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: GPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU 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::Vector < AlignSymmetric >	AlignSymmetrics

typedef IMP::Vector < CnSymmAxisDetector >	CnSymmAxisDetectors

typedef IMP::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 ()
	Return the version of this module, as a string. More...

std::string	get_module_name ()

std::string	get_data_path (std::string file_name)
	Return the full path to one of this module's data files. More...

std::string	get_example_path (std::string file_name)
	Return the full path to one of this module's example files. More...

Typedef Documentation

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

Pass or store a set of AlignSymmetric .

Definition at line 62 of file AlignSymmetric.h.

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

Pass or store a set of CnSymmAxisDetector .

Definition at line 60 of file CnSymmAxisDetector.h.

typedef IMP::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 one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

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

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

Note: Each module has its own data directory, so be sure to use this function from the correct module.

std::string IMP::cnmultifit::get_example_path ( std::string file_name )

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::cnmultifit::get_example_path("example_protein.pdb"));

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

Note: Each module has its own example directory, so be sure to use this function from the correct module.

std::string IMP::cnmultifit::get_module_version ( )

Return the version of this module, as a string.

Note: This function is only available in Python.

Definition at line 5 of file EMageFit/__init__.py.

Detailed Description

cnmultifit: command line tool

Web server

Info

Classes

Typedefs

Functions

Standard module functions

Typedef Documentation

Function Documentation