See the Tools section of the Chimera User's Guide for a listing of tools (extensions) and their individual manual pages.
There are several ways to start a tool:
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.