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[modeller_usage] Multimeric Protein Modelling

Hello Modellers,

I'm running into issues when modelling a multimeric (2 chains) protein. When using the multi-chain modelling example seen in the online manual (see below) it throws an error because the monomers aren't the same length, per the special_restraints(). How can I resolve this issue? 


# Comparative modeling by the automodel class
# Demonstrates how to build multi-chain models, and symmetry restraints
from modeller import *
from modeller.automodel import *    # Load the automodel class


# Override the 'special_restraints' and 'user_after_single_model' methods:
class MyModel(automodel):
    def special_restraints(self, aln):
        # Constrain the A and B chains to be identical (but only restrain
        # the C-alpha atoms, to reduce the number of interatomic distances
        # that need to be calculated):
        s1 = selection(self.chains['A']).only_atom_types('CA')
        s2 = selection(self.chains['B']).only_atom_types('CA')
        self.restraints.symmetry.append(symmetry(s1, s2, 1.0))
    def user_after_single_model(self):
        # Report on symmetry violations greater than 1A after building
        # each model:

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

# Be sure to use 'MyModel' rather than 'automodel' here!
a = MyModel(env,
            alnfile  = 'twochain.ali' ,     # alignment filename
            knowns   = '2abx',              # codes of the templates
            sequence = '1hc9')              # 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 comparative modeling