I couldn't find a thread about this topic yet, so I was wondering if (and how) the new template alignment feature has helped your folding.
Here's the way I used it in puzzle 411:
- The templates were not modified. When accidentally moving amino acids in a template, I reset it.
- The amino acids of the unknown protein were moved to get a "reasonable match" for a template before trying to align it.
- Breaking the unknown into smaller chains seemed to always reduce the score, so, when possible, I tried to build the longest chains of amino acids before aligning the structure.
Attached is the alignment I ultimately used. Sorry I didn't get a picture of the protein itself while the clock was running down.