Generating 400MHz external clock (Cyclone V)

--- Quote Start ---

It does look like a sine wave yes, but shouldn't the amplitude of the fundamental 400MHz sine wave still not be severely attenuated with 1GHz scope?

--- Quote End ---

The quality of the signal you observe depends on your ability to probe the circuit with a scope probe, with a ground return path right next to it.

If I want to capture clean looking waveforms for documentation, I will generally solder a wire loop to ground (eg., decoupling cap pad) next to the probe point, and wrap that wire around the scope probe tip. That provides the least inductance, without having to use fancy probe tips.

If you can see a 100mVpp sinusoid, then the LVDS receiver on the ADC clock input pin should still work ok. If the ADC is not working now, chances are you have another issue you have yet to find :)

Cheers,

Dave