It all depends on what the instrument is and what sort of command structure it responds to. The GPIB controller is limited in the fact that it can only send ASCII (or 8-bit) data to and from listeners. Whether some of the ASCII commands are understood is 100% a function of the instrument. I might recommend looking through your instrument's manual or contacting the vendor about a specific command structure that is needed to achieve the control you require.
Ryan Mosley National Instrument, Applications Engineering http://www.ni.com/exchange