Sometimes your guitar will be out of tune even after you tune it, which means your intonation is out. You can tell when your intonation is out if an open string harmonic at the 12th fret (lightly touch string at the 12th fret and pluck it) and the fretted note one octave higher (hold the string down at the 12th fret and pluck it) are not the same. Guitar intonation tuning is essentially the art of making the notes of each fret of a string equal to the chromatic reference pitches, or the natural musical scale temperaments which is achieved by adjusting string lengths at the bridge (bridge saddles). The chromatic musical scale and natural musical scale are similar, so tuning the natural musical scale of the brass instruments is preferred. This makes the twelfth fret note of a string theoretically be about one octave higher than its corresponding open string note pitch, and the seventh fret note octave pitch similar as the corresponding seventh fret harmonic pitch. If that’s a bit much for you, don’t worry, you should still be able to get through this without much problem. And just in case, this process is identical for both bass and guitar. Remember, this is only for instruments with movable bridges (such as a trapeze) or those with bridges that allow for adjustments, usually through a peg and screw as shown in the pic on the right.
Unfortunately, if you happen to have in instrument with a non-movable bridge – such as most acoustic guitars – you’re probably going to have to take it to a luthier to get you a “compensated” bridge saddle since moving the bridge is essential to fixing intonation. Also be aware than there are a few causes for bad intonation such as worn frets, among others, which cannot be fixed by bridge adjustment. If that’s the case, the repair man (luthier) can tell you if your guitar can be saved.
Tune Your Instrument
The very first thing you will need to do once you have everything covered above is to simply tune your guitar to whatever tuning you play in – although for most of us this means the standard EADGBE tuning. Remember to make sure those new strings are relieved of all of inert tension because you don’t want them to come out of tune as you’re making adjustments. As the tension on each string changes, which is typical of new strings that haven’t been worn in, it may alter the way your neck is sitting and may detune your other strings. Stick with this step until every string is open tuned as close as possible to perfect. You can pull on all of the strings to reduce any extra tension but not so hard that you break them. Remember, set up your instrument for the tuning you're going to use. If your band plays in drop D, Ab standard, G modal, or any other tuning you should tune your instrument to the tuning you are going to use because it will be our reference point in getting the intonation best for what you play. Standard E drop to D is better than standard tuning because of lower string tensions. And a side note for bassists: Throughout this process you should be using a pick, even if you do not normally play with one. The way we pluck the string with our fingers works very well when we're playing but it’s just not accurate or consistent enough for this process. For all instruments: Tune the entire instrument several times. Once you make sure your instrument is in tune and stays in tune, you can move on to the next step.
Adjust the Action
If you’re not all too happy with the action of your instrument (the distance between your strings and the fretboard) you should do it now. This means if the string is buzzing when you hold a certain fret – usually the higher ones – raise the action so that it does not! When the string is vibrating or buzzing on the next higher pitch fret, the note pitch can quickly and temporarily switch, making intonation tuning very difficult. The two pitches may briefly and temporarily blend which can make the note pitch a little sharp – and trust me, that’s not what you want. Not only that, the buzzing sometimes produces some harmonic pitches that can reduce the purity of the pitches of the higher pitch frets; in other words, the tenth fret note pitches can sound a little higher than they should. The smaller the magnitude and duration of the buzzing on adjacent frets the smaller the offsets has to be. If you alter your action after you complete the intonation setting process, you may undo all of the work you are about to do! If you do alter your action on any string, simply repeat the tuning steps above after you’re done. Higher quality guitars can usually have their strings closer to the frets with less buzzing. The closer the strings to the frets, the less the string-stretching and tension increase when pressed, the smaller the offsets have to be and the significantly better the intonation tuning will be (due to less string stretching). This is why is suggest when fixing your action, try and place the strings as close as possible to the frets; if some buzzing on next higher fret can be heard, increase the distance slightly. There may be some string buzzing permitted at frets higher than twelfth just in case you run into that.
Assesing the Magnitude of the Problem
Fret the string at the 12h fret and pick it. The pick should be moderate, not too hard, not too soft. When fretting, pay special attention to fret only as hard as is necessary to prevent the string from buzzing. Even with a standard un-scalloped fretboard it is possible (especially on guitar) to bend the string sharp several cents by fretting too hard. In normal playing it isn't generally an issue, but for this process you need maximum accuracy. When you play that string at the 12th fret, observe your tuner. If you are sharp (too high) or flat (too low) your intonations are off and an adjustment will need to be made, which brings us to our next step.
Fixing the Problem
If (when playing the string at the 12th fret) you are sharp, then the bridge is too close to the center of the string, and you need to make the vibrating length of the string longer. Here’s how you do it: Move the bridge away from the fretboard (by rotating the screwdriver away from you). FLAT: If (when playing the string at the 12th fret) you are flat, then the bridge is too far from the center of the string, and you need to make the vibrating length of the string shorter. Compare the twelfth fret note to the corresponding twelfth fret harmonic pitch with electronic tuner for meter. Fix: Move the bridge toward the fretboard (by rotating the screwdriver towards you). This is decent intonation tuning for notes between nut and twelfth fret range.
Check Your Progress
After you make a bridge adjustment, you will need to repeat the tuning step. Make sure the ENTIRE instrument is still perfectly in tune. Once you have completed the tuning step again, re-fret the 12th fret on the string you just made the adjustment on and check it on the tuner. You should see that it is not in the same place anymore. If the 12th fret note isn't perfectly in tune while the open note is perfectly in tune, you need to repeat step prior step until it is. Tune the open string note and check the fifth fret note your tuner. If the fifth fret note is still a little sharp, move the bridge (bridge saddle) back a third of a millimeter. Play some songs on one string and adjust the string length at the bridge accordingly if the intonation does not work well. If it is perfect you are done with that string. Just to double check, tune the first fret notes by adjusting string tensions (using the hardware knobs like you normally would) and compare the second to twelfth fret notes of a string with the chromatic electronic tuner pitches. If everything is good, you can now repeat the same process with the rest of the strings but don’t forget to constantly make sure you are in tune while doing this to achieve maximum accuracy!