The Stew Mac ruler measures the distance between strings taking into consideration the thickness of strings. I think this is the other method that Charles is talking about versus the method of equal center lines.
I personally like the Stew Mac ruler. With thick acoustic strings, and in particular bass strings, you might be able to tell, I can, that the bass strings appear to be closer together then the treble ones even though their center lines are all equidistant.
It's really a toss up between methods. I used to do equal distance but now use the Ste Mac ruler if for any reason the thing makes layout a snap.
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