The 411 PCM (along with many others as well) support commands from the scantool to the PCM. A crank relearn
is an example of one of these commands (also sometimes called 2-way controls). Others that are supported by
EFILive and HPTuners include:

Turning on and off cooling fans, check engine light, ignition coils and injectors
Commanding the engine to a fixed idle speed or IAC position
Commanding the engine to a fixed spark advance or air fuel ratio
Commanding the transmission to a specific gear or line pressure
Locking and unlocking the torque converter

These controls can be very helpful when tuning and troubleshooting a new setup.
I use HPTuners for this capability, as well as for my primary scantool.

-Scott