Coloring Hierarchy

Apparent color is determined hierarchically:

The command modelcolor sets color at the model level. Most coloring commands and the Color section of the Actions menu set color at the finest, overriding level (individual atoms, per-atom molecular surface patches, per-residue ribbon segments, etc.). See coloring for more discussion of coloring methods.

For molecular surfaces, coloring can come from the atom or model level, but an additional complication is that an atom or molecule model's surface color can differ from the color assignment of the atom or molecule model itself. For example, the following command sets all of the per-atom surface colors to green without changing the colors of the atoms:

color green,s
The molecular surface color source is normally the atom level, but can be controlled 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 / June 2012