pseudo.py demonstrates the use of a restraint between a real atom and a pseudo atom. This input file should work with Modeller 10.0 or later. You will also need the pseudo.atm input.
from modeller import * from modeller.optimizers import ConjugateGradients e = Environ() e.edat.dynamic_sphere = False log.verbose() # Read in a dummy PDB, which defines five real atoms - four are positioned at # the corners of a square in the xy place, and the fifth is off in space m = Model(e, file='pseudo.atm') # Define a pseudo atom as the gravity center of the first 4 atoms, and add # it to the model's restraints p = pseudo_atom.GravityCenter(m.atoms[0:5]) m.restraints.pseudo_atoms.append(p) # Create a restraint on the distance between the real fifth atom and the newly # created pseudo atom, and add it to the model's restraints. Since the mean is # zero, this will force atom 5 to coexist with the gravity center. r = forms.Gaussian(group=physical.xy_distance, feature=features.Distance(m.atoms, p), mean=0.0, stdev=0.100) m.restraints.add(r) # Calculate the starting energy of all atoms in the system, then optimize s = Selection(m) s.energy() cg = ConjugateGradients() cg.optimize(s, max_iterations=200) # Write out the final coordinates m.write(file='pseudoout.atm')
It is straightforward to add restraints of this type to a comparative modeling run - see for example, Adding additional restraints to the defaults.