Rigid bodies

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.

rigid_body(*atom_ids)
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.

Example: examples/python/rigid_body.py

from modeller import *

env = environ()
env.io.atom_files_directory = '../commands'
mdl = model(env, file='1fas')

# Keep residues 1-10 rigid:
r = rigid_body(mdl.residue_range('1:', '10:'))
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')