IMP::EMageFit Namespace Reference

Build assembly models consistent with EM images (class averages). More...

Detailed Description

Build assembly models consistent with EM images (class averages).

EMageFit is an application to build models of macromolecular assemblies using restraints from EM images (class averages).

Apart from EM images, the method relies on other types of restraints:

• Maximum distance restraints imposing a maximum distance between a pair of residues, as derived from cross-linking experiments. You can of course impose maximum distance between any part of the complex. As shown in the paper, this type of restraint is required to accurately determine the orientation between the subunits of an assembly.
• Proximity restraints forcing a pair of subunits to be within a certain distance, suitable for proteomics data.
• Excluded volume restraints preventing the components of the assembly from interpenetrating.
• Geometric complementarity restraints favoring large contact surfaces between interacting subunits. These restraints can be somewhat useful if the subunits of the assembly are expected to have large contact surfaces. Among all of the restraints considered here, they are the least useful.

EMageFit samples for good conformations of the macromolecular assembly using multiple molecular docking (optional, but it can be very useful), Simulated Annealing Monte Carlo optimization, and sampling with the discrete optimizer DOMINO. It is also straightforward to incorporate other restraints to the method.

If available, EMageFit will use the docking program HEXDOCK to do docking between subunits that are related by cross-links. But it is worth mentioning that EMageFit can also work with any other docking program, or simply using the cross-linking restraints and no docking at all.

More detail on the functioning of EMageFit can be found on the protocol page, and many of the scripts and utilities are documented on the scripts page.

Examples:

• Modeling of 3sfd

Info

Author(s): Javier Velazquez-Muriel

Maintainer: benmwebb

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

• Javier A. Velazquez-Muriel, Keren Lasker, Daniel Russel, Jeremy Phillips, Benjamin M. Webb, Dina Scheidmann, Andrej Sali, “Assembly of macromolecular complexes by satisfaciton of spatial restraints from electron microscopy images”, Proc Natl Acad Sci USA 109(46), 18821-18826, 2012.

Namespaces
	argminmax
	Utility functions to extract min/max from the inputs.
	buildxlinks
	Utility functions to handle cross links.
	csv_related
	Utility functions to handle CSV files.
	database
	Utility functions to manage SQL databases with sqlite3.
	domino_model
	Classes to manage a model using DOMINO.
	imp_general
	Utility functions that are supposedly not EMageFit-specific.
	monte_carlo
	Classes for Monte Carlo sampling using rigid body relative moves.
	restraints
	Utility functions to handle restraints.
	sampling
	Utility functions to handle sampling.
	solutions_io
	Utility functions to store and retrieve solution information.
	utility
	Utility functions.

Standard module functions
All IMP modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()
std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Function Documentation

std::string IMP::EMageFit::get_data_path

(

std::string

file_name

)

Return the full path to installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

std::string IMP::EMageFit::get_example_path

(

std::string

file_name

)

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

 IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",
model));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.