# Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class MyModel(automodel):
    def special_patches(self, aln):
        # A disulfide between residues 8 and 45:
        self.patch(residue_type='DISU', residues=(self.residues['8'],
                                                  self.residues['45']))

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

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

a = MyModel(env,
            alnfile  = 'alignment.ali',     # alignment filename
            knowns   = '5fd1',              # codes of the templates
            sequence = '1fdx')              # code of the target
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 the actual homology modeling

919a966dbd5f82febee909a124b15de13061e9aa
<mask token>


class MyModel(automodel):

    def special_patches(self, aln):
        self.patch(residue_type='DISU', residues=(self.residues['8'], self.
            residues['45']))


<mask token>

<mask token>


class MyModel(automodel):

    def special_patches(self, aln):
        self.patch(residue_type='DISU', residues=(self.residues['8'], self.
            residues['45']))


log.verbose()
<mask token>
a.make()

<mask token>


class MyModel(automodel):

    def special_patches(self, aln):
        self.patch(residue_type='DISU', residues=(self.residues['8'], self.
            residues['45']))


log.verbose()
env = environ()
env.io.atom_files_directory = ['.', '../atom_files']
a = MyModel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx')
a.starting_model = 1
a.ending_model = 1
a.make()

from modeller import *
from modeller.automodel import *


class MyModel(automodel):

    def special_patches(self, aln):
        self.patch(residue_type='DISU', residues=(self.residues['8'], self.
            residues['45']))


log.verbose()
env = environ()
env.io.atom_files_directory = ['.', '../atom_files']
a = MyModel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx')
a.starting_model = 1
a.ending_model = 1
a.make()

# Homology modeling by the automodel class
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

# Redefine the special_patches routine to include the additional disulfides
# (this routine is empty by default):
class MyModel(automodel):
    def special_patches(self, aln):
        # A disulfide between residues 8 and 45:
        self.patch(residue_type='DISU', residues=(self.residues['8'],
                                                  self.residues['45']))

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

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

a = MyModel(env,
            alnfile  = 'alignment.ali',     # alignment filename
            knowns   = '5fd1',              # codes of the templates
            sequence = '1fdx')              # code of the target
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 the actual homology modeling
