The property of color is determined by a hierarchy, where the color of an atom or bond assigned on an individual basis overrules its color assigned by residue, which overrules its color assigned by model. Even though only the overriding color is visible, the color assignments at other levels continue to exist. If an atom has not been explicitly colored, its color will be reported as "No" (none) since it is merely inheriting the color from its residue or model. If only the command line has been used for coloring, the color of bonds will be reported as "No" since they are just inheriting color from the flanking atoms rather than possessing colors of their own.
The color command assigns only per-atom colors, even when entire models are specified in the command. The commands rescolor and rainbow assign color at the residue level, and the command modelcolor sets color at the model level. See coloring for a more complete discussion of coloring methods.
The color of a pseudobond assigned on an individual basis overrules its color assigned by group. If a pseudobond has no color of its own, it will inherit the color of its pseudobond group.
If a label has no color of its own, it will inherit the color of its associated atom, bond, or pseudobond.
For surfaces, the matter is more complicated because atoms, residues, and models can have surface color assignments different from their own color assignments. For example, the command
color green,ssets 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 surfcolor or the surface attributes panel.
The display of molecules and surfaces is determined hierarchically. While display is a property of the individual atoms, bonds, and atom surfaces, there is also a display attribute at the level of the whole model. The model-level display attribute may be thought of as "display enabling," and can be toggled with the command modeldisplay or the Model Panel hide and show functions.
The Display section of the Actions menu and the display command control display at the level of atoms and bonds within molecule models; the Surface section of the Actions menu and the surface command control display at the level of atom surfaces within molecular surface models. Other model types can only be completely displayed and undisplayed, and the objdisplay command only works for these types of models.
If the display at the whole-model level has been turned off, but the display of individual atoms/bonds or atom surfaces within the model is turned on, the atoms/bonds or surface will still not be shown until model-level display is turned back on. Conversely, if individual atoms/bonds or atom surfaces within a model have been undisplayed, enabling model-level display will not turn them back on (they must be displayed at the atom/bond or atom surface level).