jeff101 Lv 1
In ED Puzzles, I think it would help to have more View Options for protein sidechains. Right now we have 3 options: Don't Show (Fast), Show Stubs, and Show All (Slow). When comparing my protein structure with the ED cloud, it would help to be able to turn off the mobile & low density sidechains while leaving on the immobile & hi density sidechains. For the usual case with hydrophobic (orange) sidechains in and hydrophilic (blue) sidechains out, large immobile nonpolar sidechains like tryptophan & phenylalanine should be visible in the ED cloud while small floppy polar sidechains should be invisible. I'm not sure what to expect for membrane proteins (hydrophobic sidechains out and hydrophilic ones in). Would large polar sidechains like arginine & lysine be buried and so less mobile & more visible in the ED cloud? Perhaps having two new view options (Show Polars and Show Nonpolars) would be enough. Maybe a 3rd View Sidechains option like Show Dense would help too. Show Dense could account for whether the protein is in a membrane or in solution.