Chimera Menus

The major menu headings are:

The menus are tear-off, as indicated by dashed lines; choosing the dashed line instead of a menu 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 open molecule models and their associated molecular surfaces. (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) depend on the current selection and the setting of Actions... Target. When nothing is selected, the various operations (Atoms/Bonds, Ribbon, Surface, Color, Label, Focus, and Set Pivot) act on all open molecule models and their associated molecular surfaces (MSMS models).


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 Tools section of the Chimera User's Guide 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 / September 2006