I have a trouble when clustering decoys of a transmembrane protein.
I use the MembraneAbinitio protocol to generate 5,000 decoys. Now I attempt to cluster them only considering the trans-membrane segments because my target protein has a very large (120 residues) cytoplasmic domain.
I notice that there is an option for clustering– “exclude_res”. I wonder how this option works? As you can see, I have more than 120 residues to exclude?