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Command: color

Usage:
color  atom-spec  colorname  [ target  string ]

Usage:
color  model-spec  sequential chainstarget  string ] [ cmap  palette ]

The color command colors atomic models, including cartoon and molecular surface representations. See examples below. See also: colordef, volume

The absence of an atom or model specifier implies “all.” Keywords can be truncated to unique strings, and their case does not matter.

For simple coloring, the colorname can be:

The sequential chains method applies a range of colors, setting a different color for each biopolymer chain in an atomic model. Only the biopolymer chains are colored, not ligand and solvent residues, even if they have the same chain ID as a biopolymer chain. Future sequential sub-options will allow setting a different color for each residue or secondary structure element along a chain, or for each model. Sequential coloring always applies to entire models (not parts of models).

The target option allows coloring only a subset of the possible displays of a given atom, residue, etc. The string can be any combination of the following letters, without commas or spaces:

The default target is all of the above, except that surface coloring is not yet implemented for sequential coloring (if atoms have been colored sequentially, however, the surface can be colored to match the atoms with the command: color byatom target s).

The cmap option specifies a palette for sequential coloring (colors listed in ascending value order):

The colors are interpolated along the range to generate a unique color for each item being colored sequentially.

Examples

Example color commands:

color /A,B:12,260-275  hot pink  target a
- color residues 12 and 260-275 in chains A and B, atoms/bonds only
color  seq chain  targ c
- assign a unique color per chain in each atomic model from red → blue through the rainbow, cartoons only
color #3  seq ch  cmap cyan
- color chains in model 3 from a medium cyan through white to dark maroon
UCSF Resource for Biocomputing, Visualization, and Informatics / September 2015