from modeller import * from modeller.scripts import complete_pdb from modeller.optimizers import conjugate_gradients env = environ() env.io.atom_files_directory = ['../atom_files'] log.verbose() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') # Read in the model mdl = complete_pdb(env, "1fdn") rsr = mdl.restraints # Select all C-alpha atoms allat = selection(mdl) allca = allat.only_atom_types('CA') # Create a pseudo atom that is the center of all C-alphas, and activate it center = pseudo_atom.gravity_center(allca) rsr.pseudo_atoms.append(center) # Constrain every C-alpha to be no more than 10 angstroms from the center for at in allca: r = forms.upper_bound(group=physical.xy_distance, feature=features.distance(at, center), mean=10.0, stdev=0.1) rsr.add(r) # Constrain the gravity center to the x=0 plane r = forms.gaussian(group=physical.xy_distance, feature=features.x_coordinate(center), mean=0.0, stdev=0.1) rsr.add(r) # Keep sensible stereochemistry rsr.make(allat, restraint_type='stereo', spline_on_site=False) # Optimize with CG cg = conjugate_gradients() cg.optimize(allat, max_iterations=100, output='REPORT') mdl.write(file='1fas.ini')