2 """This script shows how to create DENSITY representations.
3 and set up the Gaussian EM restraint.
5 These representations are useful when you are doing EM fitting with rigid bodies.
7 Preliminary step: you should convert your EM map to a GMM file
8 with the command line utility create_gmm.py (located in isd/pyext/src/create_gmm.py):
9 python create_gmm.py emd_1883.mrc 50 emd_1883.gmm50.txt -m emd_1883.gmm50.mrc
32 mol = st.create_molecule(
"Rpn4",sequence=seqs[
"1WCM:D"],chain_id=
"D")
40 mol.add_representation(atomic_res,
42 density_residues_per_component=10,
43 density_prefix=
"Rpn4_gmm",
44 density_force_compute=
False,
45 density_voxel_size=3.0)
49 mol.add_representation(mol.get_non_atomic_residues(),
51 setup_particles_as_densities=
True)
62 densities =
IMP.atom.Selection(hier,representation_type=IMP.atom.DENSITIES).get_selected_particles()
67 scale_target_to_mass=
False,
68 target_mass_scale=100000,
71 output_objects.append(emr)