Colors and Color Schemes
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Go to the Color Tables: Predefined Colors
Amino/Shapely
CPK
 
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How were these title colors chosen?
The RasMol color command allows different objects (such as atoms, bonds and ribbon segments) to be given a specified color. Typically this color is either a RasMol predefined color name or a comma-separated triple of Red, Green and Blue (RGB) components enclosed in square brackets. A typical RGB triplet is [255,255,255], which is the color white. White is also used for the Monochrome selection in the RasMol Colours menu.
- Additionally RasMol also supports:
- amino
- chain
- cpk
- group
- shapely
- structure
- temperature
- charge and
- user color schemes
for atoms, - hbond type
for hydrogen bonds, and the - electrostatic potential
color scheme for dot surfaces.
Mục Lục
Predefined Colors
The currently predefined color names are listed below with their corresponding RGB triplet.
Color Name Triple Color Name Triple
blue [0,0,255] black [0,0,0]
cyan [0,255,255] green [0,255,0]
greenblue [46,139,87] magenta [255,0,255]
orange [255,165,0] purple [160,32,240]
red [255,0,0] redorange [255,69,0]
violet [238,130,238] white [255,255,255]
yellow [255,255,0]
A table of the Predefined Colors on a black background is shown on a separate page.
If you frequently wish to use a color not predefined, you can write a one-line script. For example, if you make the file grey.col containing the line,
color [180,180,180] #grey
then the command script grey.col colors the currently selected atom set grey. (Or, you can color it gray. 🙂
Amino Colors
The RasMol amino color scheme colors amino acids according to traditional amino acid properties. The purpose of coloring is to identify amino acids in an unusual or surprising environment. The outer parts of a protein that are polar are visible (bright) colors and non-polar residues darker. Most colors are hallowed by tradition. This color scheme is similar to the scheme. Shapely can be selected from the RasMol Colours menu.
Amino Acid Color Triple Amino Acid Color Triple ASP,GLU bright red [230,10,10] CYS,MET yellow [230,230,0] LYS,ARG blue [20,90,255] SER,THR orange [250,150,0] PHE,TYR mid blue [50,50,170] ASN,GLN cyan [0,220,220] GLY light grey [235,235,235] LEU,VAL,ILE green [15,130,15] ALA dark grey [200,200,200] TRP pink [180,90,180] HIS pale blue [130,130,210] PRO flesh [220,150,130]
A table of the Amino/Shapely Colors on a black background is shown on a separate page.
Chain Colors
The RasMol chain color scheme assigns each macromolecular chain a unique color. This color 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.
CPK Colors
The RasMol cpk color scheme is based upon the colors of the popular plastic spacefilling models which were developed by Corey, Pauling and later improved by Kultun. This color scheme colors ‘atom’ objects by the atom (element) type. This is the scheme conventionally used by chemists. CPK can be selected from the RasMol Colours menu.
The assignment of element type to colors and RGB triplet is given below.
Element Color Triple Element Color Triple Carbon light grey [200,200,200] Chlorine green [0,255,0] Oxygen red [240,0,0] Bromine, Zinc brown [165,42,42] Hydrogen white [255,255,255] Sodium blue [0,0,255] Nitrogen light blue [143,143,255] Iron orange [255,165,0] Sulfur yellow [255,200,50] Calcium, Metals dark grey [128,128,144] Phosphorus orange [255,165,0] Unknown deep pink [255,20,147]
A table of the CPK Colors on a black background is shown on a separate page.
Group Colors
The RasMol
group color scheme color 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. The N termini of proteins are colored blue (similar to the CPK color for nitrogen) and the C termini, red (similar to the CPK color for oxygen). The 5′ termini of nucleic acids are colored blue, and the 3′ termini, red. Group can be selected from the RasMol Colours menu.
If a chain has a large number of heterogenous 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 aggrevated 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.
Shapely Colors
The RasMol shapely color scheme color 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 color. The shapely color scheme is used by David Bacon’s Raster3D program [4]. This color scheme is similar to the color scheme. Shapely can be selected from the RasMol Colours menu.
A table of the Amino/Shapely Colors on a black background is shown on a separate page.
Structure Colors
The RasMol structure color scheme colors the molecule by protein secondary structure. Alpha helices are colored magenta, [240,0,128], beta sheets are colored yellow, [255,255,0], turns are colored pale blue, [96,128,255] and all other residues are colored white. The secondary structure is either read from the PDB file (HELIX and SHEET records), if available, or determined using the Kabsch and Sander DSSP algorithm [8]. The RasMol
command may be used to force DSSP’s structure assignment to be used. Structure can be selected from the RasMol Colours menu.
Temperature Colors
The RasMol temperature color scheme color codes each atom according to the anisotropic temperature (B-factor) value stored in the PDB file.
Typically this gives a measure of the mobility/uncertainty of a given atom’s position. High values are colored in warmer (red) colors and lower values in colder (blue) colors. 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 color the molecule appropriately. Temperature can be selected from the RasMol Colours menu.
The difference between the temperature and charge color schemes is that increasing temperature values proceed from blue to red, whereas increasing charge values go from red to blue.
Charge Colors
The RasMol charge color scheme color codes each atom according to the charge value stored in the input file (or beta factor field of PDB files). High values are colored in blue (positive) and lower values colored 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 and temperature color schemes is that increasing temperature factor 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 command to color code a dot surface (generated by the command) by electrostatic
potential.
User Colors
The RasMol user color scheme allows RasMol to use the color scheme stored in the PDB file. The colors for each atom are stored in COLO records placed in the PDB data file. This convention was introduced by David Bacon’s Raster3D program [4]. User can be selected from the RasMol Colours menu.
If you wish to use a custom coloring scheme, it is typically much simpler to construct a short script to accomplish this than to insert values into the PDB file. The script also has the advantage that it can be invoked for any currently displayed molecule. An example of such a script is available.
HBond Type Colors
The RasMol type color scheme applies only to hydrogen bonds, hence is used in the command “color hbonds type” This scheme color 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 [10]. 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 Color 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]
Potential Colors
The RasMol potential color scheme applies only to dot surfaces; hence it is used in the command “color dots potential“. This scheme colors 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 command. Like the color scheme low values are blue/white and high values are red. The table below shows the static assignment of colors using a dielectric constant value of 10.
Potential Color Triple
25 V red [255,0,0]
10 V 25 orange [255,165,0]
3 V 10 yellow [255,255,0]
0 V 3 green [0,255,0]
-3 V 0 cyan [0,255,255]
-10 V 3 blue [0,0,255]
-25 V -10 purple [160,32,240]
V -25 white [255,255,255]
How were the title colors on this page assigned?
Answer can be found in the color tables (or peek at the HTML text).
Back to TABLE OF CONTENTS
Colors and Color Schemes
Go to the Color Tables: Predefined Colors
Amino/Shapely
CPK
