Local Rebuild Strategy is a Middlegame method that is usually aimed at specific low-scoring areas or at shapes the player finds intuitively suspicious.
Procedure[]
Choose a Target[]
Your target will be an area of the protein with one or two particularly low-scoring amino acids. These can be located using relative score coloring. Lock off an area (this is easiest to do in selection interface, by freezing neighboring segments on each end; in the original interface, these freezes must be combined with secondary structure reassignments for rebuild to work) containing these amino acids and a few others, for a total of three to five. More than five tends to become unmanageable, as the rebuilds will be harder to keep under control.
Structures[]
Choice of structure is very important in Local Rebuild Strategy. Structures not only allow the player to re-imagine what an area should look like, but they also appear to influence how the game engine rebuilds. Choose which structures you want to use with this in mind, and try to pick those that will best fit what you think the final shape should look like.
Rebuild![]
Rebuild the area you've locked off. Watch the undo graph and the area closely. There is no one thing that you're looking for, but you'll want to stop the rebuild at a time when the score is relatively high, the clashes and restraint lines are few, or when it just seems like you've hit a proper shape and can work with it. Since there are many different configurations even for a small number of amino acids, do not be afraid to let this phase of the strategy take a good long while. You'll soon learn to recognize good rebuilds when you see them.
Very short rubber bands can be helpful here too, especially on the larger locked-off sections. They become virtually a necessity at five amino acids, and above that you can use several of them to apply Local Rebuild Strategy to larger groups, although this seems to diminish its effectiveness.
Wiggle[]
You will want to try both local and global wiggle here, and see which one does better. Successful or promising local wiggle results should be followed by a global wiggle. Sometimes just global is better, for reasons I can't really explain.
Note that local wiggle may take a very long time to stabilize -- often several minutes, with a steadily increasing score the entire time. Also note that it sometimes it's possible to local wiggle yourself all the way back to the original configuration of that area -- when what you really want is to get away from it, since it was low-scoring to begin with.
Move the Locks[]
If you get poor results from the three to five amino acids you've chosen, consider adding one on an end or taking one off. You may get dramatically different and even better results.