# Modeling using a provided restraints file (csrfile)
from modeller import *
from modeller.automodel import *    # Load the automodel class

log.verbose()
env = environ()

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

a = automodel(env,
              alnfile  = 'alignment.ali',     # alignment filename
              knowns   = '5fd1',              # codes of the templates
              sequence = '1fdx',              # code of the target
              csrfile  = 'my.rsr')            # use 'my' restraints file
a.starting_model= 1                 # index of the first model
a.ending_model  = 1                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do comparative modeling