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Re: Intonation is Off on B String
One possible cause is that the nut slot is too high for that string, so that when you fret the note you are pulling it sharp just to get it to touch the fret. By the time you get to the 5th fret, the tension balances out. Another is that you press too hard, so you are stretching the string sharp when you fret just by squeezing the string.
The reason it would affect the B and not any of the wound strings, is because the wound strings aren't as susceptible to pitch change from stretching. (It has to do with the size of the core) and the high E is pretty negligible as well, which is why it's almost always the farthest forward on a compensated saddle. (electric or acoustic for that matter)
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