raster3d - Online in the Cloud

PROGRAM:

NAME

Raster3D - molecular graphics package

SYNOPSIS

The Raster3D molecular graphics package consists of a core program render and a number of
ancillary programs (balls, rastep, rods) which produce input files for rendering from PDB
(Protein Data Bank) files of atomic coordinates. Raster3D can also render images composed
using other programs such as MOLSCRIPT [Per Kraulis (1991), J. Appl. Cryst. 24, 946-950].

Raster3D is freely available. If you use the package to prepare figures for publication,
please give proper credit to the authors. The proper citation for the current version is
Merritt & Bacon (1997).

Bacon & Anderson (1988) J. Molec. Graphics 6, 219-220.
Merritt & Murphy (1994) Acta Cryst. D50, 869-873.
Merritt & Bacon (1997) Meth. Enzymol. 277, 505-524.

DESCRIPTION

Raster3D uses a fast Z-buffer algorithm to produce high quality pixel images featuring one
shadowing light source, additional non-shadowing light sources, specular highlighting,
transparency, and Phong shaded surfaces. Output is in the form of a pixel image with 24
bits of color information per pixel. Raster3D does not depend on graphics hardware.

The following image output formats are supported: AVS, JPEG, PNG, TIFF, and SGI libimage.
To actually view or manipulate the images produced, you must also have installed an image
viewing package (e.g. John Cristy's ImageMagick or the SGI libimage utilities). A filter
utility avs2ps is included in the package which can convert an AVS format output stream
directly to a dithered monochrome PostScript image.

Although Raster3D is not intended as a general purpose ray-tracing package, nothing in the
rendering process is specific to molecular graphics.

EXAMPLES

Using only programs included in the Raster3D distribution one can create and render space-
filling models, ball-and-stick models, ribbon models, and figures composed of any
combination of these. The following set of commands would produce a composite figure of
an Fe-containing metalloprotein with a smoothly shaded ribbon representation of the
protein and spheres drawn for the Fe atoms:

#
# Draw smooth ribbon with default color scheme 2,
# save description (with header records) in ribbon.r3d
#
cat protein.pdb | ribbon -d2 > ribbon.r3d
#
# Extract Fe atoms only, and draw as spheres.
# Color info is taken from colorfile.
# Save description (with no header records) in irons.r3d
#
grep "FE" protein.pdb | cat colorfile - | balls -h > irons.r3d
#
# combine the two descriptions and render to a PNG image
#
cat ribbon.r3d irons.r3d | render > picture.png

Integrated use of MOLSCRIPT/Raster3D/ImageMagick allows one to describe, render, and view
3D representations of existing MOLSCRIPT figures:

molscript -r infile.dat | render | display png:-

SOURCE

web URL:
http://www.bmsc.washington.edu/raster3d/raster3d.html

contact:
Ethan A Merritt
University of Washington, Seattle WA 98195
merritt@u.washington.edu

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