ShortScale.org

So last night I played my supersonic on stage for the very first time and ran into some crazy technical difficulties. The bottom E string kept popping out of the nut and out from under the string tree. The string does sit a little over the groove, as I use heavier strings and it doesn't quite sit inside the nut. String tree issue or nut issue?

Filing the nut may help. Does it line up otherwise?

it does! I'm going to try to file the nut down so the string rests inside rather than slightly on top of it.

Switch to 9's. Problem solved.

How heavy of a string are we talking here? If you're going to file it, you don't want to cut it deeper, you want to cut it wider. Cutting it deeper can (and probably will) cause serious problems, especially if you just use a saw or other straight blade. Ideally you should really get specialty tools to cut the nut for the diameter of string you're using. Or, pay a luthier to do it. Cutting a nut isn't rocket science, but doing it right really takes some practice.

Buy a gauged nut file like the ones on stewmac and drag it carefully through the string notch with no downward pressure until it moves smoothly/doesn't snag but is still snug in the slot. You don't have to buy an expensive guitar nut file for the job but that's where you'll find ideal gauges listed immediately, obviously.

If there's a gap in the nut slot under your string because the string is too wide to seat properly, the bass side of the low E slot on your nut WILL break off, so it's worth doing sooner rather than later.

It's always a good idea to file your nut for your preferred gauge set of strings, it helps with tuning stability issues and string breakage to get a nice smooth operation there, and is especially helpful if you use a non-locking trem... and no string nut lives forever, so exerting mad pressure on the wrong parts of them is just tempting fate.