Raster3D package for photorealistic molecular graphics

# Raster3D V3.0

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, Xfit, and coot.

Index FAQ (Frequently Asked Questions) Synopsis Brief examples of use Distribution site | Related programs Authors Citing the program References
Programs in the Raster3D package avs2ps balls label3d normal3d rastep render ribbon rings3d rods stereo3d Filters Import molecular surface descriptions from Grasp or MSMS | Hints for composing pictures Animation Black & White figures Clipping planes and Bounding planes Colors, and a Color picking tool Composing figures in other programs Coordinate systems Labels (special note: Molscript labels) Making your picture modular Shadowing Side-by-side figures and stereo pairs Tailoring your image to the output device Transparent surfaces Worked examples from the Raster3D distribution

#### 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.

New in version 3.0: Dynamic array allocation, direct rendering of labels.

#### 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 png:-

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 AVS output stream from render into a dithered black & white PostScript image:

    render -avs < description.r3d | avs2ps > picture.ps

#### SOURCE

via WWW:
  http://www.bmsc.washington.edu/raster3d/raster3d.html
contact:
  Ethan A Merritt
  Biomolecular Structure Center
  University of Washington
  merritt@u.washington.edu

#### RELATED PROGRAMS

##### Required for full installation:

libgd
  Generation of PNG and JPEG images, as well as label processing, requires prior installation of the gd graphics library. libgd itself requires other libraries, but if you have libd itself installed then you should be all set.
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). However, you can only render text labels for PNG or JPEG output, so you may be better off generating PNG images and then converting them to TIFF afterward.
ImageMagick
  For full functionality you should also obtain and install a copy of ImageMagick

##### Some other programs with direct Raster3D output modes:

Coot
  The contents of the current view window in a Coot session may be rendered in Raster3D using the <F8> hotkey. More complicated scripting from Coot is also possible. Coot web page: http://www.biop.ox.ac.uk/coot/
Molscript
  Figures composed in Molscript can be rendered in Raster3D rather than being printed as PostScript images. The Molscript web page is 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.nuigalway.ie/cryst/ortex.html. Another small molecule package running under Windows and incorporating Raster3D rendering options is WinGX, available from http://www.chem.gla.ac.uk/~louis/software.
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.sdsc.edu/CCMS/Packages/XTALVIEW/

#### LICENSE

Version 3 of the Raster3D package is distributed under the terms of the Artistic License, Version 2.0.

#### 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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