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Lately, chords are starting to sound off on my strat. I went to check the notes at the 12th fret, and the high e string is flat, way flat. Pretty easy fix right? Just shorten the string length by moving the saddle up. The problem is that it's gone up as far as it can go, as the screw isn't sitting flush with the bridge, and my high e string is still flat at the 12th fret.
Is there something I can do, or will I have to pay to get the guitar re-fretted?
Getting the guitar refretted would not solve this problem. They would simply take out the old frets and put new ones in the exact same slots.
Unfortunately, fretboard geometry mystifies me a bit. I've actually had it work out (in the same situation as you're describing) that pulling the saddle back (lengthening the string) actually resulted in having the string intonate properly.
Worst comes to worst, you may have to deal with an E string that doesn't intonate properly. Alternatively, you could put a different gauge E string.
But yeah, intonation should always be done with fresh strings.
Bridge, saddle, and height can affect intonation a bit as well, but if it's way off, it's almost certainly the string. Plus old strings produce terrible tone. Replace them often!
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Unfortunately, fretboard geometry mystifies me a bit. I've actually had it work out (in the same situation as you're describing) that pulling the saddle back (lengthening the string) actually resulted in having the string intonate properly.
Worst comes to worst, you may have to deal with an E string that doesn't intonate properly. Alternatively, you could put a different gauge E string.
But yeah, intonation should always be done with fresh strings.