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,