Puzzle 445 is broken

Case number:699969-990139
Topic:General
Opened by:anthunk
Status:Closed
Type:Bug
Opened on:Monday, August 8, 2011 - 03:54
Last modified:Wednesday, August 10, 2011 - 23:03

There are four major issues associated with the recently released puzzle 445:

1: Malformed Asparagine-- Asp 37 has the carboxyl end of the sidechain pointed at an extremely small angle to the base end. the amine end of the sidechain is affected, though by a lot less. See an image here:
http://fold.it/portal/files/chatimg/irc_99169_1312771984.png (credits to Enzyme for finding this)

2: This problem has to do with the amino acids 111 and 112. The problem is that the segment has a perpetually low backbone score, which is not solved by a rebuild of those and adjoining segments. In a related issue, the local wiggle function behaves erratically on those segments. Local wiggle moves the segments drastically, causing a dramatic score drop. This score drop is much greater than those sometimes seen on other puzzles. (credits auntdeen and myself)

3: The puzzle also has a very erratic opening. Shaking and wiggling the protein sometimes results in scores below zero, yet sometimes above 10000. Other results include 9680, 9740, and 9853. (auntdeen)

4: Finally, the puzzle also has threading problems. When threading model B onto model A, the protein has a extremely low score, and when shaken and wiggled out, extremely low backbone scores all over the protein. an image of this phenomenon: http://fold.it/portal/files/chatimg/irc_92665_1312773923.png (infajmc)

So far as we know, the bugs only appear on model B for 445.

Due to these errors, we recommend that you fix and re-release the puzzle.

(Mon, 08/08/2011 - 03:54  |  18 comments)


infjamc's picture
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I found a workaround for Problems #1 and #2:

After working on Model B for a while, save your current structure and load it as a guide. Then, apply an alignment using the "extend" template and then re-thread the protein to the guide. This will fix both the Asn 37 side chain and the bad backbone bonding angles between Ala 111 and Ser 112.

spmm's picture
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mmm asp is usually blue. the one at seg #37 on models A & B are blue. Not sure what the pic is of as it is brown.
Model A is really not doing anything at all so I would disagee with the statement that so far only Model B has problems. However I find the labelling on the aligments a bit mystical so could be wrong. Fairly obvious tho, wiggle one goes a bit green, wiggle the other, it stays red :-)

Joined: 04/19/2009

If you freeze seg # 109 & #114 then right click to wiggle just that section (at normal 1.0 CI), it will move around like a snake, scoring the entire puzzle in & out of the minuses. Current score at 10463, this will take it down as far as -6418. Fascinating to watch - but broken.

anthunk's picture
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Spmm--- the brown Asp is just a view setting applied to the protein; mine is otherwise normal, except for the error

keypad5's picture
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Regarding #2: Those backbones are problematic but they can be tidied up with rebuilds. If you rebuild from #111 to the end (#121) you'll find that the backbone can move a lot more, compared to just rebuilding #111, #112 and their adjacent segments.

I admit I did some other funky things to make it work (such as turning those segments into sheets during the rebuild and attaching a band to encourage them to straighten out) but it is possible to improve the backbone at #111-#112.

Admittedly, this is probably the least serious of the problems that Thunk has documented.

beta_helix's picture
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Thank you for reporting this, I'm looking into what went wrong right now.

beta_helix's picture
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My apologies for this problem, these puzzles have been reposted and you should be able to load in your previous solutions.

B_2's picture
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It appears that the CLOSED first iteration of 445 has been awarded points.

Was this intentional?

Should those be wiped out since the reincarnated 445 is now active?

Joined: 09/14/2008
Groups: Void Crushers

point were given , confirmed (in chat) that it is intended. not as many point as a full puzzle were handed

B_2's picture
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Why would points be granted for a puzzle that was open less than 24 hours, and not even available for many people to participate in?

This is extremely unfair that people on the far side of the planet got to rack up early points on a broken puzzle, and others never even got to see it.

Not to mention, it was probably only those people who got to vote on getting points.

This is a bad precedent to set.

beta_helix's picture
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There was no voting on getting points.
I mentioned in chat that a small amount of points would be awarded once the puzzle was closed.

There has already been a precedent when I messed up the first Flu puzzle:
http://fold.it/portal/node/989767
It had to be closed and those that had tried it received some points, nobody complained then.

I really did not think that there would be complaints for such a small amount of points, but rather I expected a lot of complaints from players who spent a day on this puzzle and got no credit at all when it had to be closed.

If you want to have a discussion on how many points should have been awarded, I can open a forum post for future cases where I mess up a puzzle (although the best thing would be for me to stop doing that!)

B_2's picture
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Then let's do the same thing you did on the broken 423 flu puzzle that you present as precedence, and just award 1 point for everyone to got started on it before it got yanked.

infjamc's picture
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One problem:

I cannot reload the solution from 445 in 445b, not even as a guide. Is this happening to anyone else?

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I can't load a solution from 445 into 445b either: attempting to do so causes an instant crash on Mac (without a crash log)

beta_helix's picture
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Yes, we are aware of this problem: http://fold.it/portal/node/990089

We will have a fix for it out as soon as we can (hopefully within 24 hours), this will require an update to the developer preview, but then those of you having trouble with this will be able to load in your previous solutions.
Until then, hopefully you can try a completely different track or trajectory.

B_2, as it took us over 1 day to close the broken puzzle, we did award a small amount of points for those who worked on it. Again, my apologies for the mistake in the previous puzzle... we'll try to be more careful in the future.

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So does that mean the points will be removed?

beta_helix's picture
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Not at all.
I am sorry for not being clear here.
Please see my reply to your post above: http://fold.it/portal/node/990139#comment-12226

I would add that 93 players tried it (http://fold.it/portal/node/990135/show_players?page=3) compare that to the 208 players that played the previous expired puzzle(http://fold.it/portal/node/990087/show_players?page=8) and it seems like a fair amount of players attempted this broken puzzle.

beta_helix's picture
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"B_2: Then let's do the same thing you did on the broken 423 flu puzzle that you present as precedence, and just award 1 point for everyone to got started on it before it got yanked."

I brought this up at our weekly Foldit meeting and we are going to stay with the assigned points.
I have described why 15 points (rather than 1) was chosen in this Forum post:

http://fold.it/portal/node/990156

I welcome any further feedback on this subject, but please continue it in the Forum as this feedback is about Puzzle 445 being broken.

Since that issue has been resolved I am closing this thread.

If you are having trouble loading previous solutions in BETA, please report it in this thread: http://fold.it/portal/node/990089

Again, I apologize for the mess created by this puzzle.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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