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_biologica... . 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.( Posted by Seth Cooper 93 2671 | Tue, 01/28/2014 - 00:59 | 7 comments )