I am novice in field of modeling.
I am doing model of homodimeric protein. I have two parts and from both of them I have template structure. Between them there is linker which is based on homologous proteins and 2D prediction helix. I want to my model that helix and symmetric homodimer.
1) If I do first model with helix and then symmetric homodimeric model - I loose helix.
2) If I do first symmetric model and them restraint helix - I loose a bit symmetry.
Is it possible to do these to restraints in one run? Or how I can handle this problem?
My .py file (#? - marks for helix in previous run)
# 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
# Override the 'special_restraints' and 'user_after_single_model' methods:
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))
# Report on symmetry violations greater than 1A after building
# each model:
#? rsr = self.restraints
#? at = self.atoms
# Add some restraints from a file:
# Residues 296-305 should be an alpha helix:
#? rsr.add(secondary_structure.alpha(self.residue_range('296:A', '305:A')))
#? rsr.add(secondary_structure.alpha(self.residue_range('845:B', '854:B')))
env = environ()
env.io.hetatm = True
# 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 = 'cpC.ali' , # alignment filename
knowns = ('cpCB', 'HXW'), # codes of the templates
sequence = 'Pase', # code of the target
inifile = 'CBPP.pdb') # use 'my' initial structure
a.starting_model= 1 # index of the first model
a.ending_model = 3 # index of the last model
# (determines how many models to calculate)
a.make() # do homology modeling
Thank you already beforehand, hopefully this is easy case for you specialists.