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For reference, Petrucci's tech said in some forum that he runs a super-low action: ~1mm at 12th fret for all strings (~1.2 - 1.3mm @24th fret). You can hear how much pop and how little bass (and how much buzz) this gives the tone in the intro solo to Hollow Years on the Live at Bukokan DVD. Petrucci's setup has been said to be absurdly low. Most low action shred setups are around 1.5 - 2mm on the high E string at the 24th fret. For more on this, see [http://www.ibanezrules.com/tech/setup/action.htm Ibanez Rules action setup page].
== Fret Buzz ==
Fret buzz is the bane of most guitarists' existence. As such, there is so much stigma and strong language around it, that more novice players can be misled about what to expect from their instrument. This section is simply designed to clarify a few things.
Fret buzz is not the same thing as fretting out or choking. Fretting out is completely unacceptable - it means the string doesn't even have enough clearance above the frets higher than the one you're fretting to make a sustainable vibration. This can be caused by having your action too low, too much truss rod tension (making the fretboard side of the neck convex), or unlevel frets. A bit of fret buzz, on the other hand, is acceptable; as long as it isn't having a strong impact on your tone.
You should gauge the amount of fret buzz you are getting by playing through an amp using a clean tone, not simply listening to the guitar when it's not plugged in. All electric guitars tend to have a little buzz, but that won't necessarily be heard by the pickups. Some people may try to completely eliminate all acoustic buzzing, making their instrument near unplayable for ABSOLUTELY NO tonal benefit.
Eliminating (reducing) fret buzz uses multiple points of attack. First, I want to make sure I'm using tight enough string gauges for the tuning I'm using (and the playability I desire). See above. The more tension on the strings, the smaller their vibration distance for a given volume, and the less fret buzz they'll produce. If I can accept a little more buzz for ease of play, I use a guitar with lighter strings. And when I say a desirable amount of buzz, I mean just a touch of it on the very initial part of my attack. I don't want it to occur through (and kill) my attack, and I DEFINITELY don't want it continue as I sustain. And again, I don't use that guitar for metal.
Next, make sure your neck is virtually flat. You need to adjust your truss rod to counter-balance the tension the strings exert on one side of the neck, but you still want the neck to have a little bow to it for the frets closest to the nut to avoid fret buzz. Again, [http://www.ibanezrules.com/tech/setup/action.htm Ibanez Rules action setup page] is a good reference. Be careful when doing a truss rod adjustment - you don't want to turn more than a quarter turn without giving the neck time to adjust to the new tension. Make sure you're turning the right direction too. If this is your first time, have an experienced friend or commercial technician demonstrate the process for you. Or do lots of internet research. Also, be sure to re-tune to ensure the neck is receiving the right amount of tension after adjustments.
Finally, I want to raise my bridge (either adjusting the saddles or the entire bridge depending on the type of bridge). I'll raise it a bit at a time, retune at least one string to test, and see how much buzz I get playing a medium amount of pick strength across at a couple frets from 1-12. Make sure you retune after any bridge adjustment. If you raise the bridge, you may be tightening the string(s), resulting in less buzz...until you actually tune to the proper note. Or vice versa. If you are adjusting via individual saddles, be sure to keep the saddles at the same relative heights as the fretboard radius. If you already have the saddles fit to the fretboard radius, it's usually best to adjust the two bridge posts when possible. Also, watch out for how floating trem bridges make contact with the posts. You generally want the knife edges to hit at a perfect 90 degrees. This will vary with the bear claw tension in the back cavity of the guitar as well as the string gauge, tuning, bridge height, saddle heights. You basically have to adjust everything at once, slowly moving closer and closer to the ideal setup.
Beyond those adjustments, the only way to get your action lower with the same amount of buzz is to have the frets re-leveled or the nut filed down. I would get a professional to do such modifications, although there are plenty of tutorials on the web that can help you. I'd try to find several of them, as some may make them sound way easier than they are. Filing and/or replacing your nut is the far simpler of the two, but you'll need precise tools to do it at a professional level.