Chimera Menus

The major menu headings are:

Except in the native Mac (non-X-Windows) version of Chimera, 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. See also: context menus



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.)


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 Volume menu is a replica of the Tools... Volume Data menu. It can be shown/hidden using Tools... Volume Data... Volume Menu on Menubar or the similar entry in the Tools menu of Volume Viewer.


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.

There are also entries related to third-party extensions (plugins available separately from the Chimera download):

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 entries in the Tools menu (individually specified using the Tools preferences). The default contents are


Start-of-line aliases defined with the command alias will be listed here. Choosing an entry from the Aliases menu executes the alias. The Aliases menu will only be present when there is at least one start-of-line alias.


Documentation pages requested from the Help menu will be shown in a browser window.

UCSF Computer Graphics Laboratory / April 2018