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 model. Similarly, the color of a ribbon segment assigned on a per-residue basis 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 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 command rainbow assigns per-atom colors and also per-residue ribbon colors, whereas ribcolor assigns only the per-residue 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 surface colors, and per-residue ribbon colors. See coloring for further 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 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.
Display is determined hierarchically. The display of individual atoms, bonds, atom surfaces, and single-residue segments of ribbon can be turned on and off; however, individual "on" settings are overruled by a model-level "off" setting. Similarly, an "on" setting of an individual pseudobond is overruled by a group-level "off" setting.
If the display at a higher level (such as molecule model) has been turned off, but the display of individual components (such as atoms) is turned on, the components will still not be shown until the higher-level display is turned back on. Conversely, if individual components have been undisplayed, enabling display at a higher level will not turn them back on (they must also be displayed at the individual level).
The Atoms/Bonds 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. The Ribbon section of the Actions menu and the ribbon command control per-residue ribbon display. Model-level display can be toggled with the command modeldisplay or the Model Panel hide and show functions.
Other model types can only be completely displayed and undisplayed, and the objdisplay command only works for these types of models.
The display of an individual pseudobond can be controlled by selecting the pseudobond and using the Selection Inspector. Pseudobond group-level display can be controlled with the PseudoBond Panel hide and show functions.