Raster3D

Overview
Raster3D is a package of separate molecular grahics programs consisting of render, ribbon, setup, and rods. ribbon, setup, and rods are pre-processors for render, which actually creates the drawings. These programs (except for ribbon) can be used to draw small molecules as well as biopolymers. Consult the Raster3D documentation for in-depth information about the program.

Representation Pre-processors
Space-filling setup is used to create space-filling representations with render:

cat {color_file_name} {pdb_file_name} | setup > {raster3D_command_file}

where "cat" is the Unix command for appending and listing files, color_file_name is a file containing RGB color specifications used by render, pdb_file_name is a molecule file in PDB format, raster3D_command_file contains the commands used to drive render, and "|" is the Unix pipe command used to transfer the input data to setup.
Dreiding and ball-stick rods is used to create Dreiding or ball-stick (use the "-b" option) drawings with render:

cat {color_file_name} {pdb_file_name} | rods -b > {raster3D_command_file}
Protein ribbon ribbon is used to create protein ribbon drawings with render:

cat {color_file_name} {pdb_file_name} | ribbon > {raster3D_command_file}

MolScript MolScript can be used as a pre-processor for render (of primary use for proteins). In this case, raster3D_command_file is created by first running MolScript.

Color Specification
Colors used by Raster3D are described in a file containing RGB values for each element type. The color file is prepended to the PDB file using the Unix "cat" command. This data is piped to the Raster3D setup program, as previously noted. A sample color file is given below:

COLOUR#######C################   0.250   0.250   0.250  1.65
COLOUR#######N################   0.000   0.000   0.800  1.50
COLOUR#######O################   0.800   0.000   0.000  1.35
COLOUR#######S################   0.125   0.125   0.125  1.70
COLOUR#######H################   1.000   1.000   1.000  1.10
COLOUR#######P################   0.125   0.125   0.125  1.70
COLOUR########################   0.150   0.150   0.150  1.70
A mask is defined to extract the element name of each atom in the PDB file (e.g. "COLOUR#######H################" extracts hydrogen). Masks can be defined to assign colors based on other features of a PDB file, such as residue names.

The first three numbers after the mask specify "R", "G", and "B", respectively. The cedit program (SGI) can be used to define colors and determine their corresponding RGB values (note that these values must be divided by 255 for use in the Raster3D color file).

The fourth number is the van der Waals radius of each element.

Creating Drawings Using Raster3D
render is used to generate a drawing:

render -sgi {output_file.rgb} < {raster3D_command_file}

where raster3D_command_file is produced using any of the aforementioned pre-processor programs.

Raster3D allows the image size to be specified, and this feature can be used to create drawings similar in quality to PostScript. The trick is to create a large bitmap image (e.g. 4000 x 4000), which is then converted to a normal size PostScript image (e.g. using tops). This has the effect of increasing the density of pixels. The following is an excerpt from a raster3D_command_file created by MolScript:

  
MolScript v1.4 (C) 1993 Per Kraulis (Raster3D support E A Merritt 1993)
165 165   tiles in x,y; SGI small screen
24 24     pixels (x,y) per tile
3         3x3 virtual pixels -> 2x2 pixels
0 0 0     RGB background colour; black
F         F = no shadows cast, T = shadows
50        Phong power
0.20      secondary light contribution
0.05      ambient light contribution
0.10      specular reflection component
4.0       eye position
1 1 0.8   main light source position
1 0 0 0   input coord/radius transformation
0 1 0 0
0 0 1 0
0 0 0 1
3         mixed objects
.               .               .

.               .               .

.               .               .
The bitmap size is specified in the second ("tiles in x,y") and third ("pixels (x,y) per tile") lines of the file. The drawing size can be approximately calculated by multiplying the number of tiles by the number of pixels/tile (3960 x 3960 in the above example).