Wiggle Power

Started by Seth Cooper

Seth Cooper Staff Lv 1

We've recently introduced a new option to control how wiggle behaves: wiggle power. This option is accessible from the behavior tab menu. This option generally trades off time for points and ideality: lower power will take less time to run, but have less ways to find points and spend less time adjusting the protein's ideality.

How does it do this? Currently, by changing which bond geometry wiggle can change. A protein's bond geometry includes the bond lengths, angles, and dihedrals (also called torsions) between atoms that define how the atoms are positioned relative to each other. For a good visual representation, see: https://wiki.cmbi.ru.nl/index.php/File:Energetics_1.gif . Low power wiggle uses only the standard set of dihedrals. These are typically called phi, psi, and omega for the backbone and chi for the sidechains; you can find more details here: http://en.wikipedia.org/wiki/Dihedral_angle#Dihedral_angles_of_biological_molecules . Medium power also uses additional bond geometry for the atoms that connect two segments, allowing it to resolve cuts. And high power further adds in some bond geometry for all of the atoms in the protein, allowing it to resolve cuts and fine-tune the entire structure. We may change precisely which bond geometry low, medium, and high power wiggle correspond to in the future, but plan to keep this general structure.

This is also closely related to a new scoring term: ideality. Roughly speaking, the bond geometry other than those standard dihedrals should not change very much from some ideal value. The ideality term lowers the score of structures when that geometry does change. For example, if you make a cut, widen the cut, and then close the cut, the bond's length will become unideal and score poorly. You can improve the ideality term of a structure's score by using medium or high power wiggle and the idealize tool.

How could the wiggle power option be used? We imagine that low and medium power wiggle will be most useful at the beginning of a puzzle to explore different structure possibilities. If a structure is already ideal, low power wiggle may be the fastest way to get a good idea of how well it can score. High power would be most useful later on, to finalize a structure and get any remaining points out of it. Although high power wiggle maybe get more points than the others right away, using it too early in a puzzle may "lock in" structures and make them harder to work with and get points from later on.

wisky Lv 1

This explains a lot to me about old wiggle's behavior (as well as new wiggle!). Thank you for the links!

Bruno Kestemont Lv 1

When I use the tool "idealize" on a zone, the score goes down (because of new clashes etc). Then I use Wiggle with high option till no gain.
Then I use Idealize again … and the score goes down.

Does it mean that the high Wiggle did not include idealize condition optimally?

brow42 Lv 1

Does rebuild respect the "idealize" constraints, or can we expect rebuilding on Low to reduce idealize over time?

bkoep Staff Lv 1

The Idealize tool resets some of your bond lengths and angles to constant values which are derived from native protein structures. For example, the peptide bond is on average about 1.33 Å long, so Idealize will extend or contract that bond to a length of 1.33 Å. This is useful when you close a cut point between two residues that are not exactly 1.33 Å apart, but will usually introduce clashes that you normally Wiggle out on low power.

Low-power Wiggle only changes torsion angles, and will not affect the length of the peptide bond. So if you close a non-ideal cut point and Wiggle with low power, the length of your peptide bond will remain non-ideal. Medium-power wiggle would be useful here for making a closed cut point more ideal without introducing new clashes.

Of course, not all peptide bonds are exactly 1.33 Å long. Sometimes the penalty for stretching that bond a little bit is offset by better packing, or a more stable hydrogen bond. This is one case where high-power wiggle is useful; it may lengthen or shorten bond lengths and angles (sometimes losing "Ideality" points, but only if this results in more points gained elsewhere).

Vredeman Lv 1

Thank you for this informative thread.
It seems as if (local wiggling) during hand folding requires a specific strategy.
This seems to mean that players need to use low, medium and high power wiggling for specific purposes.
It probably means that we should be careful to avoid global wiggles in medium and high power near the beginning but with local wiggles the powers can be played around with.
Please let me know If I got that right.
Porky

Bruno Kestemont Lv 1

So I understand that Wiggle High must have the latest word (actually, it scores the best). I wonder if there is a Lua command to set wiggle power. It would be useful to write recipes with "contextual options" (e.g. kind of fuzes beginning with idealize, then wiggle Low, then Medium then High, or using High if we are at the end of the puzzle race).