From d5220b39ed631ddc347c1c4b71c4c15ea9bf9efc Mon Sep 17 00:00:00 2001
From: Samuel HANOT <shanot@susanita.bis.pasteur.fr>
Date: Wed, 7 Mar 2018 10:57:02 +0100
Subject: [PATCH] documentation

---
 README.md | 42 ++++++++++++++++++++++++++++++++++++------
 1 file changed, 36 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index d1aeb98..d254f03 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)
-- 
GitLab