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
8 Preliminary step: you should convert your EM map to a GMM file
9 with the command line utility create_gmm.py
10 (located in isd/pyext/src/create_gmm.py):
11 python create_gmm.py emd_1883.mrc 50 emd_1883.gmm50.txt -m emd_1883.gmm50.mrc
35 mol = st.create_molecule(
"Rpn4", sequence=seqs[
"1WCM:D"], chain_id=
"D")
36 atomic_res = mol.add_structure(
43 mol.add_representation(
47 density_residues_per_component=10,
49 density_prefix=
"Rpn4_gmm",
51 density_force_compute=
False,
54 density_voxel_size=3.0)
58 mol.add_representation(mol.get_non_atomic_residues(),
61 setup_particles_as_densities=
True)
73 hier, representation_type=IMP.atom.DENSITIES).get_selected_particles()
81 scale_target_to_mass=
False,
83 target_mass_scale=100000,
87 output_objects.append(emr)