IMP.multifit_tools

Table of Contents

• multifit
• complex_to_anchor_graph

multifit

Fit atomic structures into EM density maps.

MultiFit is a protocol for simultaneously fitting atomic structures of components into the cryo-electron microscopy (cryo-EM) density map of their assembly. It can also incorporate connectivity information from proteomics experiments (such as cross links), and can work with density maps at resolutions as low as 25A.

See also cnmultifit for a similar protocol operating on symmetric complexes.

The component positions and orientations are optimized with respect to a scoring function that includes the quality-of-fit of components in the map, the protrusion of components from the map envelope, and the shape complementarity between pairs of components. The scoring function is optimized by an exact inference optimizer DOMINO that efficiently finds the global minimum in a discrete sampling space. The protocol employs the IMP::multifit module.

A webserver is also available.

Examples:

• Modeling of 3sfd

complex_to_anchor_graph

Build an anchor graph from a PDB file.

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:

• Keren Lasker, Maya Topf, Andrej Sali, “Determining macromolecular assembly structures by molecular docking and fitting into an electron density map”, Journal of Molecular Biology, 2009.
• Keren Lasker, Daniel Russel, Jeremy Phillips, Haim Wolfson, Andrej Sali, “Determining architectures of macromolecular assemblies by aligning interaction networks to electon microscopy density maps”, submitted