you can play fast runs muted or unmuted, but the important thing is to always have other strings that you're not playing strictly muted... it takes sometime till you get used to it, when shredding over scales or arpeggios (specialy when the distorion is on) you must have only one string unmuted at a time, you should practice it a lot.. acualy every body does this muting thing, even without knowing that he's doing it...

Tips for muting:
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1 - for strings above the one you're playing (lower pitched), use your palm to mute them
2 - for strings under the one you're playing (higer pitched) , use your left (fretting) hand fingers by having them to rest on the strings under those you're playing, and also use your right (picking) hand fingers ,usualy i use the thumb and index to hold the pick, so i have 3 free fingers to mute the strings..


Keep On Shredding Folks