You can also exclude certain pairs of atoms from the nonbonded list. These Python objects are added to the Restraints.excluded_pairs list.
Excludes the given two atoms from the nonbonded list.
# Demonstrate the use of excluded pairs. # In this example we approximate a disulfide linkage by creating a distance # restraint between two SG atoms in CYS residues. Since these atoms are in # different residues, ordinarily Modeller will calculate a van der Waals # (soft sphere) interaction between them. We use an excluded pair to prevent # this interaction from being calculated, as otherwise it will conflict # with the new distance restraint. # Note that this is an example only; ordinarily a DISU patch would be used # to create a disulfide linkage. The DISU patch has the advantage that it # restrains the angles and dihedrals involved with the SG-SG bond, and also # excludes these atom pairs from van der Waals interaction. from modeller import * from modeller.scripts import complete_pdb from modeller.optimizers import conjugate_gradients env = environ() env.io.atom_files_directory = ['../atom_files'] env.edat.dynamic_sphere = True env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') code = '1fas' mdl = complete_pdb(env, code) atom1 = mdl.atoms['SG:3:A'] atom2 = mdl.atoms['SG:22:A'] mdl.restraints.add(forms.gaussian(group=physical.xy_distance, mean=2.0, stdev=0.1, feature=features.distance(atom1, atom2))) mdl.restraints.excluded_pairs.append(excluded_pair(atom1, atom2)) # Retain stereochemistry atmsel = selection(mdl) mdl.restraints.make(atmsel, restraint_type='stereo', spline_on_site=False) # Optimize the model with CG cg = conjugate_gradients(output='REPORT') cg.optimize(atmsel, max_iterations=100) mdl.write(file=code+'.expair.pdb')