#2
http://www.ibanezrules.com/tech/setup/intonation.htm

"If you are using the tool that is available for the Edge, Lo Pro Edge, and TRS/Floyd Rose, attach it to the saddle and tighten it up. Loosen the saddle lock down screw [which I call the intonation screw] just enough to move the saddle, adjust the saddle, retune, and with the tool still in place recheck the last fret fretted. Adjust until correct then tighten the screw. Remove the tool and retune the string. Move to the B string and repeat. Every 2 strings recheck the tuning of all strings and make sure they are all in perfect tune before continuing. Work from the high E to the low E. When every string is correct make sure to check the trem angle again as it will move slightly as you intonate the entire bridge. Note - The saddle lock down screws are fairly soft, and in older Ibanez, also have a shallow head. I highly recommend the 2mm Allen wrench is either new or in perfect condition. If it has any rounding to the tip at all you will more than likely round off the head of the lock screw when you tighten it."