Chimera Menus

The major menu headings are:

The menus are tear-off, as indicated by a dashed line above the entries when the menu contents are shown. Choosing the dashed line instead of an entry makes the menu an independent window that remains up until explicitly closed. Unavailable options are grayed out.



Selection designates items for subsequent Actions. When nothing is selected, Actions apply to "all." (Note: Any of the entries in Chemistry, Residue... amino acid category, and Structure can also be used to specify atoms in the Command Line.) (other categorizations can be defined and listed in the top section of the Select menu, using the Selector Construction Panel)


Which items are affected by Actions (the targets) depends on the current selection. For actions under Atoms/Bonds, Ribbon, Surface, Color, Label, Focus, and Set Pivot: Inspection and file-writing actions, however, apply only to explicit selections.


A preset is a predefined combination of display settings. Choosing an entry in the Presets menu applies its settings and is much easier than adjusting the many settings individually. Presets are provided for a handful of usage scenarios; of course, many more combinations of settings are possible. See also: the preset command, the New Molecules preferences


The Tools menu contains the Chimera tools or extensions. In general, there will be several submenus of the form

where choosing an individual tool (extension) launches it. See the Chimera Tools index for descriptions of the individual tools.

If certain tools or extensions have been started and not quit during a Chimera session, their instances will appear in the bottom section of the Tools menu:


The Favorites menu contains the Preferences in addition to any subset of the Tools menu (individually specified using the Tools preferences). The default contents are


Documentation pages requested from the Help menu will be shown in a browser window.
UCSF Computer Graphics Laboratory / August 2009