These links are a work in progress and are currently divided into separate but related groups. Molecular modeling/rendering is a logical extension of molecular drawing. Molecular drawing is not to be confused with modeling and rendering. Current commercial software combines the modeling and rendering extension(s) with the drawing functions.

1. Atomic structure definitions of various types and their display. These are text files which are used to describe molecules and the various programs which process the files.

2. Links to sites using this technology.

3. 3D modeling and ray tracing information. 3D modeling is a mature technology (i.e. AutoCAD, etc.) which is being enhanced by three dimensional rendering technology. Ray tracing (3D rendering) is a developing graphics display technology which is being developed for realistic three dimensional visualization, mostly applied to computer graphics art, virtual reality, interactive games and bad television cartoons. Here, however, it is used to make the pretty pictures of molecules which you have seen on magazine covers. This is the fun part.

3.5 Animation is the next logical extension of the 3D graphics paradigm. As this technology applies to chemistry, the animation function is the least utilized of the currently available technology for the web, although excellent examples can be found. Animation technology is being used more extensively with canned packages which are licensed per computer. 'Cause that's where the money be.

Atomic Stucture Definitions

Chemical MIME Types

Chemical MIME Home Page Imperial College, Dept of Chemistry, England
Yahoo! Science/Chemistry/Chemical_Mime_Types/

Chemical Structures

3D Drug Structure Databank NIH Center for Molecular Modeling
Chemical Structure Searching Server U.S. National Library of Medicine
ChemFinder Search Cambridge Software
Klotho: Biochemical Compounds Database Washington University Saint Louis
Nucleic Acid Database Rutgers University
Protein Data Bank Brookhaven National Laboratory

Commercial Software

Chemistry Software see Chemistry Software web links

Online Structure Generation

Daylight Chemical Information Systems Inc SMILES home page
Daylight - Java Molecular Editor (JME) SMILES (requires Java Browser)
Gasteiger Research - CORINA (PDB) Erlangen University, Germany

An Introduction to Molecular Modeling article
Center for Molecular Modeling (CMM) U.S. National Institutes of Health
Chime/RasMol Home Page NSF site at University of Massachusetts Amherst
Biochemistry Online, Molecular Modeling
Daylight Chemical Information Systems Inc (SMILES)
Imperial College, Dept of Chemistry England
Journal of Molecular Modeling University Erlangen-Nürnberg, Germany
Okanagan University College, Dept of Chemistry Canada
Representation of Molecular Models Physical Chemistry Dept, University of Geneva
TORVS Research Team University Erlangen-Nürnberg, Germany

3D Modeling and Ray Tracing

Streptonigrin molecule produced with MolPOV and POV-Ray. (courtesy of the J.M. Robinson group)

Many 3D modeling/ray tracing programs exist. Persistence-Of-Vision Raytracer (POV-Ray) is a very popular freeware program with a large following and wide spread support due to the reasonable price and the superior, publication quality of the results.

Graphics File Format Page Dept of Computer Science, Univ of Edinburg
Ray Tracing Info Home Page info and links
Yahoo! Computers_and_Internet/Graphics/3D/Software/POV_Ray/

POV Raytracing

POV-Ray Persistence of Vision Raytracer (NT/95) freeware
POV-Ray Texture Library modeling textures library freeware
Lens Flare plug-in for POV-Ray Nathan Kopp
Texture Editor (eng) for POV-Ray (NT/95) shareware, Philippe Mazan, France
Texture Magic (eng) create textures, texture maps (NT/95) shareware, Germany
Gautam N. Lad's Website POV info and links
Rene' Schwietzke's Website (eng) POV info and links, Germany

POV-Ray for Molecular Visualisation

Mol POV modeler/converter (16-bit), Richardson, U of Florida freeware
PDB2POV pdb-to-pov file converter (DOS) by Eric Suchanek, Ph.D.
POV Chem pdb-to-pov file converter (DOS) by Thiessen at JHMI
Re View at Brunel University UK
SWISS-PdbViewer USA mirror at Brookhaven Natl Lab
VDM (Visual Molecular Dynamics) UIUC Theoretical Biophysics Group

Related Links

BABEL file converter at U of Arizona
BABELwin Windows interface for BABEL at Brunel UK
Thomas Baier Page POV-to-MDL utility for Moray Modeller

3D Modelers - POV-Ray

Breeze Designer 3D 2.0 freeware (NT/95/Win32s)
Moray Modeller shareware (NT/95,$90) by SoftTronics (DOS version also)
POV-Lab shareware demo (DOS,$65)

3D Modelers - Other

AC3D shareware demo (NT/95, 25L-UK)
Autodesk Inc AutoCAD, 3D Studio MAX (NT/95)
Caligari (NT/95) trueSpace2 ($200), trueSpace3 ($500)
Fractal Design Ray Dream
Kinetix 3D Studio MAX (AutoDesk)
MetaCreations Corp Ray Dream 3D ($150), Bryce 3D ($200)
Midnight Modeller shareware (NT/95,$40) beta
New Tek LightWave 3D
Pixar Animation Studios RenderMan (for Unix only)
Rhinoceros Rhino 3D (NT/95,$??) beta
Softimage Softimage (Microsoft)

3D Modeling Links

3D Cafe
Axem Textures/Backgrounds
Crossroads 3D 3D file format converter (NT/95) freeware

Updated April 10, 1998

chemistry@utpb.edu