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Where do you probe and measure the signal quality of a clock signal that has series termination? Do you probe at the end of the series resistor that is pointed towards the load? Or do you measure at the load itself?

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You can probe the clock where ever you want, but what really matters is what the clock looks like at the load. This is the clock that gets seen by the logic. The reflection from the end of the transmission line turns the nominally half amplitude voltage on the series terminated line in to a full amplitude clock pulse. If you are looking at the output of the series resistor and your scope has sufficient resolution, you will see a flat spot on the clock that is equal to the delay from the resistor to the load and back.

Note that probe capacitance and/or a long probe ground lead can distort the signal that you see on your scope.

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