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   = ('d3ckma1', 'c3fflC_', 'c2xcbA_', 'c2kc7A_', 'c3k9iA_', 'c3hymB_', 'c2r5sB_', 'c3pe3D_', ),
              sequence = 'query')
a.starting_model= 1
a.ending_model  = 1
a.make()
