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Raster3D(1)		    General Commands Manual		   Raster3D(1)

       Raster3D	molecular graphics package

       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.

       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

       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-

	    molscript -r infile.dat | render | display png:-

       web URL:

	    Ethan A Merritt
	    University of Washington, Seattle WA 98195

       render(l), rastep(l), rods(l), ribbon(l), balls(l), avs2ps(l),

	Raster3D version 3.0 is	distributed under the terms of the
	Artistic License, Version 2.0.

	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)


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