Chemistry
Amino Acid Database
Includes a 3-D image of each amino acid in the DB.
All About Atoms
All About Atoms is a very basic overview of atomic structure. Students can click on particles to learn more about them and even discover some fun facts about atoms!
Banque de molécules et d’ions ne contenant pas d’éléments de transition
About fifty files with the .pdb format to describe the geometric characteristics of simple inorganic molecules. These files were made with the atom’s coordinates to respect the experimental values. So, these files permit the illustration of classical geometries learnt in the VSEPR method.
Biochemistry Graphics
A collection of animated and still graphics which illustrates significant biochemical concepts and processes.
Brookhaven Protein Data Bank
PDB, the single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.
ChemVis
The ChemVis project is one of 23 research projects in the strategic research initiative “V3D2″ (”Distributed Processing and Exchange of Digital Documents”) of the German Research Foundation (Deutsche Forschungsgemeinschaft DFG). The group develops new tools for chemical visualization within the internet. Someproject demosare available (require a VRML97 plug-in). AGermanversion of the site is also available.
Chemistry at Imperial College of Science, Technology and Medicine
In order to use these pages you must haveNetscape 3.0 or laterandChime 1.0 or later. In additionJavaScriptmust be enabled. Here are some pages relating to molecular graphics.
The 3D Virtual Chemistry Library Project. Includes aMolecule Library.
Exercises in Molecular Symmetry. Hands on exercises with simulations of molecular motions in different symmetries.
Web compatability table for Chemists. A table of chemically applied web browser tests.
The Chemical MIME Home Page. This page provides a concise entry point for various information sources relating to chemical MIME (Multipurpose Internet Mail Extension).
ChemViz
The ChemViz group at NCSA has, within an NSF sponsored program, developed material which can put high-powered computing and communications tools into the hands of high school teachers and their students. These materials allow high schoolers and their teachers to do their own research by visualizing atomic and molecular orbitals using computational methods. There is also anFTP siteassociated with the ChemViz project.
Creating Enhanced Web Pages for Chemistry
A tutorial for enhancing your web-site with visualizations of molecules and other material. The site also includes a link list with downloadable software useful to the editor of a chemical web page.
Crystal Lattice Structures
A systematic presentation of crystal lattice structures. Coordinates in .xyz-format may be downloaded or visualized with theChemScape Chime plug-in.
Crystal Structural Models using Chime Plug-in
Structures of mineral groups with descriptions.
Examples of complexes derived from common ligands
3D structures of ligands with formula an IUPAC name. These structures can be viewed withRasMolor theChemScape Chime plug-in. FromUniversity of the West Indies, Mona Campus.
Hyperactive Molecules
This is a collection of molecules from servers around the world which can be viewed interactively. Turn off in-lined images before going to the site in England to minimize transfer time. If you want to view a molecule just click on the placeholder icon.
IMB Jena Image Library of Biological Macromolecules
The library contains visual and other information on three-dimensional biopolymer structures. It provides access to all structure entries deposited at theProtein Data Bank(PDB) or at theNucleic Acid Database(NDB). In addition, general information on the architecture of biopolymer structures is available. The major part of entries has automatically generated images and interfaces for free molecular graphics programs. However, the number of manually generated high-quality and informative mono, stereo and VRML representations is steadily increased and remains one of the peculiarities of the IMB Jena Image Library.
Indiana University Molecular Structure Center
The IUMSC site makes extensive use of Java applets to allow users to generate molecular graphics for structures determined by X-ray crystallography. Over 200 molecules have been added so far, with several thousand to eventually be added fro the IUMSC archives. “Common Molecules” page is worth looking at also, as is the “crystallography and morphology” pages.
Java 3D molecular viewer
A molecular viewer inJavaused to browse a metalloprotein database. The browser has some special features, such as showing distances and angles between selected atoms. More info is found at theMDB Main Page.
Molecular Models
Molecular models kits and other educational lab equipment sold byIndigo Instruments.
MathMol – Mathematics and Molecules
The main objective of MathMol is to provide students, teachers, researchers and the general public with information about the rapidly growing fields of molecular modeling and related areas.
MidasPlus
UCSF MidasPlus is an advanced molecular modeling system developed by the Computer Graphics Laboratory (CGL) at the University of California, San Francisco. The software is distributed as documented source code to serve as both a starting point and training tool for others interested in doing their own software development.
Models of Molecules
Databases with molecules in a format for visualizing withRasMolor theChemScape Chime plug-in.
MathMol Molecular Library:Contains water, carbons, hydrocarbons, molecules of life and drugs.
Smell Database:Structures and properties of smelling molecules.
Pomona University:Structures of Molecules Discussed in Class (Chemistry 1).
Widener University:Visualizing Molecules. This page contains a set of Lewis Dot structures, Hyperchem 3D renderings, and Protein Databank files (*.pdb) for a variety of molecules. These were developed for teaching molecular structure in General Chemistry at Widener University.
University of the West Indies, Mona Campus:Jamaican themes for Lecture Material: “The extraction of alumina from bauxite”, “The Chemistry of spices”, “Jamaican Blue Mountain coffee”, “What is at the fruit and vegetable market?”, “Jamaican Rum from sugar cane”, “Synfuel from Ethanol”, “Marine Natural Products”, “Herbal remedies”. PDB molecules are found in context in the lecture material.
Molecules of the Month:Links toMOTM Oxford,MOTM Bristol, andMOTM University of Erlangen-Nuernberg. Each month a new molecule will be added to the list on this page. The links will take you to a page at one of the Web sites at a University Chemistry Department or commercial site in the UK, the US, or anywhere in the world, where useful (and hopefully entertaining!), information can be found about a particularly interesting molecule.
Die Organik-Galerie:A selection of organic molecule images obtained by raytracing as well as .pdb and .wrl downloadable structure formats.
WWU Virtual Molecular Model Kit:A variety of instructional organic molecules.
Molecular Animations with Re View
A variety of molecular animations/simulations are available at this site, covering conformational analyses, reactions, vibrations, etc. Both animations and multistructure XYZ files are provided, enabling movies or ‘4D’-simulations to be viewed. The latter will require a special player such asReView[demo] orXMol.
Molecular Animations of Large Molecules
AVI movies of large, biological molecules (hemoglobins, agarose, DNA, collagen and more).
Molecular Dynamics Simulations on Large Systems
The objective of this project is to perform molecular dynamics simulations on extremely large systems, consisting of up to 106atoms, and to analyze the results in real time.
Molecular Models for Biochemistry at CMU
The linked pages described here have tutorials and quizzes that are based onChimeandRasMolimages of the molecules and macromolecules found in biochemistry. They are intended to complement standard biochemistry texts where more explanation is provided, but where interactive 3-D images of the molecules are not available.
Molecular Movies
Nine interactive animations describing nucleophilic substitutions, eliminations, electrophilic additions, electrophilic aromatic substitution, nucleophilic addition, and nucleophilic substitution on acid derivatives. Three demo files are playable in a web browser, if theShockwave plug-inis installed.
Molecule of the Month
Each month a new molecule will be added to the list on this page. The links will take you to a page at one of the Web sites at a University Chemistry Department or commercial site in the UK, the US, or anywhere in the world, where useful (and hopefully entertaining!), information can be found about a particularly interesting molecule.
Molecules in 3D
A few examples of molecules to be viewed in 3D. A 3D effect requires red-blue glasses.
Molecules-R-Us
A hypertext-based table of contents of the Brookhaven Protein Databank. Allows on-the-fly generation of 3D-images in various formats from the enormous database.
MolPOV
MolPOV is a graphics file converter that reads Brookhaven Protein Data Bank formated files and produces a ready-to-render input file for thePersistence of Vision (POV) ray tracer. The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format. Both programs are freeware.
NanoWorld
Images from the Center for Microscopy and Microanalysis, University of Queensland, Australia, an interdisciplinary research and service facility dedicated to an understanding of the structure and composition of all materials at atomic, molecular, cellular and macromolecular scales.
NIH Molecular Modeling Home Page
Intended as a centralized source of information concerning the methods and biological applications of molecular modeling.
Normal Modes oftrans-1,2-Dichloroethylene
Click on a peak in the IR spectrum and view the corresponding vibrational mode. RequiresChemscape ChimeandJavaScriptmust be enabled.
Nucleic Acid Database
The Nucleic Acid Database Project (NDB)assembles and distributes structural information about nucleic acids.
Orbital Viewer
Lots of atomic orbitals, arranged by quantum number and shape. The orbitals images are produced with theOrbital Viewer, an amazing software for drawing and viewing orbitals in 3D, which may be downloaded for free from this site.
Persistence of Vision Raytracer
The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Microsoft Windows 3.1/Win32s and Windows 95/NT, DOS, the Macintosh, i86 Linux, SunOS, and Amiga. The source code is available for those wanting to do their own ports.
Protein Science Kinemages
A ‘kinemage’ [kinetic image] is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be turned on or off, any point can be identified by picking it, and the change between different forms can be animated. Kinemages are proposed as a subtype of thechemical MIME standardwith the specification “chemical/x-kinemage” and file extension “kin”. Kinemages, their history, and the proposed MIME standard are described in mime_kin.txt in theMIME_kin directoryof theProtein Sciencegopher server.
RasMol Home Page
RasMol is free molecular visualization software, great for small molecules but is especially amazing for macromolecules (proteins, DNA, RNA) or macromolecular assemblies (viruses, lipid bilayers). This site provides the software itself, a gallery of images produced by RasMol, educational scripts (movies) for projection in lectures or for self-study, links to class web sites which employ RasMol, and to other free molecular visualization software.
Representation of Molecular Models Rendering Techniques
This is a nice tutorial on the ways that molecules can be represented by computer imaging. Includes discussion on structures, surfaces, rendering, etc.
Scanning Tunneling Microscopy
An STM image gallery and more from The Visualization lab of IBM.
Senses Bureau – The Wilson Group
Contains visualisations related to teaching of general and physical chemistry at the University of California at San Diego.
Silicon Graphics Teaching Laboratory
Contains a course on molecular modelling and information on MacroModel.
TORVS Chemical Internet Services
Contains searchable databases with 3D coordinates, GIFS, and VMRL scenes for Chemical Structures as well as chemical database browsers.
UK SuperJanet Demonstrations
QuickTimemovies, playable on either Mac or MS Windows using appropriate software.
Virtual Chemistry Lab at the University of Oxford
A virtual reality chemistry lab that includes a three dimensional simulation of the University of Oxford’s inorganic chemistry teaching lab and interactive on-line experiments. Examples of material available now or in the process of being built include aQuickTime3 VR tour of a laboratory, preparation of a superconductor (with videos of the special properties of such materials), and exploring the aqueous chemistry of common metal ions. This site makes extensive use of plug-ins and multimedia. You’ll need Netscape Navigator 3.0 or Internet Explorer 3.0 to view it successfully. It’s a good site to see what is possible with many emerging technologies including VRML,QuickTime,QuickTime VR, Real VR, and Macromedia Shockwave.