I tried the following using Puzzle 24
Starting at the hairpin turn near the antiparallel secondary structure I tried lining up the amino acids with the template one amino acid at a time. I used the harden tool to lock down my progress and would then keep swinging the rest of the chain around until the next amino acid covered the template. I would look closely from all angles to ensure all the blue was gone. After about 4 hours of this I had about 70% of the blue gone. All that was left were the two helices. Unfortunately, when I clicked on one of the amino acids, the whole thing blew apart :(
Apparently, one of the ribbons was upside down.
I suppose that with this strategy, a test as you go approach might be more appropriate.