MultiFit performs simultaneous rigid fitting of multiple atomic-resolution structures into density maps at resolutions as low as 25 Å. Multiple copies of a structure can be fit assuming cyclic symmetry, or multiple different structures can be fit without symmetry constraints. The method is described in:
Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Lasker K, Sali A, Wolfson HJ. Proteins. 2010 Nov 15;78(15):3205-11.The program MultiFit optimizes a score based on the quality of fit of the structures in the map, protrusions of the structures from the map envelope, and shape complementarity between pairs of structures. Chimera provides a graphical interface to running this program via a web service hosted by the UCSF RBVI. See also: Volume Viewer, Fit in Map, Fit to Segments, fitmap, measure symmetry There are several ways to start MultiFit, a tool in the Volume Data category. The atomic structure(s) and density map of interest should be open in Chimera and designated as described below.
Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. Lasker K, Topf M, Sali A, Wolfson HJ. J Mol Biol. 2009 Apr 24;388(1):180-94.
Fit [N] copies of [molecule-model / selected atoms] in map [map-model]
The stoichiometry is specified directly as N copies of the set
of input atoms, each copy to be treated as a single rigid body.
For example, if N is 7 and the input set of atoms
has stoichiometry α2β, the result will contain
7 copies of the α2&beta module, without changes
in the α-α or α-β interactions within the module.
The models to fit should be chosen (highlighted) in the table with the mouse. A model should be opened multiple times if the assembly is thought to contain more than one copy of that structure. A block of models can be chosen by dragging, or by clicking on the first (or last) line in the desired block and then Shift-clicking on its last (or first) line. Ctrl-click toggles the state (chosen or not) of a single line. The table includes:
Clicking Calculate anchor graph performs an initial assessment (also via the web service) of which regions in the density map could accommodate models. One sphere per chosen model is placed in the map to guide placement by the user prior to local fitting. The anchor graph is created as a marker model. The anchor graph will be replaced if the calculation is rerun.
Clicking the Options button reveals additional settings (clicking the close button on the right hides them again):
When the calculation finishes, the results are listed in a table in the MultiFit dialog. Each row in the table represents a solution to the fitting problem; the top 101 solutions are returned. A single solution consists of multiple models (the N copies of the input set of atoms) in their fitted positions. One or more rows can be chosen with the left mouse button to display the corresponding solution(s) in the main Chimera window. Ctrl-click toggles the state (chosen or not) of a single row. Columns in the table:
Currently, MultiFit results are not saved in sessions, other than the models displayed at the time of saving. To save a solution: