MultiFit

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.

If using Cyclic symmetry:
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.
If using No symmetry:
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:
- model ID number
- model color (a color well)
- whether Active (movable)
- whether Shown (display-enabled)
- Fit globally indicates whether to search translations all over the density map and all orientations instead of only shifts of up to ±15 Å in each direction and rotations of up to ±30° from a model's current position. The translational (shift) search increment is the map voxel size, whereas the rotational increment is set in the MultiFit options. Global fitting may take significantly longer than local fitting.
- Model name
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.

Results also depend on:

the contour level (surface display threshold) of the map in Volume Viewer, which sets the size and shape of the map envelope
certain MultiFit options

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):

Number of output assemblies (default 10) - how many solutions to the fitting problem to return to the user, after ranking by score
Resolution of the density map (Å) (default 10.0) - should be set to the resolution of the chosen experimental map; the same value is used to simulate density from the atomic coordinates, to evaluate their quality of fit to the experimental map
Sampling angle (15 to 270°) (default 30) - rotational increment for sampling model orientations
Output file location (optional) - local directory in which to place files used or produced by the calculation, including the most recent set of results, stderr, and stdout files

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:

Index - a numerical identifier, simply assigned starting with zero for the best solution found
c - structure color (a color well, which also allows changing the color)
Correlation - cross-correlation value representing the quality of fit of the structures in the map
Name - auto-generated solution name; models within a solution are named by appending an underscore and additional integer to the solution name

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:

click its row in the MultiFit dialog to display its models
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