I've never heard of putting a scope probe on a crystal damaging it, though the load resistance (typically 1Megohm to ground) and capacitance (~5pF to ground) wi

I've never heard of putting a scope probe on a crystal damaging it, though the load resistance (typically 1Megohm to ground) and capacitance (~5pF to ground) will affect the frequency. This is why the PWM-out is useful -- it gives you a buffered, divided-down version of the crystal clock.