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1766: TIM Barrel Redesign: Symmetric Trimer
Status: Closed


Name: 1766: TIM Barrel Redesign: Symmetric Trimer
Status: Closed
Created: 11/28/2019
Points: 100
Expired: 12/05/2019 - 23:00
Difficulty: Intermediate
Description: Redesign a TIM barrel protein with symmetry! We're looking for Foldit players' help in redesigning a well-behaved monomeric protein, so that it self-assembles into a trimer with C3 symmetry. The starting structure is a large (184 residue) protein previously designed in the Baker Lab. Players should bring the three symmetric units into contact, and redesign the interface between units. We expect the monomer unit may need to change shape slightly to make a good interface, so the backbone is flexible and all positions can be redesigned. In nature, proteins with this kind of fold (called a TIM barrel) are frequently found as symmetric complexes. We'd like to see if we can turn this designed TIM barrel into a symmetric complex, but this is a difficult problem for our computer programs in the Baker Lab. We think Foldit players can help!
Categories: Design, Overall, Symmetry

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Joined: 06/06/2013
Groups: Gargleblasters
puzzle too big to work

This keeps crashing with recipes that I'd use for early game. I love the concept, but it is too large :(

LociOiling's picture
User offline. Last seen 3 hours 54 min ago. Offline
Joined: 12/27/2012
late to the game, but a couple of suggestions

The crashes may be related to runaway memory use by the undo system in Foldit. It also seems related to specific poses of the protein, with some poses causing crashes while similar poses don't crash.

There are couple of tricks which may reduce the crashing, although the puzzle will still be quite slow.

The first step is to adjust the undo settings. In the Undo menu, select Graph Properties, and adjust the settings of the sliders, "Max Graph Length" and "Memory Usage". Move the sliders all the way to the left, setting max graph length to 25, and memory usage to 0%. Click on "Apply" for each setting.

As an added precaution, try closing and restarting your client, then verify the undo graph settings are still in place.

These settings limit the amount of undo information the client is keeping, and seem to eliminate crashes in at least some recipes.

The second approach is to modify recipes. This method works for Lua recipes using the "v2" interface, and can be as simple as adding one line of code.

Simply including this code near the beginning of a recipe:

undo.SetUndo ( false )

should reduce or eliminate crashes in at least some recipes.

If a recipe includes this code alone, it should be possible to undo the entire run of the recipe with just a control-z (or the equivalent) after the recipe completes. As with setting the graph properties, the result should be fewer crashes.

If you want more than one undo step, toggling undo status as follows may do the trick:

save.Quicksave ( 3 )    -- save the current solution
undo.SetUndo ( true )   -- turn undo on 
save.Quickload ( 3 )    -- reload; this should trigger an undo 
undo.SetUndo ( false )  -- turn undo off again

You'd do these steps whenever the recipe detects a gain that it wants to save. (The "3" on the Quicksave/Quickload commands can be any slot.) Thanks to berto for developing this technique.

(Another alternative is to use save.SaveSolution to create a saved solution. The advantage of SaveSolution is that the save should be available even if the recipe later crashes. Not sure about others, but Beta Folders have been slow to make use of this somewhat recent feature.)

There's more in these feedbacks:

crashes on puzzle 1766 TIM barrel redesign
Memory leak in client 20191029-32048a6a12-win_x86

Susume's picture
User offline. Last seen 8 hours 12 min ago. Offline
Joined: 10/02/2011
Decoy not scoring as well as helices

If you end up with a lot of all-helix solutions, it might be helpful to add a secondary structure requirement to future puzzles like this. Also, with so many residues, more than 7 days would be good.

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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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