You can mark groups of atoms as belonging to a rigid body. They will be moved together during optimization, such that their relative orientations do not change. These are created by making a rigid_body object and adding it to the Restraints.rigid_bodies list.
Note that all intra-body atom pairs are removed from the nonbonded list, since those distances cannot change. Thus these atom pairs will no longer contribute to any nonbonded interactions, such as Coulomb or Lennard-Jones interactions. See also selection.assess_dope().
Creates a new rigid body which contains all of the specified atoms. You can also tune the scale_factor member of the resulting object, which is used to scale the system state vector (used by conjugate_gradients() and quasi_newton() optimizations) to rigid body orientation Euler angles (in radians). (Note that no scaling is done for the position of the rigid body; thus the units of this factor are effectively radians/Å.) This can improve optimization convergence in some cases. By default the scaling factor is 1.0; values larger than 1 increase the rotational sampling, while values less than 1 will decrease it.
from modeller import * env = environ() env.io.atom_files_directory = ['../atom_files'] mdl = model(env, file='1fas') # Keep residues 1-10 in chain A rigid: r = rigid_body(mdl.residue_range('1:A', '10:A')) mdl.restraints.rigid_bodies.append(r) # Randomize the coordinates of the whole model; the rigid body remains rigid sel = selection(mdl) sel.randomize_xyz(deviation=4.0) mdl.write(file='1fas.ini')