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Bass just won't intonate, is it me?

Hello,


I have a Squire vintage jazz that finally has a good set up to it. I had it set up to the Fender specks sticky at the top of this page. The bass plays great now (the nut and action were WAY to high off the shelf) and I love the tone, but for the life of me I cannot get the third and fifth frets to be in tune on the A and E string. I have tried all day and they are both still sharp, even if the 12th fret is dead on. I used three different tuners and my ears and they are still just a hair sharp with the best I can get them. I have spent the past few years playing upright almost exclusively, is it possible that these frets are always just a hair sharp and I never noticed it until my ears got better from playing upright? I have searched and read all the info on the website and the only thing that I have not tried is new strings, which might solve the problem instantly, but I just am a little low on cash right now. New strings will have to wait; hopefully someone else has had this problem and can help.

Thank you
 
I pulled out an old Peterson strobe tuner, model 420 I believe. Using that I have gotten closer to good intonation but it is still not perfect. The E string is really giving me a problem. The G and A (3rd and 5th fret) are very sharp, and it goes very flat above the 12th fret. I will just have to get new strings and start over. I thought the strings that are on the bass were still good but after more reading it seems that sometimes you just get a bad set. I didn't mess with the intonation before the set up and it was off then, at least now the D and G are dead on, the A is very close, the E is the only big problem. Checked to make sure that all the frets are level and they seemed good, reset the neck relief as well. The bass seems to be setup correctly, I hope the new strings will fix it. Thank you for the link about intonation. I read about bending the strings over the saddles earlier today, which is the first time I ever heard of doing that. The only reason I asked weather or not it could just be me was that, when I played mostly electric, I just always set the 12th fret intonation (harmonic and fretted) tuned the string and went on my marry way after retuning the bass. Today I was practicing and noticed that the G# on the E was just a little off and checked it against a tuner, which started this whole ordeal. Just thought that it really could have just been my ear. Thank you for your help.
 
How close are the strings to the first fret? They should be as close as possible without hitting, otherwise the first few frets will be sharp.

Also, you want to "seat" the strings over the nut the same way you do over the bridge, so that there's no curve leaving the witness point.
 
Thank you everone. I have yet to have this bass out and about giging, tonight will be the first night, bringing a spare in case it drives me crazy. I think I have it set up well enough to not be a problem, if I tune the low E just a hair flat the rest are in tune up through the 12th fret. Not ideal but it works. Have to take it in to get it checked out, did all the trouble shooting and can't figure it out.
 
Oooooooooooh, yeah!

Worst cases I've seen are on ukuleles, especially sopranos, even expensive ones. The scale is short and most of the ukes I see have the nut too high. Some by a lot. The players come to me complaining about not being able to tune their ukes properly and want me to change the tuners. A few minutes work on the nut and not only does it play in tune, but it's a lot easier to play at the first two frets.