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684: Sepsis Puzzle 680 Open Phase
Status: Closed

Summary

Name: 684: Sepsis Puzzle 680 Open Phase
Status: Closed
Created: 03/11/2013
Points: 100
Expired: 03/18/2013 - 20:00
Difficulty: Intermediate
Description: This is round 2 for Puzzle 680. You will be able to load in your manual saves from 680 and use them as a starting point here. This puzzle has been opened up to allow for sharing and the use of all scripts. See if you can improve your model from the first round using these tools, or start from scratch! NOTE: If you did not manually save a solution in puzzle 680, you can go back to 680, manually save it, and the solution should appear in your manual saves for this puzzle.
Categories: Design, Overall

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Comments

beta_helix's picture
User offline. Last seen 14 hours 13 min ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this puzzle:

Please read the new Blog Entry about this puzzle: http://fold.it/portal/node/994592
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If you are new to Foldit, make sure you have completed Intro Puzzles 7-1 through 7-4 before trying this puzzle.
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This puzzle has the ResidueIE filter on (to ensure PHE, TYR, and TRP residues are scoring properly) and we've increased the Ligand Score by a factor of 10 to promote interactions with the sugar.

Tip: To see the parts of the sugar that you can bond to, check Show bonds (non-protein) and Show bondable atoms in the View menu. Make sure Show bonds (loop) and Show bonds (sidechain) are also on. Blue can bond to red, and purple can bond to either blue or red.
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Crash Warning: Do not enable the 'Show Isosurface' view option, as it will crash with this puzzle. We hope to fix this soon!
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Please note that the cuts on this puzzle cannot be closed!

They are just there to hold the region you are able to work on in place, without moving the rest of the frozen protein when you wiggle.

Joined: 06/24/2008
Groups: Void Crushers
Mutate problems

I have not been able to run any script doing mutate, I get:

string [[...}356: bagd argument #1 to GetAminoAcid (invalid argument)

beta_helix's picture
User offline. Last seen 14 hours 13 min ago. Offline
Joined: 05/09/2008
Groups: None
thank you for reporting this

We are looking into this problem:
http://fold.it/portal/node/994688

For now, since the ligand is not mutatable, if you can exclude it from your mutate scripts that hopefully might help a bit.

Joined: 09/21/2011
Groups: Void Crushers
Workaround for failing recipes

In most of them in the beginning of the file segCnt (or segCnt2 in my DRW) is set.
Just add -1 to that line.
Example V2 recipe: segCnt=structure.GetCount() change that into segCnt=structure.GetCount()-1

Joined: 06/04/2012
Filter issue

And I still believe the filter doesn't work properly. It still penalizes Tryps etc although they are placed properly. It is a bit disappointing that I didn't receive feedback anymore after i posted it on 680

brow42's picture
User offline. Last seen 1 week 6 days ago. Offline
Joined: 09/19/2011
Groups: None
Acceptor/Donors

All of the carbons are marked as Acceptor/Donor, but some are missing polar hydrogens, and Foldit refuses to bond acceptors to them.

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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, RosettaCommons