Scientists in the real world would certainly look at the pdbįiles for the old structures.

Processing their data before giving it to us to solve.įinally, if this is a new structure for an old sequence, Type of puzzle, it opens the door for more puzzles like this,Īnd the scientists won't have to spend as much time I am still hopeful I can make more progress on this ThereĪre many places where my solutions clearly jump from one chain My best solutions so far sort ofįollow one chain over here and another chain over there. (a terminal end or a recognizable sequence of residues in the Nevertheless, I haven't yet found a good starting position I have some more ideas to pursue regarding this puzzle. I had a solo rank 17 when last I checked, and PsiPred secondary structure listed above and relying a lot on One is when bound to a new drug, for example). This is a new structure for the same sequence, but maybe this Results are unknown (and perhaps they are unknown, perhaps I for one have not yet looked at the pdb files or my team's This wouldn't improve the 'quality' of density at the sidechains, but it might be useful for visualizing weak sidechain density. In the difference map, the theoretical density of the GLY helix would 'cancel-out' the EM density along the helix backbone, and the density for the (missing) sidechains would be relatively more intense.

The result would be a 'difference cloud' that highlights regions of density that are not occupied by the model.įor example, in a case like this one, where you can pick out helices but can't see the sidechains: the player might build the helices out of GLY and then compute a difference map. This means we would calculate a theoretical electron density cloud from the player's model, then subtract the theoretical cloud from the EM cloud. We could think about calculating something called a difference map, using the player's solution.

Cryo-EM only tells us where electrons are concentrated-it doesn't distinguish between electrons on sidechain atoms vs. Unfortunately, I don't think there's any direct way to emphasize the density of sidechains. Of the ED cloud, or do we directly affect the scoring as well? When we use the Trim Density tool, do we just alter the appearance Is the ED cloud here from a crystal or from a sample in solution?Īt what temperature was the ED data taken? Give us a very raw un-trimmed ED cloud? Is there some other keyĭifference between this ED puzzle and previous ones? Should weĮxpect unusually large Density subscores when we Tab on residues You trim the extra density before posting the puzzle, but here you Is this ED puzzle different from previous ones because usually Seem to have multiple NH2 and COO termini, which would We expect one continuous copy of our 187-segment chain toīe in the ED cloud, or should we expect one or more partialĬopies of the chain to appear? Several partial copies would Of a distribution of conformations so that some regions of theĬloud look fatter than others? Is some part of the ED cloudįrom proteins, ligands, or solvent molecules distinct from theġ87-segment amino acid sequence you've given us? Should Simultaneously? Could the ED cloud be showing the average Is it possible that a section of the protein, say segments 1-30,Īppears in the displayed ED cloud more than once? Could theĮD cloud be showing more than one conformation of the protein

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