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Clean Sense is not a simple input gain: You will notice that it does not affect the gain of a distorted sound, while it has an impact on the input gain of clean ones. Distortion Sense is also not a simple booster, as it does not affect the gain of clean sounds.
These Sense controls offer volume compensation for clean sounds. That means when you turn the gain to zero, you get a full clean sound at regular volume. You could not do this with an analog guitar amp. Depending on if your guitar is loud or soft, the clean sound will become loud or soft, too. This is what you control with Clean Sense. It took a while to create this capability, and handling might be a bit confusing at the beginning, because these controls respond differently than what you are used to. The Clean Sense will also ensure optimum leveling of the digital instrument input (SPDIF).
Tuning is easy: Just set Clean Sense so that clean sounds feel as loud as distorted sounds. If done correctly, there is no risk to clip the input with that guitar. The default for Distortion Sense is the middle position. If your guitar is quite hot, and you crank down Distortion Sense, it will have the same effect as if you would turn down Gain on all rigs. And if your guitar does not clean out well, this might be caused by much gain and distortion.
You can store your Clean and Distortion Sense settings for each of your guitars as local presets. So whenever you change your guitar, just load the corresponding Input preset and lock it. This way it will take affect across all rigs. The Input presets do also include the general Noise Gate settings.
Since firmware 2.2.0 Clean Sense and Distortion Sense are scaling in Decibel