#1
so i googled and found this site

http://www.projectguitar.com/tut/intonate.htm

it states that:

Start by tuning up your guitar to proper pitch, now check your High E string tuning at the 12th fret.

If your tuner shows that your sharp then adjust the High E saddle on the bridge slightly further away from the neck.

If your tuner shows that you are flat then adjust the High E saddle on the bridge slightly closer to the neck.

so i checked my open string.. then the 12th fret.
so if my tuner shows that your sharp or flat where? at the open string or at the 12th fret?

also, when the open and 12th fret is now tune. let say my 1st string. at the 3rd fret (G) is way to sharp. and the 15th fret is way to flat. how can i fix this? im using a zr trem.
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#2
open string note = 12th fret harmonics, remember that

When you tune, you make sure either that is in perfect pitch, you can use either one its the same. Then after that, you fret the 12th fret, check the pitch if its flat or sharp, start moving your saddles to the proper position
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#3
Heh, I've just sort the intonation out on my PRS SE, it sounds a lot better now, it's a VERY important part of making your guitar sound good. If I could have a quid for every time I'd heard someone playing a badly intonated guitar I would be quite a rich man by now.

Both the open string and the 12th fret should be neither flat nor sharp, so what you do is:

*Make sure the open string is in tune

*Check the same string at the 12th fret (try and apply the same sort of fretting pressure you would when you're playing the guitar normally)

*If the 12th fret note is sharp, the distance between the 12th fret and the bridge saddle for that string will have to be lengthened accordingly, the opposite applies if it's flat.

*Every time you adjust the bridge saddle you will have to go back and check the tuning of the open string and re-tune it if necessary. Keep going til they in tune with one another.

also, when the open and 12th fret is now tune. let say my 1st string. at the 3rd fret (G) is way to sharp. and the 15th fret is way to flat. how can i fix this? im using a zr trem


Assuming you're not fretting it way too hard and that there isn't any excessive wear on that fret, and the intonation has been sorted, you might need to adjust your truss rod.