I'm doing the Trinity Restored quest and everything ran fine up until I got to the gate which Karliah is suppose to unlock so i can stand on a vacant floor glyph. When I pull on the chain to open it I keep getting a message saying that I can't use this right now. I went back to an earlier save but that didn't help. Does anyone know why it keeps telling me that

You're certainly not supposed to be able to use the chain, at least not at that point in the game. And according to http://www.uesp.net/wiki/Skyrim:Trinity_Restored, Karliah is the only one who can open it.

If she starts to walk out of the cave, you can try to attack her to get her to pull the chain.