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Raster3D(1)		    General Commands Manual		   Raster3D(1)

NAME
       Raster3D	molecular graphics package

SYNOPSIS
       The Raster3D molecular graphics package consists	of a core program ren-
       der and a number	of ancillary programs (balls, rastep, rods) which pro-
       duce 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 out-
       put 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 cre-
       ate and render space-filling models, ball-and-stick models, ribbon mod-
       els, 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 pro-
       tein 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 de-
       scribe, render, and view	3D representations of existing MOLSCRIPT fig-
       ures:

	    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

SEE ALSO
       render(l), rastep(l), rods(l), ribbon(l), balls(l), avs2ps(l),
       stereo3d(l)

LICENSE
	Raster3D version 3.0 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, Al-
       bert Berghuis, and Ethan	A Merritt.  Extensions,	revisions, and modifi-
       cations by Ethan	A Merritt.

Raster3D V3.0		       14 December 2010			   Raster3D(1)

NAME | SYNOPSIS | DESCRIPTION | EXAMPLES | SOURCE | SEE ALSO | LICENSE | AUTHORS

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