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Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.

Raster 3D is a set of tools for generating high quality raster images of proteins or other molecules.

The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.

It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware.

Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc.

Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

Download current version:
Raster3D_2.9-2.tar.gz
Previous version:


Sample figures generated using Raster3D.


MSMS + Raster3D
This figure illustrates using Raster3D to draw a slice through a molecular surface, revealing interior cavities and channels.

Full size image:
PNG format (280 kByte) JPEG format (49 kByte)


XtalView + Raster3D
You can render the canvas window of an XtalView map-fitting session as a Raster3D image via a simple pull-down menu.

Full size image:
TIFF format (1048 kByte) JPEG format (248 kByte)


XtalView + Raster3D
Both XtalView and Raster3D can now represent thermal ellipsoids. This view of ellipsoids + density from the 1.25Å refinement of CTB was composed by merging files from Xfit and rastep, and then labeled using ImageMagick.

Full size image:
TIFF format (536 kByte) JPEG format (160 kByte)


ORTEX + Raster3D
Patrick McArdle has adapted the Raster3D components rastep and render for use with the small-molecule visualization tool ORTEX.

Full size image:
TIFF format (200 kByte) JPEG format (39 kByte)


New in version 2.3 "glow" lighting
Position of Bee Venom Phospholipase A2 at the Membrane Surface Using a Novel Electron Paramagnetic Resonance Technique (image courtesy of Ellie Adman).

Full size image:
TIFF format (448 kByte) JPEG format (41 kByte)


Example6: The Raster3D utility programs ribbon and rings3d can generate filled-ring diagrams of sugars, nucleic acids, and other biological molecules.

Full size image:
JPEG format (26 kByte)


Example2: A representation of the E. coli heat-label enterotoxin LT-I binding to multiple copies of a branched oligosaccharide at the cell surface. This example was created using the Raster3D utility programs balls and rods.

Full size image:
TIFF format (264 kByte) JPEG format (33 kByte)


Example3: A closer view of the sugar binding site in the LT-I toxin. This figure was created by feeding the output of Per Kraulis' program Molscript into the Raster3D rendering program.

Full size image:
TIFF format (408 kByte) JPEG format (77 kByte)


Example4: Another closeup of the same binding site in the closely related Cholera toxin. This example was created using the Raster3D utility programs balls and rods.

Full size image:
TIFF format (952 kByte) JPEG format (71 kByte)


Raster3D can render transparent surfaces. The stereo pair shown here was built up by merging a description of protein secondary structure from Molscript and the corresponding molecular surface as caculated by Anthony Nicholl's program GRASP.

Full size image:
JPEG format (54 kByte)


Pointers to other useful programs.

Coot
The contents of the current view window in a Coot session may be rendered in Raster3D using the hotkey. More complicated scripting from Coot is also possible. Coot web page: http://www.ysbl.york.ac.uk/~emsley/coot/.
Conscript
A program for generating electron density isosurfaces (an alternative to the usual chicken-wire). MC Lawrence & P Bourke (2000) J Appl Cryst 33, 990-991. Source and executables available from the Conscript web page: http://astronomy.swin.edu.au/~pbourke/papers/conscript.
ImageMagick
As a general tool for image viewing and manipulation (including annotation and format conversion) I recommend John Christy's ImageMagick, which is available from the ImageMagick web page at www.ImageMagick.org and via anonymous ftp from ftp.x.org among other places.
Molscript
Molscript version 2.0 now has an official web site at http://www.avatar.se/molscript.
Ortex
Patrick McArdle has adapted the Raster3D tools rastep and render for use with the ORTEX small-molecule package under DOS/Windows. Sample picture. Further details from web site http://www.nuigalway.ie/cryst/ortex.html.
X3DNA
Figure generation and analysis tool for RNA and DNA structures. X3DNA Web site: http://rutchem.rutgers.edu/~xiangjun/3DNA/.
XtalView
Very nice open-source crystallographic package for model-building, map-fitting, etc. with direct output to Raster3D for figure generation. XtalView web site http://www.sdsc.edu/CCMS/Packages/XTALVIEW/
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About Hugo Repetto

Ubuntu is a Linux distribution that offers an operating system predominantly focused on desktop computers but also provides support for servers. Based on Debian GNU / Linux, Ubuntu focuses on ease of use, freedom in usage restriction, regular releases (every 6 months) and ease of installation.
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