Occlusion Culling algorithm - Too many artifacts: Partial Spheres created from occlusion culling algorithm obscure view
Currently foldit allows for partial occlusion culling. This should be disabled (especially in View Options > View Protein > Sphere ) or atleast include a threshold for those whom wish to view only solid elements.
Another idea is to render the partial spheres as if they were solid instead of hollow; that is, show them like chopped potatoes or carrots instead of chopped green peppers. This would help players distinguish the voids between atoms from the interiors of atoms.
Another way to phrase my previous comment is to render partial spheres as cross-sections of solid spheres instead of as cross-sections of hollow spheres.
It might also be useful to have all the solid sphere interiors be the same color (perhaps brown), no matter what atom type they represent. The spheres could have one color on the outside (for example, red, yellow, black, blue, white as in CPK coloring for O, S, C, N, H atoms) and a different color on the inside (perhaps brown), kind of like plain M & M's candy, and all spheres would have the same color on the inside (perhaps brown) even though they might have different colors on the outside (red, yellow, etc.). This way the protein could look like a bunch of plain M & M's with some of the M & M's shown in cross-section.
There are obscure key shortcuts for changing the viewbox. You can certainly change the depth, I never use them so I don't know if you can change the close face.
These keys are listed in the (?) Help menu under Actions.
Yes, there is something in the original interface to adjust visibility (click on Action Help, left up, scroll down):
Adjust fog: alt-shift-click and drag
Adjust near visibility: ctrl+alt+click and drag
Adjust far visibility: ctrl+shift+click and drag
Mouse on a segment:
Focus on a segment: Q
Focus visibility on a segment: Shift+Q