MultiFit MultiFit icon

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.

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.
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. Results also depend on: Clicking Fit runs the calculation as a background task. Clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired. Reset deletes any existing results; otherwise, new results will be appended to those already in the dialog (rather than replacing them automatically). Close dismisses the dialog. Help opens this manual page in a browser window.

Clicking the Options button reveals additional settings (clicking the close button on the right hides them again):

MultiFit Results

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:

The solution list can be sorted by the values in any displayed column by clicking the column header. Clicking the header once sorts the entries in order of increasing value and places an up arrowhead (triangle) in the header. Clicking again sorts the entries in decreasing order and places a down arrowhead (inverted triangle) in the header.

Currently, MultiFit results are not saved in sessions, other than the models displayed at the time of saving. To save a solution:

  1. click its row in the MultiFit dialog to display its models
  2. use File... Save PDB in the Chimera menu to save the models as one or more PDB files relative to the density map model

UCSF Computer Graphics Laboratory / August 2011