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.
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Sample figures generated using Raster3D.
 MSMS + Raster3DThis figure illustrates using Raster3D to draw a slice through a molecular surface, revealing interior cavities and channels. Full size image: |
 XtalView + Raster3DYou can render the canvas window of an XtalView map-fitting session as a Raster3D image via a simple pull-down menu. Full size image: |
 XtalView + Raster3DBoth 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: |
 ORTEX + Raster3DPatrick McArdle has adapted the Raster3D components rastep and render for use with the small-molecule visualization tool ORTEX. Full size image: |
 New in version 2.3 "glow" lightingPosition of Bee Venom Phospholipase A2 at the Membrane Surface Using a Novel Electron Paramagnetic Resonance Technique (image courtesy of Ellie Adman). Full size image: |
 Example6: The Raster3D utility programs ribbon and rings3d can generate filled-ring diagrams of sugars, nucleic acids, and other biological molecules. Full size image: |
 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: |
 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: |
 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: |
 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: |
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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