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)
Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) ...
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Set of Python classes to create a multi-state, multi-resolution IMP hierarchy.
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Protocols for sampling structures and analyzing them.
Represent the root node of the global IMP.atom.Hierarchy.
Class for storing model, its restraints, constraints, and particles.
Restraints for handling electron microscopy maps.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Create movers and set up constraints for PMI objects.
Python classes to represent, score, sample and analyze models.
A dictionary-like wrapper for reading and storing sequence data.
Functionality for loading, creating, manipulating and scoring atomic structures.
Select hierarchy particles identified by the biological name.
Support for the RMF file format for storing hierarchical molecular data and markup.