Fit to Segments Fit to Segments icon

Fit to Segments rigidly fits atomic structures into segmentation regions from Segment Map. 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 at NCMI, Fit in Map, Volume Viewer, measure, molmap, mask

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

The Structure to fit should be chosen from the pulldown menu of molecule models. Any atoms in the model that are not desired for fitting, such as solvent or extra chains, should be deleted before the fitting is done.

Clicking Fit 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 the Regions menu in Segment Map 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 PDB files or removed from the table using the Fit to Segments File menu.

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

Fit to Segments Menu


UCSF Computer Graphics Laboratory / September 2010