Hierarchies

Coloring Hierarchy

Apparent color is determined hierarchically:

individually assigned atom, bond, or residue ribbon colors mask the underlying molecule model color. The model color will be apparent where the atom, bond, or ribbon segment has no individual color assignment.
an atom label (bond label, pseudobond label) without its own color assignment will inherit the color of its associated atom (bond, pseudobond)
a residue label without its own color assignment will inherit the molecule model color
a pseudobond without its own color assignment will inherit the color of its pseudobond group

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:

molecule model display must be enabled (turned on) to reveal the display settings of its individual atoms, bonds, and residue ribbon segments
MSMS molecular surface model display must be enabled to show the display settings of its individual atomic patches
(nonmolecular) surface model display must be enabled to show the display settings of its surface pieces

Model-level display can be toggled using the command modeldisplay or the Shown checkboxes (or hide and show functions) in the Model Panel.

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 2008