?
-cluster:radius==<float>Cluster radius in A (for RMS clustering) or in inverse GDT_TS for GDT clustering. Use "-1" to trigger automatic radius detection
-cluster:gdtmm==Cluster by gdtmm instead of rms (Better for loops?)
-cluster:input_score_filter==<float>Ignore structures above certain energy 
-cluster:exclude_res==<int> [<int> <int> ..]Exclude residue numbers from structural comparisons              
-cluster:radius==<float>Cluster radius
-cluster:limit_cluster_size==<int>Maximal cluster size
-cluster:limit_clusters==<int>Maximal number of clusters
-cluster:limit_total_structures==<int>Maximal number of structures in total
-cluster:sort_groups_by_energy==Sort clusters by energy.
