It depends on what you're trying to do. If you want to make sure that no one can access that file but you, even if they sit down at your computer logged in as you (your forgot to lock your screen or whatever), then there's pretty much no way for it to be transparent. You'd have to do something to check the file out and then check it back in.

Probably the least inconvenient thing would be to have an encrypted mountable filesystem image. That way it remains unlocked as long as you're using it, then you just have to remember to unmount it. TrueCrypt will do this.

You could also encrypt an individual file, but this would pretty much require that you unencrypt it and re-encrypt it every time.

Maybe if you gave us a little more intended usage pattern, it might help.