I play the notes as they are in the walkthrough and can't the music to exorcise the black mist. I've tried the notes in different order still nothing.what else is there i can try.

Before this puzzle will work, be sure that you have listened to the gramophone recoding, read the book about Nathaniel and also the journal with the snake clue.
Then you turn on the organ and play.

Thanks Mag I figured it out

Great! Enjoy the rest of the game.