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This is what I have started doing and so far I really dig the results.

1. Intonate the 6th string by using a tuner, try to get it set using the 12th fret technique, but note you may still move it slightly later (if for some reason it's off or needs to be sweetened to jive with the A).

2. Tune A string by using open E 6th string to fretted note A string. First make sure A is tuned to pitch. Check to see if open E 6th string rings in tune with fretted A string at 7th fret. If it doesn't move the A string saddle until these notes are in tune. Double check once set by comparing 5th's (Fretted E string 5th fret to fretted A string 7th fret). Your guitar should be in tune both ways.

3. Repeat this process on all the other strings. For the string what I will do is play the harmonic at the 5th fret of the G string and compare that to a fretted G on the B string (8th fret).

4. Do not use 7th fret harmonics for tuning, you'll read why if you open the link. I also use tuners to set the initial string and provide reference pitches, otherwise it's all setting the intonation so the guitar plays in tune with itself. Tuners are way too sensative and it is far to easy to get a faulty reading.

Here is a tuning method I use which IMHO sounds the best. It is taken from the American Luthier's Guild.


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