Generate cyclic atomic structures using cryo-electron microscopy data. More...

Detailed Description

Generate cyclic atomic structures using cryo-electron microscopy data.

This module implements a protocol for generating atomic structures of complexes with cyclic symmetry (such as rings), using only the atomic structure of a single subunit and a cryo-electron microscopy density map of the complex. See the IMP::multifit module for a similar protocol for handling non-symmetric complexes.

cnmultifit: command line tool

Generally, this module is not used directly; instead, the cnmultifit command line tool is used. For an example, see Modeling of GroEL.

Web server

A webserver that uses both this module and the IMP::multifit module is also available.

Info

Author(s): Keren Lasker

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:

See main IMP papers list.
K. Lasker, M. Topf, A. Sali, H. J. Wolfson, "Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly", J Mol Biol 388, 2009

Classes
class	AlignSymmetric
	A class for fast alignment of a cyclic model to its density. More...

class	CnSymmAxisDetector
	Detect cn symmetry in proteins and density maps. More...

class	MolCnSymmAxisDetector
	molecule symmetry detector More...

Typedefs
typedef IMP::base::Vector < AlignSymmetric >	AlignSymmetrics

typedef IMP::base::Vector < CnSymmAxisDetector >	CnSymmAxisDetectors

typedef IMP::base::Vector < MolCnSymmAxisDetector >	MolCnSymmAxisDetectors

Functions
em::DensityMap *	build_cn_dens_assembly (em::DensityMap *subunit_dens, const em::DensityHeader &asmb_dens_header, algebra::Transformation3D monomer_t, int symm_deg)

algebra::Transformation3D	calc_transformation_around_axis (algebra::Vector3D a, algebra::Vector3D b, float angle_rad)

float	cn_symm_score (atom::Hierarchies mhs, const algebra::Vector3D &center, const algebra::Vector3D &direction, int symm_deg)
	scores an input vector as a symmetry axis More...

void	do_all_fitting (const std::string param_filename, const std::string chimera_filename="")
	High level interface to build cyclic symmetric complexes. More...

em::FittingSolutions	fit_cn_assembly (atom::Hierarchies mhs, int dn_symm_deg, em::DensityMap *dmap, float threshold, const AlignSymmetric &aligner, bool sample_translation=false, bool fine_rotational_sampling=true)
	Fit a symmetric model to its density. More...

em::FittingSolutions	fit_cn_assembly (em::DensityMap asmb_map, const MolCnSymmAxisDetector &symm_mol, em::DensityMap dmap, const CnSymmAxisDetector &symm_map, int symm_deg, float threshold)

algebra::Transformation3Ds	generate_cn_transformations (atom::Hierarchies mhs, int symm_deg)

algebra::Transformation3Ds	generate_translations_along_symm_axis (atom::Hierarchies mhs, int symm_deg)

float	get_cn_rmsd (atom::Hierarchies mh1, atom::Hierarchies mh2)
	Find correspondence between the two rings and calculate rmsd. More...

Floats	get_rmsd_for_models (const std::string param_filename, const std::string trans_filename, const std::string ref_filename, int start_model=0, int end_model=-1)

bool	pca_matching (const algebra::PrincipalComponentAnalysis &pca1, const algebra::PrincipalComponentAnalysis &pca2, float resolution)

multifit::FittingSolutionRecords	prune_by_pca (const std::string &param_fn, const multifit::FittingSolutionRecords &sols, int dn=1)

em::FittingSolutions	symmetry_local_fitting (atom::Hierarchies mhs, int cn_symm_deg, int dn_symm_deg, em::DensityMap *dmap, int num_of_trans_to_consider)

void	transform_cn_assembly (atom::Hierarchies mhs, algebra::Transformation3D monomer_t)

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...

Typedef Documentation

typedef IMP::base::Vector< AlignSymmetric > IMP::cnmultifit::AlignSymmetrics

Pass or store a set of AlignSymmetric .

Definition at line 62 of file AlignSymmetric.h.

typedef IMP::base::Vector< CnSymmAxisDetector > IMP::cnmultifit::CnSymmAxisDetectors

Pass or store a set of CnSymmAxisDetector .

Definition at line 60 of file CnSymmAxisDetector.h.

typedef IMP::base::Vector< MolCnSymmAxisDetector > IMP::cnmultifit::MolCnSymmAxisDetectors

Pass or store a set of MolCnSymmAxisDetector .

Definition at line 46 of file MolCnSymmAxisDetector.h.

Function Documentation

float IMP::cnmultifit::cn_symm_score	(	atom::Hierarchies	mhs,
		const algebra::Vector3D &	center,
		const algebra::Vector3D &	direction,
		int	symm_deg
	)

scores an input vector as a symmetry axis

void IMP::cnmultifit::do_all_fitting	(	const std::string	param_filename,
		const std::string	chimera_filename = `""`
	)

High level interface to build cyclic symmetric complexes.

Given a parameter file, this function does all the work to build a number of fits of the monomer into a density map of the symmetric complex.

Parameters

param_filename	Name of a parameter file.
chimera_filename	If not empty, the name of a file that will be generated containing Chimera-compatible fit information.

em::FittingSolutions IMP::cnmultifit::fit_cn_assembly	(	atom::Hierarchies	mhs,
		int	dn_symm_deg,
		em::DensityMap *	dmap,
		float	threshold,
		const AlignSymmetric &	aligner,
		bool	sample_translation = `false`,
		bool	fine_rotational_sampling = `true`
	)

Fit a symmetric model to its density.

float IMP::cnmultifit::get_cn_rmsd	(	atom::Hierarchies	mh1,
		atom::Hierarchies	mh2
	)

Find correspondence between the two rings and calculate rmsd.

std::string IMP::cnmultifit::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::cnmultifit::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.

Detailed Description

cnmultifit: command line tool

Web server

Info

Classes

Typedefs

Functions

Standard module functions

Typedef Documentation

Function Documentation