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1989: Symmetric Tetramer Design: H-bond Networks
Status: Closed

Summary

Name: 1989: Symmetric Tetramer Design: H-bond Networks
Status: Closed
Created: 05/05/2021
Points: 100
Expired: 05/12/2021 - 23:00
Difficulty: Intermediate
Description: Design a symmetric protein tetramer, with 4 identical chains that assemble together! This puzzle includes a Secondary Structure Objective, so no more than 50% of your design can form helices. The H-bond Network Objective encourages players to build buried, satisfied H-bond networks at the interface between symmetric chains. H-bond networks are a great way to introduce polar residues at the interface, but it's important that all of the bondable atoms make hydrogen bonds! We've also adjusted the H-bond Network Objective so that poor-scoring H-bonds may not contribute to networks; poor-scoring H-bonds will be displayed in red. This puzzle uses the Buried Unsats Objective, with a large penalty for buried polar atoms that can't make H-bonds. In this puzzle, there are no limits on the Complex Core, but we've included the Complex Core objective so players can see the core residues that can be incorporated into H-bond Networks.
Categories: Design, Overall, Symmetry

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Comments

bkoep's picture
User offline. Last seen 6 hours 6 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -200 points per atom (not including symmetric copies).

Core Existence: Monomer (max +2800)
Ensures that at least 28 residues are buried in the core of the monomer unit.

Core: Complex (max +0)
Awards no bonuses or penalties. Click Show to see which residues count as "Core" for the H-bond Network objective.

H-bond Network (max +2400)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 12 H-bonds should cross the interface between symmetric units.
Networks must be at least 75% satisfied (i.e. 75% of all bondable atoms in a network must make a H-bond).

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.

Joined: 06/24/2008
Groups: Void Crushers
Crashing

This puzzle has crashed twice on me.

milkshake's picture
User offline. Last seen 1 hour 42 min ago. Offline
Joined: 07/17/2019
Groups: Foldit Staff
Hi Mike Cassidy, what action

Hi Mike Cassidy, what action are you performing when it crashes? Running a script, making a band, mutating a residue, etc.? If you're doing something manually, is a script running at the same time? Thank you.

blazegeek's picture
User offline. Last seen 14 hours 46 min ago. Offline
Joined: 03/30/2020
Groups: None
Crashing

This puzzle crashes on me at random, regardless of what I am doing. Manually wiggling, shaking, mutating, and idealizing have all crashed the puzzle repeatedly. I don't think I've had an opportunity to even run any scripts yet.

grogar7's picture
User offline. Last seen 8 hours 24 min ago. Offline
Joined: 10/03/2011
Crashing

Just to throw in my 2 cents worth, this puzzle is repeatedly crashing for me, too! Cause does not seem to be consistent. For example, Tvdl DRemixW will invariably crash, but sometimes it is immediately after selecting options and starting puzzle run and other times it will run through several sets of segments before crashing. Same problem with GAB_proj_beta. Has also occurred with some manual actions.

Interestingly, Maaa version 2.4.2 did not crash!

Very frustrating, especially as I suspect the problem will not be reproducible by our scientists.

Joined: 12/06/2008
Groups: Contenders
Crashing... unplayable.

Every time I try to run a mutate script or a rebuild on this puzzle, it crashes within fifteen minutes.

Unplayable. Please cancel this puzzle and replace it with one that works.

milkshake's picture
User offline. Last seen 1 hour 42 min ago. Offline
Joined: 07/17/2019
Groups: Foldit Staff
This type of crash may be

This type of crash may be somewhat difficult to reproduce and to track down, but we have ideas about what may be causing them and myself and other developers are working on the problem. We believe that low framerates, high residue count, and possibly interactions in our molecular modeling layer that are unaccounted in our graphics layer may contribute to the problem. We'll stay in communication and post patch notes when we do figure things out. I've fixed at least one crash so far related to this puzzle/caused by low frame rate, but there may be several in the same vein.

alcor29's picture
User offline. Last seen 3 hours 39 min ago. Offline
Joined: 11/16/2012
crash...

At lest 14 crashes. Main. Win10 64. Both solo and evo. Had to abandon.

milkshake's picture
User offline. Last seen 1 hour 42 min ago. Offline
Joined: 07/17/2019
Groups: Foldit Staff
Drawing bands while wiggling

Drawing bands while wiggling was the cause of the crash that has already been fixed, and will be pushed to the main client soon.

For another long-running script crash, it might help to use View Protein: Cartoon, View Hydrogens: Hide All H, and View Sidechains: Don't Show (Fast). This is a workaround and we are working on a long-term fix.

HuubR's picture
User offline. Last seen 4 hours 1 min ago. Offline
Joined: 04/13/2020
Groups: Gargleblasters
What about the HBN filter?

Tried all sorts of diffrent view settings, LWP, MWP, high CI, low CI, but nothing seemed to help. Just found out in the last half hour before closing that switching off the Hydrogen Bond Network filter does help, at least for two very persistent crahes (in two different tracks) that I had.
For what it is worth: 20210429-924409cca5-win_x86-devprev

Joined: 06/06/2013
Groups: Gargleblasters
this puzzle crashed on me & several others in my group also

the tetramers seem prone to crashing. I don't know if it is size or something else. Basic recipes that either mutate or even just drw or dremix crash frequently. Kind of frustrating

HuubR's picture
User offline. Last seen 4 hours 1 min ago. Offline
Joined: 04/13/2020
Groups: Gargleblasters
No crash with the new devprev release :-)

Tested my two saved solutions with the new devprev release (20210513-dcafd2c0c1-win_x86-devprev). With exactly the same setup, except for this new release, both solutions run smoothly.
Wish we would have had this release a couple days earlier (before the puzzle closed ;-), but still: thank you, devs!

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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, Boehringer Ingelheim, RosettaCommons