How do I set up my John Petrucci guitar?

When restringing, turn the tuner's holes toward the corresponding nut slots. This will keep the strings as short as possible for more stable tuning. The next step is to check the relief in the neck by holding the lowest string down on the second fret with your fretting hand; then hold it down on the 12th fret with your right thumb and tap on the string on the middle of these two points to show how straight the neck is. It should be no more than the thickness of a thick business card, no more than that, though it can be less. If there is no relief a little pressure in the middle of the neck should take care of it. If it does not, feel free to contact us.
With the guitar tuned to pitch in the playing position and looking down the body, the top of the body, the top of the bridge should be parallel (both front to back, bass to treble side) to or slightly higher than the body with the bottom still recessed. The saddles should not come in contact with the cover and the intonation screws. If this occurs, lower the saddles and raise the bridge. After every adjustment, it is necessary to re-tune the guitar.
Factory string setting for standard tuning starts at the bass side 2/32" (1.59 mm) to 5/64" (1.98 mm) and the treble side is 3/64" (1.19 mm) to 2/32" (1.59 mm) measured from the 12th fret to the bottom of the strings. The top of the strings should have the radius of the fretboard when you are looking at the strings in the playing position and by rotating the instrument while at the same time bringing strings into view one at a time. Remember, string height is ultimately determined by your preference and playing style, as well as the string gauge and tuning (if you you use an alternate tuning). Again, after every adjustment it is necessary to re-tune the guitar, to give you a starting reference.
Now, you are ready to play your guitar. If a string buzzes on an open string to the 5th fret and no higher, more relief is needed. If there is more buzz from the 5th to the 12th fret, the neck needs to be straighter. You should check the string height after every adjustment. If the buzzing happens throughout the neck, the string height needs to be increased.
When setting up, always consider all of the other changes that will occur with every adjustment, starting with step one, tuning up after each step you take.
For intonation, check the harmonics to the fretted note on the twelfth fret If the fretted note is sharp, you need to make the string longer by turning the intonation screw for that string (located on the tail end of the bridge) clockwise, counter-clockwise if the fretted note is flat.If you turn the screw counter-clockwise, always turn the screw clockwise afterwards. (If you don't play much above that fret, you can skip the next step). Also check the harmonics at the 19th fret after the twelfth fret is set, repeating the procedure above. Make sure that the string is coming off of the saddle straight and not at an arch.

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