but we also hope it'll be fun!
There will obviously not be any secondary structure predictions or any additional information for this puzzle.
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.
This video from our YouTube channel has Seth Cooper explaining how to add Notes to the electron density: http://youtu.be/iaVk8Yo0_MA
- 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
for every single one of 95 segments - interesting concept.
Let "Segment Information" boxes brought up by tab be taller
Use arrows to skim through the notes for each amino acid
I mention this problem I already observed several times here, because it is really important for this puzzle:
If you want to move your stub (which is really necessary in this puzzle) with the cursor tool after pressing "3", and then you press "3" again to get rid of the cursor and your mouse is directly over the cross, Foldit crashes immediately...
this makes it even more impossible =/
This ED cloud matches very well with stick view. The extra knobs on the backbone of the cloud line up with the extra twigs that show up between the sidechains in stick view.
you can clearly see the aromatic residues like phenylalanine, tryptophan and tyrosine (there are two of them each), but also prolines that are good to begin with
However, you should be careful with mutating residues, for example the phenylalanines will be mutated to histidines because they are scoring better on the surface of the protein, although they will not fit exactly into the ED
I have mentioned this before, but Chat posts about this puzzle make it sound like hoops would be useful here. See the following for details:
Is it normal that I find a segment completely out of the cloud with a density score of 90 ?
my understanding is that the cloud and associated density score and pull on the protein, continues to repeat but is only visible in the central space so building 'outside of the visible cloud' can mess you up a bit - that could be incorrect of course, but now I just build inside the cloud and turn the view off and on frequently.
Most of these electron density maps are derived from protein crystals, in which a protein forms a regular lattice—you can imagine many copies of this protein aligning and arranging themselves into a 3D grid. We only visualize one "unit cell" of the crystal in the puzzle, but the density actually repeats itself infinitely in the X, Y, and Z directions.
Does the cloud that we see correspond to about une protein? (transborder puzzle would then be wrong)
Or is it possible that the protein we are trying to find "crosses" several unit cells?
I found this explanation with pictures helped me to understand the positioning but this is one example and unlikely to be the same for every cloud we get.
and completely blocks the view of the seg you are trying to manipulate when you are zoomed in
would be much better as well, like the tools crystallographers use:
the 'dots' in foldit don't help to show direction along either the backbone or the 'arm' of a sidechain.
Thanks spmm, it's interesting to see this course for crystallographers, using quite exactly what we try to do manually with electron density puzzles.
I like the conclusion: "Most people refine ad tedium, until they are bored."
We do not succeed to go over 94 residues. Does anybody get 95 residues?
I noticed you top-scoring soloist solution had 95 residues.