Give open cutpoints a penalty

Started by Timo van der Laan

Timo van der Laan Lv 1

Sometimes an open cutpoint scores higher then when closed.
This breaks the following pseudo code:
set recent best
Repeat
-create cutpoint
-idealize near the cutpoint
-do some more (local wiggles, shakes)
-close the cutpoint
-some more wiggles/shakes
-restore recent best
And do this again for another part of the protein.
In the restore operation you can end up with an unexpected open cutpoint
Also after this it possible that restore best score has an open cutpoint.

Giving a penalty of 50 pts for each open cutpoint, or 100 pts if any open cutpoints would making use of the new cutpoint functions a lot easier.

Timo van der Laan Lv 1

I think you are missing the point. You would never want a score of an open cutpoint be higher than the same position when the cutpoint is closed.
Because then you have a high score with a cutpoint open, and that is just not what you want.
A not counting high score destroys the logic. Also when you later use the a key or control b to restore the best score, you get one with an open cutpoint.