Hi all, I'm using Modeller 9v3 (Linux) and 9v1 (WindowsXP). I perform a rudimentary automodel with the script below. On both systems I get 200 output models, all of which appear to have an identical number of residues and atoms, however the script just hangs when it executes the cluster command.

---------------- # Homology modeling by the automodel class from modeller import * from modeller.automodel import *

log.verbose() env = environ()

# directories for input atom files env.io.atom_files_directory = './'

a = automodel(env, alnfile = 'sequences3.pir', knowns = ('prot1','prot2','prot3'), sequence = 'protx', assess_methods = (assess.GA341, assess.DOPE)) a.starting_model= 1 a.ending_model = 200

a.make()

a.cluster() -----------------

I've then used the clustering script found at http://salilab.org/modeller/wiki/Cluster_PDBs with the 200 models, which uses transfer_xyz. This time the script ends with a segmentation fault (Linux) or closes unexpectedly (Windows XP). There are are no errors reported in the log file in either instance, it simply executes fine up to the point where clustering is requested and gets no further.

As this hasn't been mentioned before I assume it's not a bug. Has anyone else had this problem and overcome it?

Thanks! James