pseudo.py demonstrates the use of a restraint between a real atom and a pseudo atom. This input file should work with Modeller 9v1 or later. You will also need the attachment:pseudo.atm input.
#!python
from modeller import *
from modeller.optimizers import conjugate_gradients
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.gravity_center(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[4], 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 = conjugate_gradients()
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.