oh, and i figure that the alignment needs the structure's sequence in
there - right? this would actually save me some keystrokes.

Yes, and the target sequence (i.e. the protein that you crystallized) needs to be first. One annoying thing about MUSCLE is that it sorts sequences and (currently) won't let you disable this behavior, so you may need to do some cut-and-pasting. Maybe we need to modify the Python wrapper to do this automatically. (Although I think it would be even easier if Sculptor did the alignment automatically.)

-Nat