Guitar setup/intonation guides?

I use my electronic tuner and intonate by matching octaves at the 5th and 17th fret across all strings. First read about this method from Peterson. Seems to work nicely. It particularly seems to true up 1st position chords like C, G, etc. When I do a careful job, I can take the fretted notes of an open C, run them up an octave, and I am still in tune to the open G and E. This technique assumes that you have individual string saddles to adjust.

Harmonics or fretted?

From the Peterson site:

Intonate Your Guitar

So by now you have looked over your guitar and made sure that everything is in good working order, and it is time to get your instrument intonated. Before intonating your guitar, there are a few guidelines and general good practices that you should keep in mind. Review the Intonation Introduction page for some tips that will keep your instrument in good working order. Keep in mind that you should ALWAYS change the strings on your guitar before doing your final intonation.

Standard Intonation Procedure
After deciding on string gauge, setting string height (nut & bridge), neck relief — factors that will later affect the guitars intonation considerably — the individual string lengths need to be adjusted. For this task, use Equal temperament (EQU) in the StroboStomp’s TMPR menu.
Lower the pickups away from the strings to avoid "doubling" and electromagnetic pull.
Lay the guitar flat on a bench to adjust it, but always check the intonation with the instrument in the playing position, as the readings will be visibly (and later audibly) different.
You should always aim to freeze or "cage" the image on your Peterson Strobe Tuner display, the less movement the more accurate the results.
Where setting the intonation is concerned, an often-used technique is the 12th fret & flageolet comparison method.
In this method, the open string is first tuned...
Then the open string (you can also use the flageolet tone or "harmonic" over the 12th fret) is compared to the string fretted at the 12th fret..
...saddle position is carefully adjusted as follows:
If the fretted note is flat compared to the open string or flageolet tone, move the bridge saddle forward to shorten the string (turn the saddle screw counter-clockwise)...
If the fretted note is sharp compared to the open string or flageolet tone, move the bridge saddle back to lengthen the string (turn the saddle screw clockwise)...
Always re-tune the open string after adjusting the saddle position before re-checking the result...
...and check the string fretted on the 12th fret again...
Adjust until both fretted note and open string (or flageolet tone) are identical in pitch.

While this is a common system, it is not always the most satisfactory.

One popular alternative is to adjust each string so that it is in tune at two points an octave apart from each other on the fret board using a strobe tuner.
Using the 5th and 17th fret as an example:Tune a string at the 5th fret.
Check the string at the 17th. If sharp, move the saddle back, thus lengthening the string (turn the saddle screw clockwise). If flat, shorten the string by moving the saddle forward (turn the saddle screw counter-clockwise).
Always re-tune the open string after adjusting the saddle position before re-checking the result. Remember to fret the string using the pressure that you would normally apply while playing. Keep repeating this process until each string is in tune as much as possible at both the 5th and 17th frets.
This method takes time, and has to be repeated if you change string gauges, but if properly executed, yields very satisfactory results.
Now, before you play music with a lot of 5ths on your guitar (e.g. power chords), tune the guitar using the GTR, P5 or G5 setting , depending on which model of strobe tuner you own, otherwise use the EQU (default) setting to tune your guitar.

Sounds like the standard way of doing it to me..... I usually make sure it's all in tune and the open string is in line with the 12th. From there I will go to my most used root notes and if there is any sharp or flatness in those I'll fine adjust until they are right, then make sure I'm still in tune and the 12th is still in tune and usually that means the whole guitar is pretty solid. That's just my way of doing it.

You need a strobe to do intonation work, IME.

This all doesn't fix poor intonation of cheap guitars. Just the set up. A guitars intonation is about fretwork and the consistency. All you're doing is setting the open strings's intonation (and you should-don't get me wrong)...and sometimes that IS all it takes....here's hoping it is.

Any tuners in particular to recommend for studio use and setups? I have a handful of guitars that need attention but feel the Boss pedal tuner isn't the one for the job.

Love those Old Peterson strobe tuners. No one that came in the studio could work it, would always hand the guitar off to me, but to me it was easier than one you clip on the end. Insanely accurate, and I would agree with you on it only being the tuner for intonation work, if you're really setting up a guitar for recording use. Another one that's good is the old boss one with the needle, those work pretty good too for intonation setups.

You know what I find hilarious about that comment? My "everyday", easy, sitting around jamming, throw in the case and go tuner...is an old Boss with a needle!

thanks popmann & matt… will check out those tuners & techniques… 12th harmonic isn't always kosher

WOW...why did I wait so long to borrow this Peterson? Seriously, I don't think I've ever had my electrics more in tune. Thanks for the help, guys!

Is the new string the same length as the old one? The only time I tried DR's was with bass and I didn't like them.

Strings can be bad, yes. Why not get a baritone guitar to get that low. That's what they're made for. Different scale length...fret spacing...I would imagine completely different string sets and gauge relationship.

You're welcome, JK.