SegFit rigidly fits atomic structures or maps into segmentation regions from Segger. Along with that tool, it is part of the Segger package described in:

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC. J Struct Biol. 2010 Jun;170(3):427-38.
See also: Segger documentation, Fit in Map, Volume Viewer, fitmap, measure, molmap, mask

There are several ways to start SegFit, a tool in the Volume Data category (including from the Volume Viewer Tools menu).

The Structure or Map to fit should be chosen from the pulldown menu of models. It can be a density map or a molecule model (atomic structure). Any atoms in the molecule model that are not desired for fitting, such as solvent or extra chains, should be deleted before the fitting is done.

Clicking the Fit button at the bottom of the dialog performs the fitting. The default settings are to fit the structure to the selected regions using the principal axes method. The regions are made transparent; region transparency/opacity can be adjusted further using Segger or the main Chimera menu Actions... Surface.

Fit information is shown in a table:

One or more rows (fits) can be chosen with the mouse. The structure is repositioned as each fit is chosen. The chosen fit(s) can be saved to files or removed from the table using the SegFit menu.

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

SegFit Menu


UCSF Computer Graphics Laboratory / November 2020