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.
- the ribbon inside color is a model attribute; if assigned,
it will be used for the insides of all protein helix ribbon segments
in the model regardless of how the rest of the ribbon is colored
- 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 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