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']

aln = alignment(env)
aln.append(file='4WLBA.aln', align_codes='all')

class MyModel(automodel):
    def select_atoms(self):
        return selection(self.get_insertions(aln, minlength=1, maxlength=30, extension=0, include_termini=True))

a = MyModel(env, alnfile = '4WLBA.aln',
            knowns = '4WLB_flexprotA', sequence = '4WLBA')
a.starting_model= 1
a.ending_model  = 1

a.make()