Electron Density (ED) Puzzles
|Opened on:||Wednesday, October 28, 2015 - 13:43|
|Last modified:||Thursday, March 31, 2016 - 07:55|
Below are some questions about Electron Density (ED) Puzzles, based on Puzzle 1152:
(1) If you press Tab on a segment to show its Segment Information, does the ED only contribute via the "Density" subscore? Does the ED ever contribute via "Other", "Reference", or any other subscore?
(2) On Puzzle 1152, I have seen the "Density" subscore be nonzero, sometimes positive and sometimes negative, even when the protein is far away from the ED cloud. Is the exact same ED cloud tiled repeatedly through 3D space but only shown for one small region of 3D space? What do negative "Density" subscores mean?
(3) When you press the "Center Protein on Density" button, the overall score you get depends on the "Threshold" setting. Does the overall score depend on any of the other settings in the Electron Density Window (see the image on the left below)?
(4) I would like to play around with the settings in the Electron Density Window while a Recipe is running, but I worry that I will press the wrong thing, change how my protein is scored, and so mess up what the Recipe is doing. Is "Center Protein on Density" the only thing in the Electron Density Window that will directly alter the overall protein score? If I vary things like the "Threshold" but never press "Center Protein on Density", am I only affecting how the ED cloud is displayed? Can selecting "None" as opposed to "Solid" or "Wireframe" affect the overall protein score?
(5) Is it possible to list values for "Red", "Green", "Blue", "Alpha", and especially "Threshold" in the Electron Density Window like you already list for the "Clashing Importance" in the Behavior Window? This way, we could easily tell each other what settings we find work best. Right now, we have to say things like "Threshold to far left", "Threshold at the center", or "Threshold over the m in mouse". It would be easier if we could say something like "Threshold=0.05" instead.
(6) http://foldit.wikia.com/wiki/Electron_Density_Puzzles is helpful. Are there other places you would recommend for help with ED Puzzles? I think many players have trouble seeing things within the ED cloud. It would be nice if there was one place that described every item in the Electron Density Window, explaining things like "Alpha" and "Backface Culling", for example.