My score drops by a lot whenever I align. Shouldn't the alignment algorithm make the alignment bonus improve when I align the protein to the ED, regardless of whether the ED is correct or not?
(Currently (8698) my OTHER score is -84 vs -157 aligned. I did a reset and wiggle, that is -80 vs -97 aligned, after fuzing -84 vs -109)(minimum threshold maximum cloud while aligning)

Your intuition is correct - aligning should always increase your score.

However, the problem is that aligning isn't easy - we cant just find the perfect answer like we can for aligning a QTTN. When you press the align button, it does a bunch of complicated math to make a best guess of how to orient the protein, and then does a type of wiggle to let it settle into the density. This doesn't always get the right answer, so your score can actually drop. If you already have the protein well aligned within the density, pressing the "Refine Alignment" (I think that's what it's called...) will JUST perform the wiggle part, and will only ever increase your score.

It might make sense to have the Align button only actually replace your current alignment if the score you end up with is better. I can try this out and put it in if it works well.

Alright, I've discovered why aligning is resulting a score decrease -

The problem is that when you press align, foldit tries to orient the protein in the way such that it gives you the most ED alignment score. Now, for a protein with a single chain, this works great. But this puzzle has two pieces, and it is trying to fit each piece into the density separately. So the relative position of the two pieces is changing when you press align. This is somewhat desirable, since you *are* matching the density better.

However, I think it is still better for align to only align, so that it can never *decrease* your score.