Draft color command matrix. Comments to Bob Hanson
color [object or element name] [NONE, color, color scheme]
OBJECT NONE1 color2 color scheme3

atom objects:

(if the object is omitted, ATOMS is assumed)
ATOMS, DOTS, LABELS5, POLYHEDRA4, STARS4, VECTORS,
along with the biomolecule-specific terms
BACKBONE, CARTOONS, MESHRIBBON, RIBBONS, ROCKETS, STRANDS, TRACE.

bond objects:

BONDS, HBONDS6, and SSBONDS

 

model objects:

AXES, ECHO, HOVER, ISOSURFACE7, MEASUREMENTS, PMESH7, and UNITCELL

 

element name8:

(British or American spellings of the full element names of all the elements in the Periodic Table, and "unknown" or "dummy" when the atomic symbol in the coordinate file is not recognized, for example "X" or "Xx".)

 
Notes:
1 In Jmol the option NONE can have one of four different meanings, depending upon the context:
  1. In the context of color ATOMS NONE or just color NONE, it means "not specified: revert to the default coloring scheme" (either Jmol or Rasmol, depending upon the setting of set defaultColors), which might have been modified using the color [element] command.
  2. In the context of coloring bond objects and atom objects other than ATOMS itself, (for example, color BONDS NONE or color RIBBONS NONE), it means "not specified: return to the state of inheriting the color of the associated atom," which might not be the default color.
  3. In the context of coloring model objects such as HOVER and AXES, it means "black."
  4. With the background command, as in background LABELS NONE it means "remove completely."
2 Colors in Jmol can be either a name, such as "green", or a red-green-blue color triple in brackets expressed as three decimal numbers, for example [255,32,0], or as one hexidecimal number, for example [xFF2000]. The color can be preceeded by TRANSLUCENT or OPAQUE to add additional visible character to the colored element. Biomolecular displays, such as ribbons, traces, and cartoons, are rendered by default in the color of alpha carbon atoms for proteins and the phosphorus atoms for nucleic acids.
3 Color schemes include AMINO, CHAIN, CPK, FIXEDTEMPERATURE, FORMALCHARGE, GROUP, MONOMER, PARTIALCHARGE, RELATIVETEMPERATURE, SHAPELY, and STRUCTURE

4 Available in PreRelease only; not available in Jmol 10.00.00.

5 Color schemes for labels are available starting in Jmol PreRelease 10.00.39. In Jmol 10.00.00, labels could not be colored using color schemes.

6 HBONDS has an additional option, TYPE, which allows for coloring hydrogen bonds in a biomolecule based on a scheme related to the number of residues between the atoms associated with the bond.

7Available in PreRelease only; not available in Jmol 10.00.00. To color a pmesh or isosurface, first select the specific surface you want to color using either the pmesh [name] or isosurface [name] command, then color ISOSURFACE [color|NONE] or color PMESH [color|NONE].
8Available in PreRelease only; not available in Jmol 10.00.00. See also element colors
- Changes in chemical element colors persist, regardless of loading a subsequent model, until they are reset using the 'set defaultColors' command.
- Customizing the element color is independent of the currently selected atom set.
- The element color is overridden when another color scheme is applied, such as 'STRUCTURE' or 'CHAIN'.

Jmol Color Schemes
AMINO Renders each of the 20 standard amino acid residues as well as ASX and GLX in a different color (for a total of 22 colors for amino acids) along with one additional color for anything that is not a standard amino acid residue, AGX, or GLX (including nucleotides, solvents, and non-amino ligands). See also SHAPELY.
CHAIN Renders each chain in the structure in a different color. This color scheme is particularly useful for distinguishing the parts of a multimeric structure or the individual helices of a DNA double helix.
CPK Colors objects based on the default color scheme, either Jmol or Rasmol, as set by the set defaultColors command and possibly modified using the color [element] command.
FORMALCHARGE and PARTIALCHARGE Distinguishes atoms based on charge. Uses a series of shades of reds for negatively charged (electron-rich) groups and shades of blue for positively charged (electron-poor) groups. The greater the degree of charge, the deeper the color. Uncharged groups are white. The range of values for formal charge is -4 through +7; the range for partial charge is -1 to +1.

Rasmol/Chime note: While CHARGE can be used in place of FORMALCHARGE, the way Jmol reads and displays charge is quite different from the way Rasmol does so. Jmol currently reads partial charge only from CML files (the scalar record with dictref="jmol:charge") and from Gaussian calculation output, not from PDB files. The Rasmol "color charge" command simply takes the "temperature factor field" (columns 61-66 of the PDB file), normalizes it to fill a red-to-blue spectrum (instead of a blue-to-red one), and displays it. For PDB files, Jmol reads the "charge on atom" field (columns 79-80 -- in chemical "2-" format, not "-2") as formal charge; for CML files, Jmol reads the atom record "formalCharge" attribute. If Rasmol-like "charge" behavior for PDB files is desired in Jmol, request it.
GROUP Uses a reverse rainbow spectrum (blue -> green -> yellow -> orange -> red) to color the specified groups (for example, residues or nucleotides) according to position along a chain of groups. The spectrum is applied only across the specified or selected groups in the chain. For proteins, the N terminus is blue and the C terminus is red. For nucleic acids, the 5' terminus is blue, and the 3' terminus is red. If any atom in a group is selected then the group is considered selected.

Note: The color group command
  1. operates within every chain independently,
  2. operates on the selected or specified set of groups, not the entire chain, and
  3. uses the group index within the chain, not the number assigned to the group in the model file.

Notes to ResMol users: The group index is relative to the groups of the chain that are currently selected. This differs from RasMol/Chime where group index is relative to the full chain. In addition, the "set hetero" command is not implemented. If you want to exclude "hetero" groups, then do not select them.
MONOMER A variation on color group, but relating to "monomers" in a "polymer" rather than "groups" in a "chain". A "polymer" is a series of connected "monomers" (at least for these purposes). Thus, if chain "A" has a break in it, color monomer recognizes the 2 pieces of chain "A" as separate polymers, coloring each from red to blue independently, despite the fact that both parts are designated as chain "A" in the coordinate file. HETERO groups may participate in a polymer, depending upon how the pdb/mmCIF file is marked up, and as long as they have a backbone pattern that Jmol can recognize as a sequence of individual units.
SHAPELY Like AMINO, coloring each of the standard amino acids and nucleotides differently, but using a different color scheme than AMINO.
STRUCTURE Uses four different colors to distinguish protein secondary structures: alpha helices, beta sheets, turns, and loops. The secondary structure is either read from the PDB file (HELIX and SHEET records), if available, or determined using an algorithm. Also distinguishes between RNA and DNA by color.
FIXEDTEMPERATURE and RELATIVETEMPERATURE Color codes each atom according to the temperature-factor (B-factor, or Debye-Waller factor) value stored in the PDB or mmCIF file. Typically this gives a measure of the mobility or uncertainty of a given atom's position, and a high crystallographic B-factor may indicate an incorrect structure. High values are colored in warmer (red) colors and lower values in colder (blue) colors. This feature can be used by the model creator to indicate any characteristic of the atoms of the model and is often used to associate a "scale" value (such as amino acid variability in viral mutants) with each atom in a PDB file. For FIXEDTEMPERATURE, the index is relative to an absolute scale of 0 to 100; for RELATIVETEMPERATURE, the color is relative to the lowest and highest B-factor values within the file.

Rasmol/Chime note: TEMPERATURE can be used in place of RELATIVETEMPERATURE.