The direct sound duration, string length, strike point, along with the spectrum profile all affect the the timbre - (though that said, I've found I use different settings for these in different registers - only available in Pro)
Generally applicable:
Microphone positioning and the equalizer have a profound effect on timbre, if you'd like a darker/softer spirit per se.
Note that the equalizer (not the effects equalizer) works in pre-processing... from the manual:
"The fact that it works in pre-processing allows automatic volume compensation: for example, when increasing the medium spectrum, it will increase the medium frequencies in each note while keeping the natural balance across the keyboard. In other words, the middle notes will not get suddenly louder than the other ones. Another advantage of pre-processing is that it allows very fine variation in the EQ curve, unlike on a standard 3 band EQ. You can add (click) or remove (double click) control points and modify the curve by dragging them with the mouse."
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