Raster3D V2.6


The Raster3D molecular graphics package consists of a core program render and a number of ancillary programs that read atomic coordinates from PDB (Protein Data Bank) files to produce scene descriptions for input to render. Raster3D can also render images composed using other programs such as Molscript and XtalView.
Index  
Programs in the Raster3D package Filters
  • Import molecular surface descriptions from Grasp or MSMS
Hints for composing pictures

SYNOPSIS

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 plus one matte channel.

Raster3D does not depend on graphics hardware. The rendering program currently supports output to files in AVS, JPEG, TIFF, PNG and SGI libimage format. 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). The Raster3D rendering program can be integrated with ImageMagick to expand the flexibility of output formats and interactive use.

Ancillary programs are provided for the generation of object descriptions based on atomic coordinates stored in PDB format. Although Raster3D is not intended as a general purpose ray-tracing package, nothing in the rendering process is specific to molecular graphics. Some of the algorithms used have been chosen for speed rather than generality, however. They work well for molecular graphics images, but possibly would produce odd results if used for very different types of image.

Raster3D currently supports rendering six object types: spheres, triangles, planes, smooth-ended cylinders, round-ended cylinders, and quadric surfaces. It also supports the definition of material properties (transparency, bounding planes, color, reflectivity) that apply to groups of objects within the rendered scene.

Version 2.1 added support for additional "object types" which are really modifiers for characteristic properties of existing objects. These have since been expanded to include the specification of explicit surface normals, colors, and transparency at the vertices of the current object.

Version 2.2 added support for transparency.

Version 2.3 added support for file indirection, additional anti-aliasing options, internal light sources, and a separate alpha blend (matte) channel in the rendered image. There is a new shell script, stereo3d to automatically generate a side-by-side stereo pair from a Raster3D input file.

Version 2.4 added support for generalized quadric surfaces (ellipsoids, cones, etc). Input lines beginning with '#' are treated as comments. It introduced the utility program rastep which generates "thermal ellipsoid" representations of atoms based on the Biso or Uij entries in a PDB file (ANISOU cards). The option of coloring based on B values was added here and elsewhere.

Version 2.5 added support for Z-clipping, output to a JPEG image file on stdout, piped output to ImageMagick for automatic conversion to additional image types, and file indirection of header records. It also upgraded support for handling labels (object types 10,11,12) using PostScript. See r3dtops and label3d documentation.

Version 2.6 adds support for bounding planes, and removes the previous limit on stacking transparent objects. The installation process has been modified so that all user-configurable options are collected into the files parameters.incl and Makefile.template.

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 as AVS image file 
# 
cat ribbon.r3d irons.r3d | render > picture.x
One can alternatively use Molscript to produce a Raster3D input file by using the -r switch. 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 avs:-
A similar example using xv as an image viewer, and assuming that TIFF support has been built into the render program:
molscript -r < infile.dat | render -tiff image.tif 
xv image.tif
The same image rendered as a side-by-side stereo pair:
molscript -r < infile.dat | stereo3d -border -png stereo_pair.png

The Raster3D distribution also includes a filter utility which will convert the 24-bit color output stream from render into a dithered black & white PostScript image:
render < description.r3d | avs2ps > picture.ps

SOURCE

anonymous ftp site:
ftp.bmsc.washington.edu /pub/raster3d/
via WWW:
http://www.bmsc.washington.edu/raster3d/raster3d.html
contact:
Ethan A Merritt
Dept of Biological Structure
University of Washington,
Seattle WA 98195-7742
merritt@u.washington.edu

RELATED PROGRAMS

Required for full installation:
PNG
Support for direct output of PNG images requires prior installation of the libpng and libz libraries. If these are not distributed with your operating system you can get the source from http://www.libpng.org/pub/png/. PNG files allow transparent backgrounds and alpha blending, and can be viewed using a web browser.
TIFF
In order to build in support for the direct output of TIFF image files, you must separately obtain and install a copy of the TIFF library (libtiff.a). Several implementations are available, including one by Sam Leffler which may be obtained via anonymous ftp from sgi.com. Some recent TIFF libraries no longer support LZW compression due to concerns about patent enforcement by Unisys. This makes TIFF much less useful than it used to be. Consider using PNG format instead, as it has most of the good features of TIFF and also can be viewed by web browsers.
JPEG
In order to build in support for output of JPEG images you must have a copy of the JPEG library. If your system does not already have this library installed, you can obtain it directly from the Independent JPEG Group development project via anonymous ftp from ftp.uu.net/graphics/jpeg/.
ImageMagick
In order to view the rendered images on a workstation screen you must also obtain and install an image viewer. Two commonly available viewers are John Christy's ImageMagick (also available via anonymous ftp from ftp.x.org ) and John Bradley's xv.
Ghostscript
Used only by the label-processing tools r3dtops and label3d.
Some other programs with direct Raster3D output modes:
Molscript
Figures composed in Molscript can be rendered in Raster3D rather than being printed as PostScript images. The features of Raster3D version 2.0 are supported by Moslcript version 1.4 (with a couple of additional patches that come in the Raster3D distribution). To obtain Molscript please contact Per Kraulis directly (Email: pjk@avatar.se). There is now a Molscript web page at http://www.avatar.se/molscript.
ORTEP and the small molecule world
ORTEX V7 (an interactive descendent of Carroll Johnson's ORTEP program) now supports Raster3D as an output mode. ORTEX runs under DOS/Windows, and is available from http://www.ucg.ie/cryst/software.htm. Another small molecule package running under Windows and incorporating Raster3D rendering options is WinGX, available from http://www.chem.gla.ac.uk/~louis/software.
TkRaster3D
an X11-based front-end (GUI) for the Raster3D programs developed by Hillary Gilson at NIST, http://www.cstl.nist.gov/div831/TkRaster3D/
VMD
Biomolecular visualization tool from the Theoretical Biophysics group at the University of Illinois, http://www.ks.uiuc.edu/Research/vmd/
X3DNA
Figure generation and analysis tool for RNA and DNA structures. X3DNA Web site: http://rutchem.rutgers.edu/~xiangjun/3DNA/.
Xfit/XtalView
General crystallographic model building, map fitting, and analysis program by Duncan McRee, available in both academic and commercial versions, http://www.scripps.edu/pub/dem-web/index.html

Several auxiliary programs are available from the ftp site above which may be useful, though they have not been kept up to date with the current Raster3D version. These include two attempts to aid in the composition of Raster3D images (atoms, preras3d) and tools for conversion to half-toned monochrome images and annotation and display of the images (viewtools). Most of the code was written specifically for SGI workstations, and may not transport well to other platforms.

AUTHORS

Originally written by David J. Bacon and Wayne F. Anderson. Ancillary programs by Mark Israel, Stephen Samuel, Michael Murphy, Albert Berghuis, and Ethan A Merritt. Extensions, revisions, and modifications by Ethan A Merritt.

CITING THE PROGRAM

If you use the package to prepare figures for publication, please give proper credit to the authors; the proper citation for the most recent version of the package is Merritt & Bacon (1997) as given below.

REFERENCES

Bacon, D.J., & Anderson, W.F. (1988) ``A Fast Algorithm for Rendering Space-Filling Molecule Pictures''. (abstract of paper presented at the Seventh Annual Meeting of the Molecular Graphics Society). J. Molec. Graphics 6, 219-220.
Kraulis, P.J. (1991) ``MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures''. J. Appl. Cryst. 24, 946-950.
Merritt, E.A. & Murphy, M.E.P. (1994) ``Raster3D Version 2.0 - A Program for Photorealistic Molecular Graphics''. Acta Cryst. D50, 869-873.
Merritt, E.A. & Bacon, D.J. (1997) ``Raster3D Photorealistic Molecular Graphics''. Methods in Enzymology 277, 505-524.

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