Dear Modeller
I am repeating my question again regarding multi chain modeling, i have been successful in developing two chain alignment by giving model-multichain.py command but when i want to create pentamer model it shows error, can you tell me which py file i can use for it or how i can change this py file given below
# Homology 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
log.verbose()
# 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: self.restraints.symmetry.report(1.0)
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 = 'multchain.ali' , # alignment filename knowns = '3EAM', # codes of the templates sequence = 'hGLR') # 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 homology modeling model-multichain.py lines 1-37/37 (END)
The above given python is used for dimer to be produce help me generate pentamer structure directly by given any python file.
Regards