They were retrieved manually?
Well, it's my only share with the "code-like" name: FLAG_691_SUBMIT_1
(which is kinda why I thought they were fetched by database protocol or program or something and that's where something misfired)
If it turns out that isn't the case, was the save altered in any way?
We think we've discovered the problem with wiggle sticking in symmetry. There is an option that we use for non-symmetric puzzles that doesn't exist for symmetry in Rosetta. We're coordinating with the Baker lab to try and implement it or find a workaround.
For some reason, our database contains multiple entries saved by you with that name. Most of them are duplicates, but one is different from the others (it has Phe 35 and Gly 37, and one of the beta strands is slightly different). This one must have been overlooked when we grabbed your solution before. I don't know which solution is the one you intended to submit, but they are very similar.
Regarding your observations about the helix being lengthened and the sheets being shortened—that's just a visual result of a secondary structure prediction method we ran on your solution for puzzle 691. When we processed your solution to make it the starting point for puzzle 725, your helix and strand assignments were lost, so we reassigned secondary structure with these predictions. In fact, the atomic coordinates of your solution were unchanged. In any case, we'd like to keep player-assigned secondary structure when we repost player solutions in the future, so we've changed our puzzle-posting protocol to accomodate this.
I see, well thanks. It could've been the combination of the minute differences and just the secondary structure being assigned differently that made me think it was "off" more. :/
Thanks again for looking into this, and sorry if I made a giant fuss. :p