You know, it just takes trial & error. I have a set of tones in my head that I go by and achieve on whatever kit I play. Then again, I try to adopt a "no-touch" policy on kits other than my own. As in "don't change a thing" unless it's a necessity.
As far as that "tune this drum to this pitch" thing that DW uses, I cannot agree with that. There's too many intaqngibles that stop that theory from working 100%. Besides, I like my toms tuned slightly outside of that "perfect long pitch" that would denote "perfect" shell/head resonance.
Tune for your own ears, not from the "manufacturer's suggested pitch".
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