Closed since about 11 years ago
Advanced Overall Design Electron DensityThis puzzle is unlike anything we have ever posted before! We have given you extremely accurate electron density, but no sequence information. This protein has 95-residues, but your starting model only has 5 Alanines that are floating in the density. You'll need to insert residues and mutate them as you make your way through the density. We know this won't be easy, some might even suggest that this task is impossible... but we know that if anyone can do it: you can!
We are giving you two weeks to work on this... good luck!
would be much better as well, like the tools crystallographers use:
http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html
the 'dots' in foldit don't help to show direction along either the backbone or the 'arm' of a sidechain.
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.
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.
