puzzle picture
1249: Electron Density Reconstruction 1
Status: Closed

Summary

Name: 1249: Electron Density Reconstruction 1
Status: Closed
Created: 06/20/2016
Points: 100
Expired: 06/27/2016 - 23:00
Difficulty: Intermediate
Description: The structure of this protein has already been solved and published, but close inspection suggests that there are some problems with the published solution. We'd like to see if Foldit players can use the same electron density data to reconstruct a better model. Secondary structure predictions (from PSIPRED) are marked on the starting structure, and provide clues about where the protein might form helices and sheets!

Sequence:
SRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLLVHLDQSIFRR
Categories: Electron Density, Overall, Prediction

Top Groups

RankGroupScorePoints
1Anthropic Dreams13,648100
2Go Science13,64771
3Gargleblasters13,62449
4Beta Folders10,44533
5Contenders10,13322

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Comments

Joined: 10/23/2014
Groups: Contenders
Unable to play

Clicked to open puzzle 1249 and foldit crashes within seconds. Have tried five times now. Running Windows 10.

Susume's picture
User offline. Last seen 2 days 22 hours ago. Offline
Joined: 10/02/2011
Also unable to play

Have crashed 4 out of 4 times when opening puzzle. In a new client, once with network timeouts enabled and twice with disabled. Also when switching to 1249 from another puzzle. Puzzle screen comes up, protein is visible, scoreboard loads, then screen goes gray and crash message from Windows.

Win 7 64, 20160609-a37c535a0d-win_x86-devprev

bkoep's picture
User offline. Last seen 14 hours 40 min ago. Offline
Joined: 11/15/2012
Groups: None
Possible stopgap

This seems to be a problem with the "electron_density_panel/threshold" setting in the options.txt file. We're working on a fix for this bug; in the mean time, players can try deleting their options.txt file before starting a new client.

Susume's picture
User offline. Last seen 2 days 22 hours ago. Offline
Joined: 10/02/2011
or just edit

Or if you are comfortable editing your options.txt file, set
"electron_density_panel/threshold" : "0.50"

Joined: 10/23/2014
Groups: Contenders
Stopgap seems to work

After comparing the old and newly created options.txt files made the following setting change.

"electron_density_panel/threshold" : "0.500000"

Appears to be working fine now.

gitwut's picture
User offline. Last seen 32 weeks 3 days ago. Offline
Joined: 05/18/2012
Groups: Contenders
Poor quality cloud image

If the structure is known (or almost known) why is the density cloud image so poor? I've played with all the settings and I can't seem to make out a single structure from it.

I'm not a fan of either the Electron Density or Contact Map puzzles, but if the structure is reasonably known, wouldn't a contact map puzzle have been a better choice for this puzzle?

jeff101's picture
User offline. Last seen 2 days 1 hour ago. Offline
Joined: 04/20/2012
Groups: Go Science
Cloud image quality

Is the ED a superposition of ED from several different subspecies?
Just considering different disulfide bonding patterns gives many
possibilities (http://fold.it/portal/recipe/43861#comment-28861).
The Recipe bandsomeSS (http://fold.it/portal/recipe/101275)
makes it easy to band a particular combination.

Perhaps next week we will have a Contact Map puzzle for the same protein.

bkoep's picture
User offline. Last seen 14 hours 40 min ago. Offline
Joined: 11/15/2012
Groups: None
Good questions!

This density has the potential to look much clearer. When generating this map, we took some steps to limit model bias (a phenomenon in which a poor model can be used to make a deceitfully clear map), but this process also removes some genuine information from the density. Model bias is probably not a huge problem in this particular case, but we wanted to allow Foldit players the opportunity to meet the greater challenge. It is very likely we will repost this puzzle in the future with a refined density map.

In general, an electron density map will contain much more information than a contact map. A model that fits electron density data is much, much more reliable than a model that fits contact data.

Joined: 09/24/2012
Groups: Go Science
very slow ED panel

It's abnormally slow when trying to change treshold, and it crashes unexpectedly (on open or later) on windows

Joined: 10/30/2012
Groups: Beta Folders
still crashing, loads OK, but

still crashing, loads OK, but crashes when i try and adjust the density

Joined: 10/30/2012
Groups: Beta Folders
args passed:

args passed:
'C:\Foldit\foldit3\Foldit\Foldit.exe'
starting the init thread!..
boinc base url: https://fold.it
checking updates...
binary
local: 'cc851479fcf63a3ea048c70a4d550955'
remote: 'cc851479fcf63a3ea048c70a4d550955'
database
local: '4aa3799f5de6b1475e948fb77682d90f'
remote: '4aa3799f5de6b1475e948fb77682d90f'
resources
local: 'f3f5689675a05a73fb3d5d1f6e8950e6'
remote: 'f3f5689675a05a73fb3d5d1f6e8950e6'
cleaning up old components:
binary 00000000000000000000000000000000
binary cc851479fcf63a3ea048c70a4d550955
database 4aa3799f5de6b1475e948fb77682d90f
resources 00000000000000000000000000000000
resources f3f5689675a05a73fb3d5d1f6e8950e6
CRASH: 455069
SoundTheme::load: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_00.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_01.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_02.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_03.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_04.ogg
loading: cmp-resources-f3f5689675a05a73fb3d5d1f6e8950e6\resources\sounds/organic_01/rotamer_land_05.ogg
SVM classifier successfully loaded
Feature list successfully loaded
Valid classifier feature list
Duplicate hotkey Ctrl+Shift+E (Show constraints, Show ligand constraints)
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASN:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 13
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue MET:CtermProteinFull 13
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 12
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 12
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASN:CtermProteinFull 12
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 12
buildid: 20160609-a37c535a0d-win_x86
about to create view_options_button_
Duplicate hotkey Shift+L (Show outlines, )
setting side chain mode to: 0 Don't Show (Fast)
Playing: sounds/organic_01/splashscreen.ogg
Converting any old-style quicksaves and autosaves...
Reading in vall_torsions file: cmp-database-4aa3799f5de6b1475e948fb77682d90f\database\sampling/rna/1jj2.torsions
Lines read from vall_torsions file: 2754

Joined: 06/06/2013
Groups: Gargleblasters
won't load without crashing for me

known klutz about manipulating software. but it crashes the minute I try to do anything. not workable for me. Windows 7 system

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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