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 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:
- 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 / June 2012