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Originally Posted by VHFan
Ahem....I hate to jump in here EJ....but I think you have a type-O.
The open string the the harmonic in the center on it (12th fret) will always be exactly the same...regradless of the lenght of the string.
What you have to do is match the open string up to the note when you fret the 12th fret. If the 12th fret note is sharp move teh saddle back...flat move it forward to the nut.
I only know this because I do it a lot.
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Thanks VH.
We intonate in the first place because the saddles are not perfectly distanced. This was recently demonstrated when I bought (and took back!) a Boss chromatic tuner to check my intonation. I did check the tone based on the fretted note and the harmonic, then decided to use my ear since I was the one playing!
Actually, mathematically perfect intonation involves measuring to the middle of the twelth fret wire from each saddle and matching it with the distance of the nut to the middle of the fret wire. It just doesn't always sound "perfect".
However, the string height does need to be considered for the intonation because if the string height is just high enough, it would take additional pressure to move the string down and create more tension on the string throwing it out of the harmonic range, which as mentioned is the easiest way to intonate. You should also fret the note to compensate for string height since when you actually play you are fretting rather than playing harmonics. Getting the tone at the 12th fretted and 12th harmonic is where you want to put your money. There are also debates on 5th and 17th frets accuracy, but we'll save that for later.
Of course, as you mentioned you do it a lot where as I hardly do it at all.
"Nothing but a Good Time" would be indicative of intonation problems since some of the chords are played above the twelth fret as well as below. If I recall correctly when your wife threw her bra on stage at the gig last month, you both thought the guitar sounded good. Coincidence? Only my hairdresser knows for sure! But, yes, I would strongly recommend you intonate based on fretted notes and harmonics at the twelth since it is your playing that will impact the intonation. That is why so many guys come back from the guitar store with unhappy setups because they weren't a part of the setup process.
And let me add that because of debates such as this, Buzz Feiton has a system that supposedly resolves these questions. I don't know about the BF system first hand, but if anyone else does I would love to hear about it
The 12th is not the same as open, thats for sure. Also, I've got a d tuna on it, I've heard several ways that people tune with that on. Could someone just explain how to do a few of these things for me? It'd be a great help! 
My amp goes to 11!Nigel Tufnel
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