Dear Ben Webb, Thanks for everything you have been very helpful. I'm trying to include one model I generated in the optimization scrip fro FAQ: from modeller import * from modeller.automodel import * log.verbose() env = environ() a = automodel(env, alnfile='align1.ali', knowns='templ1', sequence='targ1') # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Very thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() How can I do it? And how can I automate it including on this script to optimize only the best model: from modeller import * from modeller.automodel import * log.verbose() env = environ() a = automodel(env, alnfile = '1', knowns = ('2', '3'), sequence = 'bar', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model= 1 a.ending_model = 10 a.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model: %s (DOPE score %.3f)" % (m['name'], m[key]) a.make() Thanks again, -- Atila Iamarino L.E.M.B. - Laboratory of Molecular Evolution and Bioinformatics Av. Prof. Lineu Prestes, 1734 - USP (University of São Paulo) - ICB Zip: 05508-000 Phone: +55 11 30917290 / +55 11 30918453