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.
For example, the amino acid Leucine at residue 37 is highly predicted to be part of a sheet. However, the Valines at residues 6-7 & 97 have an equal probability of being anything.
I believe it is possible to improve this density cloud clarity:
1) The current density map seems to have been saved with a step of 2 (judging by the rough angles of the blobs) giving us a much rougher image to work with than with a step of 1.
2) Plus some dust cleaning (removing small blobs) would also greatly enhance our ability to navigate and distinguish the shape of the protein.
Please, could you re-submit the puzzle with a smoother/cleaner density cloud?
This puzzle seems to have disappeared from my list of available science puzzles. It is not supposed to have expired for several hours. Explanation?
we're looking into it.
The puzzle should be back up, Seth took care of it. Thanks for letting us know.