bayesianem, an IMP module for Bayesian multi-scale modeling of macromolecular structures based on cryo-electron microscopy density maps

Usage:

First, import the module:

import IMP.bayesianem
import IMP.bayesianem.restraint

Then, select the model densities that you want to assign to the EM:

sel = IMP.atom.Selection(hierarchy=hier, representation_type=IMP.atom.DENSITIES)
densities=sel.get_selected_particles()

Finally, create the restraint (replace gmm.txt by your target gmm), and add it to the model.

gem = IMP.bayesianem.restraint.GaussianEMRestraintWrapper(densities,
                                                 target_fn=‘gmm.txt',
                                                 scale_target_to_mass=True,
                                                 slope=0.01,
                                                 target_radii_scale=3.0,
                                                 target_is_rigid_body=False)
gem.add_to_model()
gem.set_label("Total")
output_objects.append(gem)

Info

Author(s): Samuel Hanot, Massimiliano Bonomi, Riccardo Pellarin

Maintainer: Riccardo Pellarin

License: LGPL

Publications:

• M. Bonomi, S. Hanot, C. H. Greenberg, A. Sali, M. Nilges, M. Vendruscolo, R. Pellarin. "Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling", Structure 27, 2019.