It would be helpful to have the possibility to let the ED cloud fade from one color to another (or 'rainbow', 'iron' color palette) to indicate the depth in the cloud, where the color of the cloud changes as seen from the current viewpoint or fixable from a particular viewpoint when rotating / moving after fixing it. The 'iron' palette is used in thermal imagery (as seen in my avatar).
and, in addition to that, have the possibility to 'slice' the visibility of the ED cloud in a plane, with varying thickness. Currently the rest of the cloud makes it more difficult to distinguish features behind others.
I'd like to be able to see cross sections of the electron density and the protein inside it.
Cross sections could be done with rectangular x,y,z coordinates and just show parts of the protein and electron density with values of z between zmin and zmax, making the rest of the protein or electron density invisible. It might even be useful to let players also pick ranges for x and y. Then we could focus on cubes or other rectangular shapes within the protein/electron density.
Another way to do cross sections would be to let the user pick a point within the protein or electron density to be the origin. Then use spherical coordinates around that origin to show layers, like in an onion, out to a radius that the user can set.
Have no idea of how any of the previous comments would work out in a practical sense but DO KNOW that greater visibility is an absolute must between density cloud and protein in form as created by the user. Otherwise these Density puzzles need to be thrown out the window, and let us get back to unsolved proteins. I want something I can break my teeth on and am sick and tired of stuff I cannot see…