A current status rumination on the Wiggle power issue.

Case number:699969-997184
Opened by:alcor29
Opened on:Wednesday, March 5, 2014 - 17:51
Last modified:Thursday, March 6, 2014 - 20:36

After five weeks of random experimentation my conclusion is that I am still at sea, probably because I am missing quite a bit of understanding. This is the way I am seeing things now (feel free to enlighten, chastise, insult me, etc.):

If we idealize in the opening by idealizing or folding on High power, either by hand or by script, we then find that the ideality scores prevents most moves or scripts from gaining any energy ground because the rise in the ideal score, driven by geometry checks( I think), cancels whatever gains we make. This is experienced by folders as “hardening” of the protein. Most importantly then we are in effect no different from Rosetta. So why bother funding the whole foldit experiment at all.

If we start all folding in low power we are essentially at the point the client was prior to NC and old scripts work because the checks are few and the ideality penalties scores are very low therefore allowing energy gains.

So we come to Medium, which increases the geometry checks a little or separates out what was done prior to NC within the old wiggle. It is currently experienced by me and perhaps others as essentially doing nothing that couldn’t be done by the including or re-including it in another power choice, especially Low power. Nevertheless it or some similar compromise seems to be the only possible answer to the problem, or to at least point to it. If you still think there is a benefit from exploring the resource of the human brain as opposed to a Rosetta program, all you can do is improve the ideality slightly. My question then is why not put Medium's function back under Low and just have one wiggle; or perhaps another path would be lowering the ideality penalty score would work better, since both methods don't increase the permutations a folder has to encounter by finding different combinations of wiggle power with CI, etc. And perhaps more importantly, it also might simplify the effort needed to modify our pre-NC scripts to include both ideality penalties and wiggle power variations.

(Wed, 03/05/2014 - 17:51  |  3 comments)

spmm's picture
User offline. Last seen 41 weeks 4 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers

Medium also stiffens the protein which imo removes the ability to experiment with poses on low wiggle power, so putting medium into lowWP would be a step backwards in terms of player flexibility and for me at least my enjoyment of the game.

Joined: 09/21/2011
Groups: Void Crushers

I dont ever use medium, because that does the protein flexibility no good at all. And I would like to see the default on wiggle power to be LOW and no change at all except when the player asks for it. So any loading, changing tracks, changing puzzles should not interfere with the setting.

alcor29's picture
User offline. Last seen 2 days 13 hours ago. Offline
Joined: 11/16/2012

I never use medium either for similar reasons, nor am I recommending it. Perhaps I wasn't totally clear.

Since high would be the equivalent or Rosetta, and low would be, I assume, almost or identical to pre-NC, it seems then paradoxically, that if the scientists want us to make proteins that are closer to reality, (ideality) the answer seems to lie somewhere around medium or as I mentioned lowering the penalty for ideality or some such stratagem. I am sure there are other answers which they are working on, I am just stating my very limited understanding of the situation I find myself in and hoping for further elucidation either from experienced super folders like yourself, or from a developer, to see if I'm sort of on the right track.

For the record, my preference would be to see it go back not just to pre-NC but back to when wiggle was just wiggle even without a "more precise wiggle." I play for fun, or to distract myself from the real crises in my life. I prefer to do a puzzle in one day. I do what I can and then abandon. I don't like to grind or spend a day or three running a single script. In fact I was considering doing a feedback suggesting we have some "blitz" folding puzzles which would be up for just 24hrs to see what folks could do just by intuition and without too much exploring or grinding, but I thought the better of it since I felt it would be met with a hue and cry of post-NC outrage.

hanks for commenting, Timo. I hope this makes it a little clearer.


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons