The overall goal of my coloring scheme is to separate functionally-distinct portions of the scene. In the cellular landscapes, colors are typically used to separate functional regions, such as the inside, outside, and membranes of cells, organelles or viruses. In digital images of biomolecular assemblies, colors are used to distinguish subunits or domains with different or related functions.
I use a few overarching design parameters for this coloring scheme. First, I break the color wheel into several sectors, and use these to tell the broad strokes of the story, for example, separating DNA from proteins in an assembly or separating a cell from the surrounding environment. I typically use five of these sectors: blue-green to blue, shades of green, yellow/orange/red, magenta to purple, and earth tones.
Second, within each color sector, I try to choose values that visually integrate the entire collection of entities, while providing enough difference to distinguish the different entities. For example, I commonly push neighboring subunits in a complex to slightly bluer or slightly greener hues to highlight their arrangement or symmetry. In addition, I often use slightly desaturated colors to give some color texture, for example, coloring carbon atoms with a slightly desaturated hue of the subunit color.