IMP::restrainer Namespace Reference

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Detailed Description

This module provides a higher level interface for using experimental proteomics data with IMP.

Introduction

Restrainer is an IMP module that provides convenient way of inputting molecule definition and experimental data into IMP. This module will take experimental data in XML format, and translate it into IMP restraints to construct models at a variety of different resolutions or levels.

The XML input data is divided into 3 parts:

1. Representation
   • Each component in the system can have either atomic or geometric shape representation.
2. RestraintSet
   • Restraint can be added for each component, between and among components in the representation.
3. Display
   • Colors for the representation components can be defined and an output file can be generated in chimera format.

The XML schema is provided to check the validation of the input data. The visualization of the XML schema can be seen here.

To check if the XML files are valid use the schema.xsd which can be found as part of the restrainer data.

xmllint --schema schema.xsd --noout *.xml

The process of preparing the input data for restrainer can be best shown using simple examples.

Examples:

• restrainer examples
• All examples using IMP.restrainer

Author(s): Elina Tjioe, Keren Lasker, Jeremy Phillips, Ben Webb

Version: SVN.r12662

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:

• Daniel Russel, Keren Lasker, Ben Webb, Dina Schneidman, Javier Velázquez-Muriel, Andrej Sali, “Putting the pieces together: integrative structure determination of macromolecular assemblies”, PLoS Biology, 2012. This paper provides an overview of the key concepts in IMP and how to apply them to biological problems.
• Frank Alber, Friedrich Foerster, Dmitry Korkin, Maya Topf, Andrej Sali, “Integrating diverse data for structure determination of macromolecular assemblies”, Annual Review of Biochemistry, 2008. This paper provides a review of the integrative structure determination methodology and various data sources that can be used.

Classes
class	Display
	A class to display the configuration. More...
class	Main
class	Representation
	Store Representation. More...
class	Restraint
	Store Restraint. More...
class	SimpleConnectivity
	Simple connectivity restraint. More...
class	SimpleDiameter
	Simple diameter restraint. More...
class	SimpleDistance
	Simple distance restraint between two particles. More...
class	SimpleEMFit
	Simple EM fit restraint. More...
class	SimpleExcludedVolume
	Simple excluded volume restraint. More...
class	XMLDisplay
	Construct Display from XML file. More...
class	XMLRepresentation
	Construct Representation from XML file. More...
class	XMLRestraint
	Construct Restraint from XML file. More...
Functions
SimpleConnectivity	create_simple_connectivity_on_rigid_bodies (const core::RigidBodies &rbs, Refiner *ref=IMP::core::internal::get_rigid_members_refiner())
em::DensityMap *	load_em_density_map (char const *map_fn, float spacing, float resolution)
core::RigidBodies	set_rigid_bodies (atom::Hierarchies const &mhs)
Variables
	SimpleConnectivities = list
	SimpleDiameters = list
	SimpleDistances = list
	SimpleEMFits = list
	SimpleExcludedVolumes = list

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Function Documentation

em::DensityMap* IMP::restrainer::load_em_density_map	(	char const *	map_fn,
		float	spacing,
		float	resolution
	)

Load EM density file (.mrc or .em file).