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Raster3D(1)						      General Commands Manual						       Raster3D(1)

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 pro- duced, 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-contain- ing 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: contact: Ethan A Merritt University of Washington, Seattle WA 98195 SEE ALSO
render(l), rastep(l), rods(l), ribbon(l), balls(l), avs2ps(l), stereo3d(l) 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 modi- fications by Ethan A Merritt. Raster3D V3.0 14 December 2010 Raster3D(1)

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AVS2PS(1)						      General Commands Manual							 AVS2PS(1)

avs2ps - convert AVS image input on stdin to monochrome PostScript on stdout SYNOPSIS
avs2ps [-b] [-dpi xxx] < infile.avs > avs2ps converts a 24-bit color image file in AVS format into a dithered monochrome PostScript image with the same number of pixels as the input file. avs2ps may be used as a filter for the output of the render program to produce a PostScript file directly. avs2ps is machine independent, and does not impose restrictions on the tile size in the original image. It supersedes the programs mol- ras3d and hdither in the viewtools package. EXAMPLES
Produce an unbordered black & white image suitable for printing on a 300 dpi PostScript printer. render < infile.r3d | avs2ps > Add a border, and prepare image for a 400dpi printer render < infile.r3d | avs2ps -b -dpi 400 > OPTIONS
-b Draw a border around the figure. By default avs2ps will produce a borderless image 0.5 inch in from the bottom left of the page. -dpi xxx By default avs2ps writes header records into the PostScript output file which are correct for a 300dpi printer (e.g. an HP IIIsi). If there is a mis-match between the header records and the actual resolution of the printer the image quality is substantially degraded. This option allows one to specify a different printer resolution (e.g. -dpi 400 for a Next printer, or -dpi 95 for GhostScript on a 1280x1024 workstation screen). DESCRIPTION
avs2ps converts the input stream to a grey scale image and then applies an empirical algorithm for dithering and error propagation to pro- duce a monochrome output image. SOURCE
anonymous ftp site: web URL: contact: Ethan A Merritt University of Washington, Seattle WA 98195 SEE ALSO
render(l), raster3d(l), avs AUTHORS
Ethan A Merritt. Dithering algorithm derived from code by Randy Read and Albert Berghuis. Raster3D 8 May 1999 AVS2PS(1)
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