Access to Tools

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:

by choosing its name from the Tools menu
by choosing its name from the Favorites menu (if it has been listed there, using the Tools preferences)
by clicking its icon in the toolbar (if the icon has been placed there, using the Tools preferences; whether the toolbar is shown is controlled in the General preferences)
by specifying --start toolname when starting Chimera from the system command line
automatically upon Chimera startup (if previously set to do so, using the Tools preferences)
by opening a file whose type is specific to the tool

Some tools can also be started by choosing the corresponding function from the Model Panel. Depending on the tool, something may happen right away, or dialog boxes requesting input files or parameter settings may appear.

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.