Raster3D

The Raster3D molecular graphics package consists of a core program render and a number of ancillary programs which produce input files for rendering from Brookhaven PDB files of atomic coordinates. Raster3D can also render images composed using version 1.4 of Molscript


SYNOPSIS

Raster3D uses a fast Z-buffer algorithm to produce high quality pixel images featuring two light sources, specular highlighting, Phong shaded surfaces, and shadowing. Output is in the form of a pixel image with 24 bits of color information per pixel.

Raster3D does not depend on graphics hardware for operation. Four image output formats are supported: AVS, TIFF, SGI libimage, and a private format which is backwards-compatible with earlier versions of Raster3D. 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). An alternate version of the rendering may be built which directly outputs JPEG images [only].

Ancillary programs are provided for the generation of object descriptions based on atomic coordinates stored in Brookhaven PDB format. Although the rendering program is not specific to molecular graphics, Raster3D is not intended as a general purpose ray-tracing program. Some of the algorithms used have been chosen for speed rather than generality; that is, they happen to work well for the types of images the program is intended for, but may 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.

Version 2.1 added support for two additional "object types" which are really modifiers for characteristic properties of existing objects. One of these allows specification of explicit surface normals at triangle vertices; the other allows specification of surface reflectance properties specific to individual objects.

Version 2.2 added support for transparent objects, including transparent molecular surfaces.

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

Version 2.4 The render program now supports generalized quadric surfaces (ellipsoids, cones, etc). There is a new 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 colouring based on B values has been added here and elsewhere. Triangles now may be colored by interpolation of colors assigned to the three vertices. Input lines beginning with '#' are treated as comments.

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 Version 1.4 to produce a Raster3D input file by using the -r switch. Raster3D is not able, however, to render any labels specified by the Molscript input. 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 > input.r3d; stereo3d input.r3d; xv stereo.tiff 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

SUGGESTIONS FOR BETTER PICTURES

Topics covered:

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:
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.
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.

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.
TkRaster3D
an X11-based front-end (GUI) for the Raster3D programs developed by Hillary Gilson at NIST, http://www.carb.nist.gov/TkRaster3D
VMD
Biomolecular visualization tool from the Theoretical Biophysics group at the University of Illinois, http://www.ks.uiuc.edu/Research/vmd/
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
The avs2ps utility for direct production of black & white PostScript images is now included in the Raster3D distribution. It replaces earlier machine-dependent programs in the viewtools kit.

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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