Weird helix scores too well

Case number:699969-997269
Topic:General
Opened by:auntdeen
Status:Open
Type:Bug
Opened on:Sunday, March 16, 2014 - 04:37
Last modified:Thursday, March 20, 2014 - 11:02

There still seems to be something wrong with scoring.

Puzzle # 858 should be a basic refinement puzzle. However, this solution has horribly misshapen helices, but is high scoring - I ran a Quaking Rebuild on it which gained nicely but produced this mess.

We have all seen helices bend, curl funny, etc. But the wide looping at the top of the one on the left is just plain wrong.

http://fold.it/portal/files/chatimg/irc_99169_1394935918.png

This was in Main, Mac OS 10.7

(Sun, 03/16/2014 - 04:37  |  10 comments)


Joined: 04/15/2012
Groups: Beta Folders

Yep, I've seen one that was a very nice shade of green that was bent at a 90 degree angle (maybe more, can't remember). I think that may have to do with the fact scoring is not based on SS... Though maybe it should be?

Joined: 12/06/2008
Groups: Contenders

You might want to check the sidechains that make up the "weird" part. If they are not sidechains that are commonly found in a helix, perhaps that odd area might actually be a loop.

I always take given secondary structures with a grain of salt. They are only predictions, yes?

Joined: 04/19/2009

Normally I would have done that... but this is the revisited Mouse Puzzle and usually the structures given in an old puzzle are mostly correct :)

bkoep's picture
User offline. Last seen 10 hours 52 min ago. Offline
Joined: 11/15/2012
Groups: None

Thanks for bringing this up, auntdeen. It turns out there was a slight problem in the way the score function was set up for this puzzle (my fault, sorry). The problem only affects Puzzle 858.

Joined: 04/15/2012
Groups: Beta Folders

Well, that explains a lot. :)

Joined: 02/08/2012
Groups: None

As an experiment, I'd love to see scoring based on SS. Maybe on devprev. Just to see the gains and losses and hoe much of a difference it would make.

Joined: 04/15/2012
Groups: Beta Folders

I would love a custom score weighting option in general, though the core wouldn't count. Also, maybe being able to have tools act differently depending on the score weighting being used (like CI does with wiggle, and other such tools).

bkoep's picture
User offline. Last seen 10 hours 52 min ago. Offline
Joined: 11/15/2012
Groups: None

drumpeter, can you elaborate on your idea of "scoring based on SS"?

Do you mean you'd like to see something that considers the helix/strand/loop "designation" that has been assigned by the player? This would mean, for instance, that your score could change simply by selecting a segment and changing its SS designation without actually moving the protein.

Or do you mean something that would reward segments with regular helix/strand shape and penalize segments with irregular helix/strand shape (like the funny helix in auntdeen's screenshot above)? This type of scoring is already used by Foldit to some extent, but could possibly be augmented in a devprev puzzle.

Joined: 04/15/2012
Groups: Beta Folders

I'm not him, but...

Maybe both. I would like to see the first approach as a non-global scoring mechanism (you see it, but score isn't reported until you turn it off).

Joined: 09/21/2011
Groups: Void Crushers

Or maybe punish helixes because it looks like Foldit is rewarding that structure too much.

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