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@ by A.J. Oostenbrink |
Chemistry, Teaching, Graphics & Visualizations
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| Amino Acid Database Includes a 3-D image of each amino acid in the DB. |
| Animated Infra-Red Spectroscopy (AIRS) This website contains animated infra-red spectra for a variety of organic compounds. Each spectrum allows access to animated molecular vibrations for many of its peaks. Clicking on a particular peak will download the animation of the corresponding vibration. From Michigan State University. |
| All About Atoms
Deze site is geeft een basis overzicht van de atoom structuur. Studenten kunnen klikken op neutronen, protonen en electronene om meer of deze onderwerpen te leren. |
| Animated GIF's and Protein Chemistry The utility of animated GIF's goes far beyond the ability to rotate your companies logo or having bouncing buttons or whatever ridiculous things are being created these days. This page demonstrates the concept by multiple views of Carboxypeptidase A with peptide substrate rotating on an axis. This way one can get a feel for the 3-D structure of the enzyme with its substrate bound in the active site, as well as the position of some key side groups. |
| Molecular database without transition elements !!!!!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 This is a collection of animated and still graphics which illustrates significant biochemical concepts and processes. It has been taken for the most part from the Integrated Biochemistry Learning Series, a HyperCard-based course in Medical Biochemistry. |
| 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. |
| C4-Computers in Chemistry at Cabrillo College A library with more than 400 "live" molecules, including almost all commonly studied compounds. Sets of chemistry problems incorporating Chime models. Most features of this site require Netscape Navigator 3.01 or later and the Chime plug-in. Cabrillo College Chemistry Department also offers a Chime Tutorial. |
| ChemVis Chemical Visualization on the Internet: Embedded dynamic and interactive high-end graphics in digital documents for the visualization of complex factual relationships. Some demos are available. |
| Chirality http://www.colby.edu/chemistry/OChem/DEMOS/Chirality.html Dr. Thomas Poon, Colby College, Movie and explanation. |
| Chemistry at Imperial College of Science, Technology and Medicine The purpose of the project is to develop an on-line library of three-dimensional molecules and their associated properties to be encoded in a combination of standard molecule molfile format and VRML (Virtual Reality Modelling Language), and instruments and other laboratory equipment to be encoded inter-alia in VRML. |
| ChemViz ChemViz NCSA(Chemistry Visualization) is an interactive chemistry program which incorporates computational chemistry simulations and visualizations for use in the chemistry classroom. The chemistry simulations support the chemistry principles teachers are trying to convey, and the visualizations allow students to see how matter interacts at an atomic level. |
| Creating Enhanced Web Pages for Chemistry Includes a list of some helper applications that can be used to visualize chemical data and aA tutorail: how to author a web page that includes enhancements that make use of the chemical MIME |
| Crystal Lattice Structures This page offers a concise index of common crystal lattice structures. A graphical representation as well as useful information about the lattices can be obtained by clicking on the desired structure. |
| Crystal Structural Models using Chime Plug-in Crystal Structures of mineral groups (diamond, salt, carbonates, ...) |
| IMB Jena Image Library of Biological Macromolecules The IMB Jena Image Library of Biological Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. |
| 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.. |
| Metalloprotein database and browser: Java 3D molecular viewer A molecular viewer in Java used to browse a metalloprotein database. |
| J. Lauher's Fullerene Structure Library A Fullerene Structure Library |
| MathMol - Mathematics and Molecules MathMol (Mathematics and Molecules) is designed to serve as an introductory starting point for those interested in the field of molecular modeling. |
| Models of Small Molecules in .pdb Format Databases with molecules in a format for visualizing with RasMol or the ChemScape Chime plug-in. |
| Molecular Animations of Large Molecules AVI movies of large, biological molecules (hemoglobins, agarose, DNA, collagen and more). |
| Cluster Science Collaboration The Cluster Science Collaboration (CSC) is an academic group promoting fundamental research in atomic clusters. These aggregates (for example nanotubes, bucky balls), ranging in size between few and millions of atoms, bridge the gap between molecules and the bulk, and exhibit a variety of unusual phenomena |
| Molecular Models for Biochemistry at CMU Tutorials and quizzes that are based on Chime and RasMol images of the molecules and macromolecules found in biochemistry |
| Molecular Movies
***** Magnificent iInteractive animations, describing nucleophilic substitutions, eliminations, electrophilic additions, electrophilic aromatic substitution, nucleophilic addition, and nucleophilic substitution on acid derivatives. All demo files are 10 times playable (freeware) in a web browser, if the Shockwave plug-in is 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 To GO The NIH Molecules To Go Utililty combines a full text search of the PDB database with a FORM interface to customize the format ( TEXT, IMAGE, INTERACTIVE ) of the selected structure.Molecules To Go" is a World Wide Web (WWW) Forms interface which facilitates access (browsing, searching and retrieval) to the molecular structure data contained within the Brookhaven Protein Data Bank (PDB). Through the Molecules To Go request FORM, one may request a PDB data file to be returned in one of several different formats: |
| MolPOV MolPOV is a graphics file converter that reads Brookhaven Protein Data Bank format files and produces a ready-to-render input file for the Persistence of Vision ray tracer (POV-Ray). The PDB files can be from the Brookhaven PDB itself or from any molecular modeling program that can store structures in the PDB format. A POV setup dialog can be used to edit many of the basic scene features and rendering options. In addition, the program allows launching of the POV program to view the rendering immediately. |
| Nucleic Acid Database The Nucleic Acid Database Project: repository of three-dimensional structural information about nucleic acids |
| OrbVis - Calculation and 3D-Visualization of MOs OrbVis is an online service for the calculation and visualization of molecular orbitals. The service will visualize all MOs of any reseonable structure you create. It employs a combination of a VRML2.0 plugin and a JAVA1.1 applet with many display options to control the visual appearance. |
| RasMol Home Page Protein Explorer, a RasMol-derivative, is the easy-to-use software for looking at macromolecular structure (proteins, DNA, RN, viruses, lipid bilayers)and its relation to function. And it's free! The site provides the necessary plugins. |
| Representation of Molecular Models Rendering Techniques Contains different representations of molecular models and rendering techniques. |
| Scanning Tunneling Microscopy An STM image gallery. |
| TeleSpec IR Spectra Simulation on the WorldWideWeb. The aim of the project TeleSpec is to provide a tool for the simulation of infrared spectra, especially for compounds whose spectra are not available in any database. |
| Spinus WeB NMR Spectra Simulation: Predicts the proton NMR spectra of organic compounds. Chime plug-in required. |
| University of Arizona QuickTime Movies QuickTime movies organized by lecture topic: Molecular Recognition (DNA); Protein Structure; Infra-Red Spectroscopy; SN2 Reaction Mechanism; PDB files can be viewed interactively with the Chime plug-in or RasMol. |
| Virtual Chemistry Lab at the University of Oxford ***** The award winning Virtual Chemistry Laboratory designed and built by Oxford students to provide online learning resources for chemistry.With virtual experiments, lots of links. |
| Virtual Reality Modeling Language in Chemistry Site with a database with thousands of molecules. |
Widener University Visualizing Molecules. |