Access to Tools

A tool or extension can be started by

choosing its name from one of the categories in the Tools menu
choosing its name from the Favorites menu (if it has been placed there; controlled in the Tools preferences)
clicking its icon in the toolbar (a tool's icon can be placed in the toolbar using the Tools preferences; whether the toolbar is shown is controlled in the General preferences)
using the --start option when starting Chimera from the system command line
opening a file whose type is specific to the tool

Depending on the tool, something may happen right away, or dialog boxes requesting input files or parameter settings may appear. Detailed descriptions of the individual tools (Chimera-associated programs) can be found in the Tools section of the Chimera User's Guide.

The Tools preferences also allow specification of whether a tool should start automatically upon Chimera startup.

Instances of certain tools or extensions that have been started during a Chimera session are available from the Tools menu, allowing them to be raised, hidden, or quit. For example, if the Command Line has been started, it can be hidden by choosing Tools... Command Line... Hide; if a Multalign Viewer window displaying the alignment file apoex.fa becomes obscured by other windows, it can be raised with Tools... MAV - apoex.fa... Raise.