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Tool: Fit to Segments

Fit to Segments rigidly fits atomic structures or maps 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.

Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps. Pintilie G, Chiu W. Biopolymers. 2012 Sep;97(9):742-60.
See also: Volume Viewer, Fit in Map, fitmap, Segger website

Dialog and Basic Usage

Fit to Segments can be started from the Volume Data section of the Tools menu (more...).

The Structure or Map to fit should be chosen from the pulldown menu of models. It can be a density map, an entire atomic model, or the selected atoms only. If an entire atomic model is chosen, any parts not desired for fitting (such as solvent, ligands, or extra chains) should be deleted from that model.

Clicking the Fit button at the bottom of the dialog performs the fitting. By default, the structure is fit to the selected set of one or more segmentation region(s) using the principal axes method. The regions are made transparent; region transparency/opacity can be adjusted further using the Segment Map shortcuts options or its Regions menu.

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 Fit to Segments menu.

Clicking Help shows documentation in a browser window.


Fit to Segments Menu


UCSF Resource for Biocomputing, Visualization, and Informatics / July 2019