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E string intonation

I've got a Ernie Ball Musicman Stingray that i really like the tone on, but if i set up the intonation the way i think it's supposed to be set (same note on an open string and 12th fret) The first several frets on the E string are 3 or 4 cents sharp. This is only true on the E string. Does this mean the neck is damaged? Those frets are damaged? (they don't appear to be). I adjusted the truss rod to flat and there doesn't appear to be any things i can adjust on the nut. Thoughts?

thanks
 
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Could be that the nut slot is a bit high. Could also be that the witness point is not set at the nut. Or a combination of both. Or a "bad" string. Or too much squeeze when fretting, especially with jumbo frets.

I'd start by ensuring the witness point is properly set. Then I would look at the height of the nut slot.
 
Measure the distance from the center of the crown of the 12th fret to the 13th fret. double it. Then measure the distance from the leading edge of the nut to the center of the crown of the 1st fret. I do this with light marks on something like a sticky note so I can be precise. In addition to all the above, including the nut slot depth, leading edge, nut slot slope back to the tuner, fresh strings, double-checked intonation, etc., if this is not precise it will also cause the bass to play sharp on the first few frets. I have a bass that this measurement was off and the bass simply would not play in tune until the nut ws repositioned.

Most likely it is nut slot issues as set forth above.

But if nothing else works, or you want higher action, you can always put a sliver of nut on the inside edge of the nut on the fretboard, as set forth by Stephen Delft. Link: Stephen Delft's Compensated Nut . Music Man has a version of a compensated nut, but it requires re-machining of the nut slot: 1-5/8" 4-string Bass Compensated Nut Blank
 
I've got a Ernie Ball Musicman Stingray that i really like the tone on, but if i set up the intonation the way i think it's supposed to be set (same note on an open string and 12th fret) The first several frets on the E string are 3 or 4 cents sharp. This is only true on the E string. Does this mean the neck is damaged? Those frets are damaged? (they don't appear to be). I adjusted the truss rod to flat and there doesn't appear to be any things i can adjust on the nut. Thoughts?

thanks

12th harmonic = 12th fretted for setting intonation...leave the open string out of the equation. Set witness points first. Quit jacking around with the relief...set it for optimal relief and leave it alone (for now). If the first few frets are still sharp, we'll move on to other steps. You'll need, at a bare minimum, a pocket rule and set of feeler gauges.

Riis
 
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I've got a Ernie Ball Musicman Stingray that i really like the tone on, but if i set up the intonation the way i think it's supposed to be set (same note on an open string and 12th fret) The first several frets on the E string are 3 or 4 cents sharp. This is only true on the E string. Does this mean the neck is damaged? Those frets are damaged? (they don't appear to be). I adjusted the truss rod to flat and there doesn't appear to be any things i can adjust on the nut. Thoughts?

thanks
Could be a dead string. I just had the same problem on a P base I purchased used. G string. Changed the strings and all was fine.
 
Change the strings. Honestly I wont worry with 3-4 cents sharp, on the fretted notes. I do not think, I ever checked in 39 years of playing. I just do harmonic and fretted 12 . Make sure those are set . Also how what is the gauge of your string. Heavy E's also will be not in tune fretted

The SR special have a compensated nut, If it really bothers you maybe you can ask Ernie Ball to sell you one.
 
Oops... Then I was lied to!
Yah, some will be right on, some will be sharp, some will be flat.

But the real question is - intonated compared to what? In the video about true temperment frets, it is said that these squiggly frets are true in pitch like a piano. But pianos are tuned to be slightly out of pitch on certain intervals because, like fretted instruments, they use equal temperment which is a compromise so that the out-of-tune-ness is the same regardless of the key of the piece being played. Otherwise some keys would sound good and others horribly out of tune.

If the true temperment frets provide provide true temperment in a given key, they will be bad in another.
 
Yah, some will be right on, some will be sharp, some will be flat.

But the real question is - intonated compared to what? In the video about true temperment frets, it is said that these squiggly frets are true in pitch like a piano. But pianos are tuned to be slightly out of pitch on certain intervals because, like fretted instruments, they use equal temperment which is a compromise so that the out-of-tune-ness is the same regardless of the key of the piece being played. Otherwise some keys would sound good and others horribly out of tune.

If the true temperment frets provide provide true temperment in a given key, they will be bad in another.
Sitting here looking that the piano in my church while I do my little rehearsal before everyone else shows up…… We play traditional hymns and now that I think real hard about what you just told me…. It does make sense. Our church piano is tuned 4-5 times a year but hymns in E-flat or C have always sounded just a bit off to me and I always blamed it on my string stretch. Or a cold or hot day changing the piano tuning a smidge. I believe I can take this newfound information and make some positive changes. I appreciate that.
 
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