Both molecules in the asymmetric unit to be fitted will in general be chemically equal. However, by special arrangement, unequal molecules may be fitted as well (usually in the form of two concatenated 'PDB-style' datafiles as input) see.
Atoms to be used for the fit (at least 5 pairs) should be clicked in pairs. The Fit sequence starts and ends by clicking on the menu-item FITbyCLICK.
For more information on molecule fitting see FIT and AUTOFIT.
The Right click position attempts the best fit of molecule #n on molecule #m. The Left click position also attempts a fit of inverted molecule #n on molecule #m, keeping the best fit.