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Subfragment
Subfragment is an option that calculates secondary fragments; i.e., it uses a previous fragment as the source rather than the entire molecule. When Subfragment is selected from the Options menu, both Box mode and Multifragment are selected automatically because Subfragment requires both of these options to be active.
When Subfragment is on and a newly drawn fragment box lies completely inside the previous fragment box, then the fragmentation masses are calculated based on the enclosing fragment rather than the entire molecule. This is indicated by r= (i.e. residual mass =) in the results. For example, if M1 and M2 are the masses resulting from a standard fragmentation, then M2=MW-M1, where MW = the molecular weight. However, if M1 is then Subfragmented to M3 and M4, then M4=M1-M3 rather than MW-M3.