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== String Gauge ==
Most stock guitars come in standard E tuning with 9's (.009-.042). These are easy to bend and are good for lead work, but I find them a bit lacking if you want a heavy rhythm sound. Because they are relatively loose, you'll get a strong attack on them that quickly fades to a whimper. In my mind, that sounds kind of vintage, not modern and heavy. For standard E tuning, I prefer 10's (.010-.046). If you like to play in drop D, you may prefer strings with a heavy bottom (.010-.052). The heavy bottom is nice, even if you don't play in a drop tuning - you generally don't need to make as strong bends on your thicker strings as you do on the thinner ones. Given that I'm a Petrucci nut, I basically use the [http://www.johnpetrucci.com/gear.htm exact same string gauges ] (Scroll down a little and there's a chart for all his tunings with the gauges used).
Also, thinner strings are easier to mute. This is mostly why I like them for lead work - you are less likely to have an unwanted string ring out. I find I sometimes like the sharper attack too, but not always. You will also have an easier time playing legato (hammer-ons and pull-offs) with thinner strings. I have two guitars tuned to standard E. One has 9's, the other 10's.
If you are tuning all your guitar strings down, you don't want 9's, or even 10's. I find I need at least 11's to play in standard D, at least 12's to play in standard C, and at least 13's to play in standard B. If you are additionally going to drop the 6th string a full step, I highly recommend getting a set of heavy bottoms. Again, see the chart on the Petrucci site linked above, or [http://www.surveyor.com/guitar/stringtension.html visit this website], which has a Java Applet to calculate string tension using gauges and tunings. Here are the values I use for most of my guitars: notice you can specify the scale length, tuning, and type of strings. The first is D'Addario EXL120's, then D'Addario EXL110's, then D'Addario EXL110-7's with an additional .080 nickel wound string (for my Ibanez RGA8 8 string). Notice the 8 string has a longer scale length, but I tune it down a half step, acheiving roughly the same string tension.
len 25.5"
And a final point - thin strings are more likely to have fret buzz with the attack. As I just mentioned, they will stretch more and thus be more likely to slap against frets above the one you are fretting. This can sound kind of nice for blues work, where you aren't always picking aggressively - it really emphasizes when you do. For metal, where you are constantly picking quickly and aggressively, it will make your playing sound like noise; it will be near impossible to hear the desired note pitch. This also depends on your...
== Action ==
Action can generally be described as the distance between your strings and your frets when you are not fretting them, usually measured as the distance between any string and the top of the 12th (or sometimes 24th) fret. This depends on your nut height, your bridge height, and your truss rod tension. Properly setting up your action is way beyond the scope of this guide; we are only focusing on how action affects your tone, assuming whether you can set up your guitar correctly for your desired action.
High action is often regarded to have "better" tone (see below), but can be more difficult to play. This is mainly due to poor setup in other areas, which causes a lower area to have too much fret buzz. It can also be more difficult to get a good intonation (making you sound out of tune). Low action runs the risk of fret buzz, especially when other aspects of your setup are bad or you pick aggressively and use a thick pick. For metal, fret buzz is a no-no (too noisy). I like a medium to low action across the board - high enough so that I don't get a strong buzz when I pick the strings at a low to medium stength.
A lot of people think action has little impact on tone, other than the amount of fret buzz. That might be true on a low-quality instrument or one that hasn't been set up properly because by the time you get the action low enough so that it affects tone, it's already getting quite a bit of sustaining buzz. With a great instrument well set up to allow a really low action with virtually no sustaining fret buzz, action has a strong impact on tone. At higher action, the strings don't have as much twang or pop to their attack and sustain a strong bass response. As you lower the action, the strings will occasionally hit the frets. This pop during attack can be regarded as good or bad. It tends to add a little brightness to the tone.
My advice here is not to try to basically EQ your guitar tone through the action. And if you have a strong bass response, you can always EQ it out later, whereas you can't EQ it in if it wasn't there to begin with. A boost pedal does a much better job of filtering out too much mud than a low action.
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].