It is highly unlikely that you will see the protein change conformation in the GUI display. The view of the protein will change, but the overall position of the atoms will not change significantly.
The timescale each WU works on is very small, so major positional changes are only visible over the larger timescale of several WU generations.
The only exception to this is if your WU initiates a Folding/Aggregation Event, in which one section of the protein passes very close to another, this maybe visible in the GUI display.
The upcoming PS3 FAH client is about to bring a change to that topic - you can see the protein move!
Check videos on:
If you want to see the WU itself then use any of the 3rd party WU viewing tools.