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1020: Revisiting Electron Density Puzzle 663
Status: Closed

Summary

Name: 1020: Revisiting Electron Density Puzzle 663
Status: Closed
Created: 11/25/2014
Points: 100
Expired: 12/13/2014 - 14:00
Difficulty: Advanced
Description: NOTE: The deadline for this puzzle has been extended to December 13 at 14:00.

We're revisiting this old electron density puzzle to test some recent changes to Foldit! In this puzzle, there are bits of density which don't belong to the copy of the protein that you're working on. However, the protein you're working on should fit entirely within the density box. You'll have to decide which bits of density to match with, and which bits to ignore. Try to fit the protein into the density to get the best score! Secondary structure predictions are posted in the puzzle comments along with info about available tools in the game.
Categories: Electron Density, Overall, Prediction

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Comments

bkoep's picture
User is online Online
Joined: 11/15/2012
Groups: None
Secondary structure predictions

Here is the sequence logo predicted by the SAM server.

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

beta_helix's picture
User offline. Last seen 2 hours 47 min ago. Offline
Joined: 05/09/2008
Groups: None
Available Electron Density tools:

Cutaway view hint:

If you hover your mouse over a segment and type shift-Q, the game will hide parts of the protein and cloud that are not in the same plane as that segment - it cuts down on how much cloud you see at one time and makes it easier to focus. Q returns to normal view.
__________________________________________

Electron Density Features:

- Notes can be added to the electron density if present. To add one, press TAB with the mouse over the density while the density panel is open. Use the recycle button in the note panel to erase one.

The above video from our YouTube channel has Seth Cooper explaining how to add Notes to the electron density.

- There is a button in the Electron Density Panel to focus rotation on the density. You can use the HOME or Q keys to refocus on the protein.
- The density score of a residue may be viewed in the tab menu

Joined: 09/24/2012
Groups: Go Science
shortcuts on a Mac?

these short cuts does not react like this on my Mac with azerty keyboard shift Q changes the view settings,not tis one)
Does anybody know?

Susume's picture
User offline. Last seen 13 hours 31 min ago. Offline
Joined: 10/02/2011
More time please

Given that people are trying out the tools and re-familiarizing themselves with how to approach this kind of puzzle, a few extra days to work on it would be very helpful.

Joined: 10/30/2012
Groups: Beta Folders
agree. more time

agree. more time

spmm's picture
User offline. Last seen 48 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
if you extend please don't leave it to the last minute to do so

extending into a new working week on Sunday night doesn't help that much thanks

bkoep's picture
User is online Online
Joined: 11/15/2012
Groups: None
Deadline extended

Thank you everyone for the feedback!

The deadline for this puzzle has been extended to December 13 at 14:00.

Joined: 09/24/2012
Groups: Go Science
expiration date computing error

The remaining time calculated in the client is erroneous (it says "2 days...")

LociOiling's picture
User offline. Last seen 20 min 21 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
the client doesn't refresh the expiration time

The client doesn't refresh the expiration time shown in the main window. The updated expiration time is shown in the puzzles menu (ctrl+P or whatever). One solution is to open the puzzles menu, select the same puzzle, and click "play". This procedure preserves any density notes...which may or may not be helpful.

spmm's picture
User offline. Last seen 48 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
Density bonus too strong?

It looks as if unless you place each piece exactly first time the ED score will drag it out of position and it will be impossible to recover from that.
Possibly because of the density and delicacy of the sheet positions, this is highlighted in the scores for this puzzle.
I don't think the extra bits in the visual cloud are causing the problem, there are landmarks, but the density score is making wiggle the enemy.
I also noticed rotating and moving the chain well outside of the visual representation of the density cloud caused big score changes, given that we are always spining and turning, not knowing where the actual edge is provides for additional confusion.

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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