Better, but still…
I think number of residues (locked o not) is essential.
Maybe you can create same puzzle in few variants:
1 - only locked backbone
2 - locked backbone and unneeded ss
3 - all unneeded ss are gly (bb locked)
4 - all unneeded aas are cut out
In that way we can simple run same script few times after reset puzzle, compare times and choose best option for future :)
We have thought many times about whether it is better to just remove the areas of the protein that are frozen and unimportant but then you are left with an ugly fractured mess instead of a nice looking protein so it's hard to see what is going on.
When I have a chance, I'll try to post some of those puzzles you suggested as Contests so you can all run some benchmarks.
Remind me if I forget to do this! :-)
Maybe full protein as guide in addon to cutted out part?
Looks like loaded guide not messing much in performance.