IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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Build assembly models consistent with EM images (class averages). More...
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:
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:
Author(s): Javier Velázquez-Muriel
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:
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 | |
std::string | get_module_version () |
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... | |
std::string IMP::EMageFit::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
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
std::string IMP::EMageFit::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
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.