For my part, I manage by usually reducing the Threshold to a point where I can see most of the shapes of the sidechains which is the point where the dust particles (small part of the cloud around the main cloud) mostly disappear. I know it is difficult for many people to see the two together. Only by visualizing the density cloud AND the sidechains that you can decide if they belong together. In other words, high Density Score is not equal to good position in cloud. Also you have to consider that the chain may be sideways to the cloud even though that particular sidechain density is high. And the "surrounding" before-and-after sidechains may be the wrong ones for that area of the density cloud. Please keep in mind that even if a particular sidechain has a high density score, it does not mean that sidechain belongs there. I'll try and do some testing tonight if no devs get back to us on this to determine whether or not the Density subscore relies on any given position in the cloud or if there's an implicit bonus for a "correct" cloud position that bolsters the bonus. I think it's a much more effective strategy to match landmark residues within the visible cloud, and align the sequences as such. In other words, I expect that if we were to shift that hypothetical lucky Trp53 into the main unit cell that's visible, we would find that it doesn't correspond well to a good cloud shape for it, but rather it just happens to be buried in a portion of the cloud that's large enough to house it, but not the correct shape or place for it. For one, it's pretty serendipitous to get that positive density subscore in the first place, and from what I can actually tell from experience, it doesn't matter if the residue in question is in the correct part of the cloud (since the whole point is that we don't necessarily know how it fits into the cloud) but rather the Density subscore is focused on whether or not a given residue is overlapped by any part of the cloud. I understand where you're coming from, and how an extended chain that's longer than one unit cell might stretch some residues into a positive density bonus, but I don't think this unit cell visibility is actually useful. With the protein would also help identify which part of theĬloud overlapped so well with Trp53. Of the cloud had such a large density and therefore such a Translate the protein so that Trp53 moved into the Unit CellĬontaining the visible cloud. Was nowhere near the usual visible ED Cloud, one could easily One saw a very large Density subscore for Trp53 when Trp53 Parts of the cloud, and this might give insight into howĪn extended protein should fold in order to make all of itsĬontacts with just one Unit Cell's ED Cloud. Identify which segments of the protein overlap with which Unit Cell's Electron Density Cloud, one could more easily With these tools, if the protein overlaps with more than one Identical, the protein's score should not change for these Screen, and A Z or PageUp PageDown could translate the TheĪrrows could translate the protein left right up or down on the To translate the protein from one Unit Cell to another. I think it would also help if one could use certain keyboardīuttons (perhaps the arrows and A Z or PageUp PageDown) Overlap could be colored like normal, but the otherĬlouds could be colored slightly differently, a bit likeĬopies of the main monomer in a Symmetry Puzzle. I think it would help if one could display all the clouds Moved through space in a fixed direction, one wouldĬross from one Unit Cell to another at regular intervals. This lattice ofĬlouds / Unit Cells is periodic in all directions. Many identically-shaped boxes (also called Unit Cells),Īnd each Unit Cell contains one cloud. I think this lattice of clouds can be imagined to contain Protein does not appear to overlap with the visible cloud. Protein have nonzero Density subscores even when the These invisible clouds let segments of the There are many invisible copies of the cloud extending inĪll directions. When the visibleĬloud is far from the protein, one has to remember that Near the protein and sometimes it is not. In Electron Density Puzzles like 1598, one can turn on theĮlectron Density Cloud to view it.
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