diff --git a/README.md b/README.md index d1aeb9833975ef90622da9e668179fbc432bf1b9..d254f036ce0756546b261baaf0a4c8872aab7fdf 100755 --- a/README.md +++ b/README.md @@ -1,14 +1,44 @@ -\brief New module created by make-module.py on Mon Apr 4 14:07:34 2016 +\brief bayesianem, an IMP module for Bayesian multi-scale modeling of macromolecular structures based on cryo-electron microscopy density maps -Fill in this file with a description of your module. +# 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)_: (full names of author(s)) +_Author(s)_: Samuel Hanot, Massimiliano Bonomi, Riccardo Pellarin -_Maintainer_: (GitHub name of active maintainer) +_Maintainer_: Riccardo Pellarin -_License_: None +_License_: LGPL _Publications_: -- None +Bayesian multi-scale modeling of macromolecular structures based on cryo-electron microscopy density maps +Samuel Hanot, Massimiliano Bonomi, Charles H Greenberg, Andrej Sali, Michael Nilges, Michele Vendruscolo, Riccardo Pellarin +bioRxiv 113951; doi: https://doi.org/10.1101/113951 (submitted)