My early inclination to believe rigged wiggles was a bit off. It turns out that when moving segments further apart their segments have less and less interaction so the score changes smoothly. When one moves the segments back together the sidechains will interact more strongly so the backbone has to overcome this interaction so the scores jerk and may even go negative then more positive.
I know this isn't much.
I have published two scripts, rebuild worst and minima finder.
Use rebuild worst when you are tempted to use a rebuild routine and want to focus on the worst scoring segments. If you convert your protein's secondary structure to loops it will have greater freedom. Wiggle worst leaves your secondary structure as it is.
Don't use minima finder without understanding what it does. It first tries to rebuld a segment then, if that fails, it wiggles it and its neighbors. It doesn't find the best solution just the best it can find quickly.
I thought foldit used pass by value. It passes tables by reference. This means one needs to build one's own copy function for tables. Rebuild Worst has the copy function in it. Since Foldit doesn't implement foreeach I can't create a generalized routine that works with string indexes.
Rebuild Worst aslo has a bubble sort routine in it that will sort a table of tables on any column. I read from the end towards the beginning to gets ascending scores from worst to best.
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