Chain Colours

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.

 Charge Colours

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.

 CPK Colours

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.

 Group Colours

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.

 NMR Model Colours

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.

 Shapely Colours

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.