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.
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
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?
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.
agree. more time
extending into a new working week on Sunday night doesn't help that much thanks
Thank you everyone for the feedback!
The deadline for this puzzle has been extended to December 13 at 14:00.
The remaining time calculated in the client is erroneous (it says "2 days...")
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.
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.