puzzle picture
742: 65 Residue Trimer Design
Status: Closed

Summary

Name: 742: 65 Residue Trimer Design
Status: Closed
Created: 07/08/2013
Points: 100
Expired: 07/15/2013 - 18:00
Difficulty: Intermediate
Description: This is a 65 residue symmetric trimer design puzzle; there will be three symmetric chains to manage. Remember, a symmetric protein relies not only on how well-folded each chain is, but also on how well they interface together. See the blog post about this for more information. There are 2 filters enabled on this puzzle: the Residue IE Score monitors that all PHY, TYR, and TRP residues are scoring well, and the Core Existence filter checks that at least 30% of the residues are buried in the core of your design. The Baker Lab will run folding simulations on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 3 designs that you want us to look at, even if they are not the best-scoring solutions.
Categories: Design, Overall, Symmetry

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Comments

marie_s's picture
User offline. Last seen 1 year 36 weeks ago. Offline
Joined: 05/18/2008
Groups: None
wiggle is hard at the start ans bands are useless

I cannot use bands as they behave like they have lenght negative and high strenght

jamiexq's picture
User offline. Last seen 17 hours 40 min ago. Offline
Joined: 07/31/2011
wiggle sticks

As has been the case for a while, wiggle sticks on these design puzzles - just stops cold - yet on non-design puzzles, wiggle goes on and on and on for days

Joined: 03/20/2012
Groups: None
Also...

Seems to act like a Centroid puzzle. Did anyone else notice this??? Wasn't anything in the Puzzle Description about that though... hmmm.

Any script that uses Shake isn't doing anything at all, how a script deals with that differs from script to script obviously. Ditto for Shaking by hand, nothing happens.

Wiggle and Bands seem fine though... at least on the scripts I tried.

beta_helix's picture
User offline. Last seen 12 hours 5 min ago. Offline
Joined: 05/09/2008
Groups: None
We are looking into this...

Thanks for letting us know.

Did anyone that played the BETA Tetramer Design with Wiggle Fix
puzzle run into any of these issues?

http://fold.it/portal/node/995414

If not, hopefully we can pinpoint why this one is different than that one!

spdenne's picture
User offline. Last seen 27 weeks 4 days ago. Offline
Joined: 10/01/2011
Groups: Void Crushers
I played the BETA puzzle, but

I played the BETA puzzle, but all I remember was that it did wiggle, unlike the experience it was trying to fix.

I've had no problems with bands in 742. I do get Wiggle taking a very long time for 1 iteration.

20130705-05dcd7a009-win_x86-devprev

spmm's picture
User offline. Last seen 27 weeks 3 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
bands are a problem in main

In main, I found the same as Marie, bands need to have the strength set to <0.6 or they go bonkers, rebuild was also quite odd. It seemed as if CI was set very low but in either case and after closing and reopening the puzzles and checking CI the problem persisted.
Wiggle was the least of my problems so no comments on that apart from the apparent low CI effect, ie not wiggling enough for CI=1.
Win 8, latest main version.

beta_helix's picture
User offline. Last seen 12 hours 5 min ago. Offline
Joined: 05/09/2008
Groups: None
this is specific to 742, right?

Thanks for these details, spmm.
Is this behavior specific to Puzzle 742, or happening on all puzzles in main?

spmm's picture
User offline. Last seen 27 weeks 3 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
specific to this puzzle

apologies didn't see this question - the band thing in main (Win8) is only on this puzzle - I have 3 versions and they all do the same thing. So I have to set any band to <0.5 actually 0.6 was a bit optimistic, they stick (stop) and then, as Marie says, suddenly act as if CI was negative. Wiggling on low CI produces the same 'less than zero' effect, or nothing at all.
Wild and woolly :D
Having glimpsed spdenne's latest creation it is obviously not a universal problem :D

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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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