Pi helix trick revisited

Started by infjamc

infjamc Lv 1

In the recently posted Beginner Symmetry puzzle, it's possible to turn the alpha helix into a pi helix for a huge boost in the score:

I don't think this was intended. For future purposes, could constraints be placed (say, require a minimum distance between the first and the last residues) on this type of puzzle to discourage the use of high-scoring but unnatural artifacts?

beta_helix Staff Lv 1

Thanks for catching this infjamc, this is why we wanted to start with a simple first symmetry puzzle, to try to catch these bugs that went unnoticed in the Developer Preview.

infjamc Lv 1

Well, maybe bug isn't the right term– I see it more as exploiting a known weakness in the score function, which gives more points to "stronger" hydrogen bonds (i.e. you get more points because the pi helix is more densely packed). In the interest of full disclosure, I'd say that this bug gives one at least a 400-point advantage (my score was in the 9600s before posting the screenshot).

infjamc Lv 1

  1. Enter a full-atom viewing mode that displays polar hydrogens (e.g. via the Ctrl+Shift+V hotkey on Windows systems).
  2. Add a rubber band between the backbone hydrogen atom of residue n to the oxygen atom of residue n+5, starting with n=1. Then, set the length of the band to zero.
  3. Repeat Step #2 for the length of the helix.
  4. Wiggle, then shake. If done correctly, the alpha helix would curl up into a pi helix. (Note that this trick obviously doesn't work if there's a proline in the middle.)

infjamc Lv 1

Either that, or decrease the number of points it's worth.

On a side note, I've just discovered another bug. This has been confirmed by several of my teammates:

  1. Load Puzzle 479.
  2. Load a teammate's solution as a guide.
  3. Press the G key. You should see the guide fly away, and you can't get it back unless you restart the puzzle.

auntdeen Lv 1

Changing status back to Open and priority to High:

I reset the puzzle. Started one script - killed it after literally 2 minutes. Started another, and within one minute my score jumped to rank #11 - with this unlikely result:

No way should this score so high. A teammate was able to duplicate this with the same results.

Sigh - puzzle should be cancelled.

We had both done the dev update this evening, if that has anything to do with it.

spmm Lv 1

  1. Add a rubber band between the backbone hydrogen atom of residue n to the oxygen atom of residue n+5, starting with n=1. Then, set the length of the band to zero.
  2. Repeat Step #2 for the length of the helix.

I'm obviously not getting this, hydrogen = white; oxygen = red - starting from the glutamine at seg #1=n - which has 3 white knobs close together > to the Leucine at seg#6, which only has backbone bonds. alanine at 11, leucine at 16, glutamate at 21 etc.

The residues themselves don't have apparent red knobs to bond to, even with bondable atoms turned on.

with band length set to zero - then wiggle - ends up in a ball?

infjamc Lv 1

Oops, looks like I wasn't being clear enough. What I meant in Step 2 was this:

Starting from the alpha helix configuration, band the backbone hydrogen of every residue to the oxygen of the residue that's 5 amino acids ahead. (In other words: ignore the side chains completely.) Namely, 1 to 6, 2 to 7, 3 to 8, etc. Clashing importance and band strength should both be left at 1.00.

Maybe a screenshot from the starting configuration would help? (See attachment)