It's definitely possible to do a single FFT on a single capture. The main trick to that is to just setup the trigger mode to be Single (control at bottom left portion of the screen). To get an unpadded and untruncated FFT with the exact time window you want (50s) takes some extra steps.
Here's what I did to try out your example:
- The properties window is really handy to confirm what's going on with sampling, so start by opening it: View -> View Properties
- Setup the AWG to output a 5Hz sine
- If necessary, setup input channel (A) to appropriate voltage range (so it's not over-voltage)
- Setup the input channel (A) to be 5 sec/div and enter a specific sample count in the sample control (about the middle control in the top row of controls near the menu) "16384 S"
- Change triggering to single
- Open a separate view to the spectrum mode: Views -> Add View -> Spectrum
- Open the Spectrum Options and set Spectrum bins to 16384
- Click the Go button
Once the run is completed, the FFT will be computed and shown:
I did this all with the demo mode, so it may differ with specific scopes' sampling properties. But the overall principle should be the same.