from modeller import * 
from modeller.automodel import * 
log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in
env.io.atom_files_directory = './:../atom_files'
a = automodel(env,
              alnfile  = 'modeller.pir',
              knowns   = ('c3tpaA_', 'd1dpea_', 'c2wokA_', 'd1jeta_', 'c3m8uA_', 'd1uqwa_', 'd1lnwa_', 'd1i5za1', 'd1sfxa_', 'd2oz6a1', 'c3g3zA_', 'c3bj6B_', 'd3broa1', ),
              sequence = 'query')
a.starting_model= 1
a.ending_model  = 1
a.make()
