The RasMol 'colour' command allows different objects (such as atoms, bonds and ribbon segments) to be given a specified colour. Typically this colour is either a RasMol predefined colour name or an RGB triple.
Additionally RasMol also supports 'alt', 'amino', 'chain', 'charge', 'cpk', 'group', 'model', 'shapely', 'structure', 'temperature' or 'user' colour schemes for atoms, and 'hbond type' colour scheme for hydrogen bonds and 'electrostatic potential' colour scheme for dot surfaces.
The 24 currently predefined colour names are listed below with their corresponding RGB triplet and hexadecimal value.
Note that the rendering of the hexadecimal-equivalent colors shown here will depend on many factors. Thus, they only approximate how RasMol will render the RGB colors on your computer.
If you frequently wish to use a colour not predefined, you can write a one-line script. For example, if you make the file 'grey.col' containing the line, 'colour [180,180,180] #grey', then the command 'script grey.col' colours the currently selected atom set grey.
The RasMol 'alt' (Alternate Conformer) colour scheme codes the base structure with one colour and applies a limited number of colours to each alternate conformer. In a RasMol built for 8-bit color systems, 4 colours are allowed for alternate conformers. Otherwise, 8 colours are available.
The RasMol 'amino' colour scheme colours amino acids according to traditional amino acid properties. The purpose of colouring is to identify amino acids in an unusual or surprising environment. The outer parts of a protein that are polar are visible (bright) colours and non-polar residues darker. Most colours are hallowed by tradition. This colour scheme is similar to the 'shapely' scheme.
The RasMol 'chain' colour scheme assigns each macromolecular chain a unique colour. This colour scheme is particularly useful for distinguishing the parts of multimeric structure or the individual 'strands' of a DNA chain. 'Chain' can be selected from the RasMol 'Colours' menu.
The RasMol 'charge' colour scheme colour codes each atom according to the charge value stored in the input file (or beta factor field of PDB files). High values are coloured in blue (positive) and lower values coloured in red (negative). Rather than use a fixed scale this scheme determines the maximum and minimum values of the charge/temperature field and interpolates from red to blue appropriately. Hence, green cannot be assumed to be 'no net charge' charge.
The difference between the 'charge' and 'temperature' colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge values go from red to blue.
If the charge/temperature field stores reasonable values it is possible to use the RasMol 'colour dots potential' command to colour code a dot surface (generated by the 'dots' command) by electrostatic potential.
The RasMol 'cpk' colour scheme is based upon the colours of the popular plastic spacefilling models which were developed by Corey, Pauling and later improved by Kultun. This colour scheme colours 'atom' objects by the atom (element) type. This is the scheme conventionally used by chemists. The assignment of the most commonly used element types to colours is given below. Follow the link for the complete table of elements.
Note that except for green, white, blue, and orange, these colour names are not the ones specified as "Predefined colours" in RasMol; thus, they can only be specified on the command line as RGB triplets.
In the CPK colouring scheme, RasMol will attempt to assign a colour to each element from the periodic table from a list of 16 colours (the colour codes listed are to help in understanding the mapping and are not used by RasMol)
For X-ray crystallographic models of proteins and nucleic acids (i.e. without hydrogens) the display can be 'brightened' by converting the O, C, and N atoms from the RasMol default cpk colors to "true red, white and blue" using RasMol's predefined color scheme. Use the following sequence of commands to try it:
select all select oxygen color red select carbon color white select nitrogen color blue select all
Extension of this idea to other atoms and color schemes is straightforward.
The RasMol 'group' colour scheme colour codes residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue through green, yellow and orange to red. Hence the N terminus of proteins and 5' terminus of nucleic acids are coloured red and the C terminus of proteins and 3' terminus of nucleic acids are drawn in blue. If a chain has a large number of heterogeneous molecules associated with it, the macromolecule may not be drawn in the full 'range' of the spectrum. 'Group' can be selected from the RasMol 'Colours' menu.
If a chain has a large number of heterogeneous molecules associated with it, the macromolecule may not be drawn in the full range of the spectrum. When RasMol performs group coloring it decides the range of colors it uses from the residue numbering given in the PDB file. Hence the lowest residue number is displayed in blue and the highest residue number is displayed as red. Unfortunately, if a PDB file contains a large number of heteroatoms, such as water molecules, that occupy the high residue numbers, the protein is displayed in the blue-green end of the spectrum and the waters in the yellow-red end of the spectrum. This is aggravated by there typically being many more water molecules than amino acid residues. The solution to this problem is to use the command 'set hetero off' before applying the group color scheme. This can also be achieved by toggling 'Hetero Atoms' on the 'Options' menu before selecting 'Group' on the 'Colour' menu. This command instructs RasMol to only use non-hetero residues in the group color scaling.
The RasMol 'model' colour scheme codes each NMR model with a distinct colour. The NMR model number is taken as a numeric value. High values are coloured in blue and lower values coloured in red. Rather than use a fixed scale this scheme determines the maximum value of the NMR model number and interpolates from red to blue appropriately.
The RasMol 'shapely' colour scheme colour codes residues by amino acid property. This scheme is based upon Bob Fletterick's "Shapely Models". Each amino acid and nucleic acid residue is given a unique colour. The 'shapely' colour scheme is used by David Bacon's Raster3D program. This colour scheme is similar to the 'amino' colour scheme.
The RasMol 'structure' colour scheme colours the molecule by protein secondary structure. Alpha helices are coloured magenta, [240,0,128], beta sheets are coloured yellow, [255,255,0], turns are coloured pale blue, [96,128,255] and all other residues are coloured white. The secondary structure is either read from the PDB file (HELIX, SHEET and TURN records), if available, or determined using Kabsch and Sander's DSSP algorithm. The RasMol 'structure' command may be used to force DSSP's structure assignment to be used.
The RasMol 'temperature' colour scheme colour codes each atom according to the anisotropic temperature (beta) value stored in the PDB file. Typically this gives a measure of the mobility/uncertainty of a given atom's position. High values are coloured in warmer (red) colours and lower values in colder (blue) colours. This feature is often used to associate a "scale" value [such as amino acid variability in viral mutants] with each atom in a PDB file, and colour the molecule appropriately.
The difference between the 'temperature' and 'charge' colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge values go from red to blue.
The RasMol 'user' colour scheme allows RasMol to use the colour scheme stored in the PDB file. The colours for each atom are stored in COLO records placed in the PDB data file. This convention was introduced by David Bacon's Raster3D program.
The RasMol 'type' colour scheme applies only to hydrogen bonds, hence is used in the command 'colour hbonds type'. This scheme colour codes each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor. This schematic representation was introduced by Belhadj-Mostefa and Milner-White. This representation gives a good insight into protein secondary structure (hbonds forming alpha helices appear red, those forming sheets appear yellow and those forming turns appear magenta).
Offset Colour Triple +2 white [255,255,255] +3 magenta [255,0,255] +4 red [255,0,0] +5 orange [255,165,0] -3 cyan [0,255,255] -4 green [0,255,0] default yellow [255,255,0]
The RasMol 'potential' colour scheme applies only to dot surfaces, hence is used in the command 'colour dots potential'. This scheme colours each currently displayed dot by the electrostatic potential at that point in space. This potential is calculated using Coulomb's law taking the temperature/charge field of the input file to be the charge assocated with that atom. This is the same interpretation used by the 'colour charge' command. Like the 'charge' colour scheme low values are blue/white and high values are red.