High wiggle leaves huge ideality score loss

Started by AsDawnBreaks

AsDawnBreaks Lv 1

See attached screenshot. This is on 845. Several segments scoring -300 to -500 in ideality. High wiggle should really be able to resolve something that bad…

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AsDawnBreaks Lv 1

Better after some local wiggles on single segs, but it really should be fine with a global wiggle and local wiggling smaller stretches.

nemo7731 Lv 1

After idealize I do a LPW before to switch to high power. My feeling is that HPW is unable to deal properly with low scoring segments whether or not they are ideal.

nemo7731 Lv 1

Sorry, I wasn't clear enough. Idealize first, then do a LPW before to switch back to HPW.
A zero lenght band prior to idealize is sometimes required to avoid the protein to explode.

jflat06 Staff Lv 1

Believe it or not, this is actually working as intended.

The Baker Lab has discovered recently that deviating from the ideal values for these degrees of freedom can provide better predictions in some cases.

The idea with high power wiggle is that it lets you 'trade off' ideality for increases in some of the other score terms. So even with the bad ideality terms, you're getting even better gains somewhere else that offset these.

That said, we are evaluating the usefulness of high-power wiggle and we may find it isn't helpful in the case of Foldit.

Susume Lv 1

I hope you won't take out high power and leave us with just the current low and medium. Consensus on my team seems to be that medium is not good for much, score-wise. We are mostly using low, and high only at certain times. If there is some functionality in medium that you want us to use because it makes better predictions, it has to pay off more in the score function.

jflat06 Staff Lv 1

The functionality of medium-power wiggle is to introduce the degrees of freedom for peptide bonds. Normally you shouldn't have to worry about these, since the should stay at their ideal values and aren't allowed to vary.

However, some of the tools in the game let you modify these degrees of freedom, allowing you to create unidealities. The biggest culprit here is the Cut tool. With the cut tool, you can botch two amino acids together in extremely unideal states that score terribly. Once you get in that state, there are options like the idealize tool that will get rid of these unidealities, but not without global changes.

Because of that, we've included these degrees of freedom in medium-power wiggle. That way, you can wiggle out these poorly idealized regions on the protein into more reasonable states.

This functionality has actually always been in Wiggle. Prior to the New Chapter, these extra degrees of freedom were only added on the even iterations of wiggle. Some players had noticed before that the even iterations would take a lot longer - this is why.

The design was such that even if you managed to get some unidealities into your pose, they would be resolved by Wiggle automatically over time. With the New Chapter, we decided that since you don't always need these peptide degrees of freedom, it would be simpler and faster to let you have the ability to run them only when you needed them.

As for why we kept medium as the default - we wanted to preserve the behavior that the default "Wiggle" of Foldit would address unidealities, just like it did before.

As for high power wiggle, we are evaluating the scientific usefulness. We understand it's great for getting points, but unless it's fulfilling some scientific purpose in Foldit, it might be best to remove it, since it might even be causing some issues as well.