PeterH:
You need to toggle the RTS signal.
Not necessarily.
RTS and DTR are not the same.
You will need to toggle which ever signal is wired up to the autoreset circuitry on your board.
When the FTDI serial cable is used, RTS is connected to the auto reset circuitry.
On the Uno boards, DTR was wired up when FTDI chips were used.
Now with the Atmel chip that replaced the FTDI chip, it is under f/w control inside
that Atmel chip, but the default code that shipped in it, looks for the virtual
DTR signal and so DTR will need to be toggled rather than RTS.