Raster3D Version 3.0


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FAQ
Home Page
Sample images
Documentation
Download current version
Raster3D_3.0-3.tar.gz
RPM packages for linux
executables for OSX
Older version
Raster3D_2.9-2.tar.gz

Raster3D 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.

The current version is 3.0 (last changed: 29-Mar-2014)

New in this version: Dynamic array allocation (no need to recompiler for big structures). Labels are processed directly by the render program; no need to render labels separately using PostScript.

Distributed files

Source code
Source and documentation for core programs avs2ps, balls, normal3d, rastep, ribbon, rods, rings3d, stereo3d and render. Makefiles are provided for various linux, unix, OSX environments.
Latest (February 2011): Raster3D_3.0-3.tar.gz
RPMS for linux (not quite current)
I have built several rpm packages. Each probably is usable on a variety of linux configurations.
The statically-linked 32 and 64-bit executables should run on any i586/x86_64 linux distribution. We have tested on Mandriva installations ranging in age from 2007.0 to 2010.1, RHEL 4, and CentOS 5. The source files and example scripts for Raster3D are present in all RPMs.
For systems that do not use RPM as a distribution mechanism, download the source tarball or check for a Debian package.
Current version
Raster3D-3.0-3.x86_64.rpm Mageia 4 (gfortran 4.8.2)
Previous version (December 2010)
Raster3D-3.0-2.src.rpm Source RPM (should work on any RPM - based system)
Raster3D-3.0-2.i586.rpm Mandriva 2010.1 (gfortran)
Raster3D-3.0-2.x86_64.rpm Mandriva 2010.1 (gfortran)
Raster3D-3.0-2.x86_64.ifort.rpm CentOS 5 (Intel ifort)
Raster3D-static-3.0-2.i586.rpm (gfortran 4.4.3; statically linked)
Raster3D-static-3.0-2.x86_64.rpm (gfortran 4.4.3; statically linked)
Old versions
Raster3D-2.9-2.src.rpm Source RPM (should work on any RPM - based system)
Raster3D-2.9-2.i586.rpm Mandriva 2010.0 (gfortran)
Raster3D-2.9-2.x86_64.rpm Mandriva 2010.0 (gfortran)
Raster3D-static-2.9-1.i586.rpm (gfortran; statically linked)
Raster3D-static-2.9-1.x86_64.rpm (gfortran; statically linked)
Debian/Ubuntu
Debian package repository
Executables for OSX
This is a tarball containing executables built using the Intel ifort compiler on 32-bit OSX version 10.5. It also contains the full source, documentation, examples, etc, and a matching shared library for libgd version 2.0.36 that the render executable is linked against. The libgd source is available here.
Raster3D_3.0-2.osx.tgz

Contributed files

raster3d-Win32.zip
Precompiled win32 binaries for 2.6c contributed by Suhaib Siddiqi. Installation instructions are here. Totally unsupported.

Sample Images

Image Gallery
Several figures produced using Raster3D. Each is available here in either TIFF or JPEG format.
Examples
Images produced by the demonstration/verification scripts in the Raster3D distribution

References

original implementation:
Bacon, David J. and Anderson, Wayne F. (1988). "A Fast Algorithm for Rendering Space-Filling Molecule Pictures." Journal of Molecular Graphics 6, 219-220.
version 2.0:
Merritt, Ethan A. and Murphy, Michael E.P. (1994). "Raster3D Version 2.0: A Program for Photorealistic Molecular Graphics" Acta Cryst. D50, 869-873.
version 2.3:
Merritt, Ethan A. and Bacon, David J. (1997). "Raster3D: Photorealistic Molecular Graphics" Methods in Enzymology 277, 505-524.

License

Artistic License, Version 2.0

Authors

Rendering core originally written by David J. Bacon and Wayne F. Anderson; extensions, revisions, modifications, ancillary programs by Mark Israel, Stephen Samuel, Michael Murphy, Albert Berghuis, and Ethan A Merritt

Pointers to other useful programs

Coot
The contents of the current view window in a Coot session may be rendered in Raster3D using the <F8> hotkey. More complicated scripting from Coot is also possible. Coot web page: http://www.biop.ox.ac.uk/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: x3dna.org.
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/

Biomolecular Structure Center at the University of Washington / merritt@u.washington.edu