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Ah, nuts!!!

Trying to dial in my bass. It’s a relatively new Squier PJ. Just wanted your guys opinion on the attached pics. The E string seems to be riding high in that nut groove. Should I file down the groove? The strings are med-light guage (45-100). I had to lower the bridge saddle way too much (almost bottoming out) to get the action decent. Thanks for any guidance on this.
 

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I am looking at pic 2, see how the string is curving over the nut?
The same thing is probably happening at the bridge.
The solution is to massage the string to have a clean "break" angled not curved.
There are threads addressing this. See "witness points."
Then see where you are at action wise. Nut looks good to me in pix.
Hope this helps!
 
I am looking at pic 2, see how the string is curving over the nut?
The same thing is probably happening at the bridge.
The solution is to massage the string to have a clean "break" angled not curved.
There are threads addressing this. See "witness points."
Then see where you are at action wise. Nut looks good to me in pix.
Hope this helps!
Thanks for the input. Yes, the string is definitely curved and not a nice, sharp, clean angle. I’ll look up “witness points” to see what massaging the string is all about. Massaging the string... hmmmmm. Lol.
 
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It’s not so much about how much of the string is out of the nut, until it starts popping out of the slot, anyway. It’s about the action over the first fret. So, yes, set the witness points then check the first fret action.
I checked out the “witness points” thread but I don’t understand what to do. Just start “working/massaging” the string into the nut groove?
 
I checked out the “witness points” thread but I don’t understand what to do. Just start “working/massaging” the string into the nut groove?
Press the string down just in front of the nut (first fret side). Press it just hard enough to get the arch out of the string so that it forms a nice straight line - same at the bridge. Ignore how much of the string sits above the top of the nut - it's irrelevant. Instead look at the clearance between the first fret and the string. It should be about the same as the clearance over the second fret when you are fretting at the first fret.
 
Press the string down just in front of the nut (first fret side). Press it just hard enough to get the arch out of the string so that it forms a nice straight line - same at the bridge. Ignore how much of the string sits above the top of the nut - it's irrelevant. Instead look at the clearance between the first fret and the string. It should be about the same as the clearance over the second fret when you are fretting at the first fret.
I just did that. Looks better. Intonation set. Thank you!
 
Press the string down just in front of the nut (first fret side). Instead look at the clearance between the first fret and the string. It should be about the same as the clearance over the second fret when you are fretting at the first fret.

That's the most important point - I just had one of my basses setup for BEAD from a local Luthier, he made a new nut from bone, and polished my frets for $60. He got those clearances just perfect.