Coloring Hierarchy

Apparent color is determined hierarchically:

The commands color, rangecolor, and rainbow can assign atom-level colors and residue-level ribbon colors. The command modelcolor sets color at the model level. The Color section of the Actions menu assigns individual atom and bond colors, per-atom molecular surface colors, and per-residue ribbon colors. See coloring for more discussion of coloring methods.

For molecular surfaces, an additional complication is that an atom or molecule model's surface color can be different from the atom or molecule model's own color assignment. For example, the command

color green,s
sets all of the per-atom surface colors to green without changing the colors of the atoms. Unless explicitly set otherwise, the visible surface color(s) typically match the visible atom color(s), determined by the hierarchy described at the top of this section. The level in the hierarchy used as the source for visible surface colors can be changed with the command surfcolor or the molecular surface attributes panel.

Display Hierarchy

Display is determined hierarchically:

Model-level display can be toggled using: The Atoms/Bonds section of the Actions menu and the display command control individual atom and bond display settings; the Surface section of the Actions menu and the surface command control display at the level of individual atomic surface patches. The Ribbon section of the Actions menu and the ribbon command control per-residue ribbon display.

The display of an individual pseudobond similarly depends on pseudobond group display status, but usually also on whether its endpoint atoms are displayed. An individual pseudobond can be undisplayed (without undisplaying its endpoint atoms) by picking it and using the Selection Inspector. Pseudobond group-level display can be controlled with the Shown checkboxes (or hide and show functions) in the PseudoBond Panel.

UCSF Computer Graphics Laboratory / January 2009