Auto-Wiggle Power and Idealize Secondary Structure

Started by jflat06

jflat06 Staff Lv 1

We're introducing several new features soon, and we're here to give a brief description of what they do.

Auto Wiggle Power

We've heard requests by many players to make Low Power Wiggle the default. Our reasons for not making this change might not be obvious. There are tools in the game that allow you to introduce unideal peptide bond lengths and angles, and we want the default behavior to be capable of resolving these issues. Low Power isn't capable of addressing these issues, but Medium Power can.

However, as many of you have noticed, there are a couple of problems with Medium Power Wiggle. The first is that it is slow. This is because Medium Power Wiggle modifies bond lengths and angles for every peptide connection in the protein. Thus, there are more variables for Wiggle to try changing, which takes more time. The second is that since Medium Power Wiggle has more freedom of which variables to change, it can find better shapes and get 'stuck'.

We'd love to have the unideality-resolving power of Medium Power with the speed and looseness of Low Power - that's the purpose of Auto-Wiggle. When you start a Wiggle, Auto Wiggle Power figures out the bare minimum of extra computation to resolve the unidealities, instead of just including all bond lengths and angles like Medium does.

The result is that instead of adding ~400 extra degrees of freedom like you would with Medium Power, you're now only adding on average ~4 with Auto Wiggle Power. And if you have NO unidealities, it will function identically to Low Power Wiggle.

We hope you like it!

Idealize Secondary Structure

Another request we've seen is to make forming Helices and Strands easier.

Since Secondary Structures are so critical as building blocks for proteins, we agree! Our current tools for forming a perfect helix or strand are Rebuild and Tweak. Neither of these tools is particular good at that task, so we've decided to give you a dedicated tool: Idealize SS.

Idealize SS turns a helix or strand into a perfect helix or strand. Like Idealize, it simply sets these values, so there will be global changes even when run on a local region. If you want to prevent this, you'll have to use cuts.

Idealize SS is available in the right-click menu of the Original Interface or by any non-empty selection in the Selection Interface.

Bruno Kestemont Lv 1

ISS sounds good but, like idealize and remix, frustrating to use in hand fold (because of the cuts).
Will there be a lua command soon?

OR you could add an option: when used on selected part, it "cuts" automatically then close cuts.

OR when froozing one segment before and after, same behaviour as cut-close ends.

Same behavior as for rebuild would be nice: if you want to perfect one zone, simply froze it's ends, then try everything you want with right click: rebuild, local wiggle, local shake, idealize, remix, IdealizeSS …

AsDawnBreaks Lv 1

Jeff was in chat yesterday, and explained why it swings: It DOES create cuts, and can't close them any better than we can.

jflat06 Staff Lv 1

Idealize SS does not use cuts - I was referring to Rebuild.

But the point about Idealize SS not being able to close cuts reliably is accurate.

The idea behind Idealize SS is that you simply want a helix. If we attempt to do loop closure and resolve cuts automatically, that introduces side effects and also adds a possibility for failure. Loop closure failure is the same reason why Tweak sometimes gets stuck, and not all Rebuild tries succeed in changing the structure.

Instead, we opted to let players decide whether inserting cuts is necessary. And if you do choose to use cuts, then you also have more control over how they are resolved, letting you resolve them more reliably than the computer would.

The intended use case for Idealize SS is also more for the early stages of folding, particularly in design and denovo. In these stages, it's useful for just forming the secondary structures properly for use as building blocks.

Timo van der Laan Lv 1

One thing that still is not resolved, is that sometimes the wiggle power goes back to its default without that being asked for, and only to be realized once a tool has started and sometimes run for a long time because it was not showed in the behavior box.
Please, please do never change the wiggle power unless specificly asked for by the player. (If you really want to keep that behavior add an explicit warning that wiggle power has changed to the default.)
So changing puzzle, changing track, loading a save should have no influence on wiggle power.