Have a look at the modeller.parallel module and friends: http://salilab.org/modeller/manual/node69.html http://salilab.org/modeller/manual/node408.html#SECTION:parallel As an example, you need to have something like this: from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class from modeller.parallel import * # Load the parallel class, to use multiple processors j = job(modeller_path=os.path.join(modellerPath, "bin/modslave.py")) j.append(local_slave()) # 1 Processor j.append(local_slave()) # 2 Processors j.append(local_slave()) # 3 Processors...and so on env = environ() ..... Regular Modeller definitions..... a.use_parallel_job(j) # Use the job for model building a.make() # do the actual homology modeling Regards, João [...] Rodrigues @ http://stanford.edu/~joaor/