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To intonate a guitar the length of the string has to be altered so that the 12th fret harmonic matches the fretted note at the 12th.
If you have changed string gauge, adjusted the truss rod or set string height then the intonation will need setting as the LAST thing you do.
The method of adjusting the string length differs on Guitars, but is generally a small slot-head or Philips machine screw going through the saddle on each string or pairs of strings. On a Floyd Rose vibrato the adjustment is a bit more complicated and I won't go into detail here unless requested.
To start, first plug your guitar into a good tuner, preferably a strobe tuner but any old tuner will do.
You can start with any string but it will make sense for me to start with describing the low E string: First tune the 12th fret harmonic to a perfect 'E'. If you don't know how to do this then ask someone who does to show you, as it is fairly hard to understand without seeing it. In theory just rest a finger of your left hand lightly directly ABOVE the physical 12th fret wire and pluck the string with your right hand to hear a bell like note.
Anyway tune this harmonic to E, then hold down the 12th fret and pluck that too, ideally it should be a perfect E as well, the same as the harmonic, if not then its time to get out the screwdrivers!
Taking the harmonic as your constant, if the fretted note is FLAT, then you have to SHORTEN the string, if it is SHARP, you need to LENGTHEN the string.
Adjust the string length as necessary for each string by turning the saddle screw, making sure you retune the harmonic after each adjustment until the harmonic and fretted 12th match perfectly.
Then your guitar should play perfectly in tune!
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