Miriam Leach wrote: > I wondered if somebody could help me. > Is it at all possible to cluster existing pdb files ? If so can you tell me how > to arrange the input arguments I tried using > > a=automodel env, alnfile = '', > knowns = ('pdb1', 'pdb2'... > with cluster(cluster_cut).

automodel.cluster() will make a representative of all the models built from one automodel run, by clustering. You can't use it to cluster arbitrary PDB files.

> Any help/example scripts would be very much appreciated

See http://salilab.org/modeller/wiki/Cluster_PDBs

Ben Webb, Modeller Caretaker