Websites Using Jmol

Jmol users, please add your (X)HTML website here. There are also pages where you can add your link to applications that embed Jmol (Applications Embedding Jmol), or where you can add your link to a Wiki that uses Jmol (Wikis Using Jmol).

• 3Dchem.com The Molecule of the Month website from the University of Oxford, now updated to make use of Jmol, showing hundreds of small molecules, inorganic polyhedra and protein structures - Karl Harrison, Oxford, UK.
• Aptanomics Intranet The Jmol applet is used to explore the structure of molecules in our database. - Aptanomics SA, Lyon, France.
• Apuntes de Biología Molecular by M. Gonzalo Claros - Universidad de Málaga, Málaga (Spain).
• Biomodel Teaching resources and self-guided learning for structure and interaction of biomolecules: amino acids, carbohydrates, stereoisomerism, lipids, lipid bilayer, proteins, nucleic acids, nucleic acid-protein complexes, biopolymers - in Spanish, by Angel Herraez, Universidad de Alcalá (Spain).
• BioROM Ayudas para el aprendizaje de bioquímica, biotecnología y biología molecular - Material in Spanish, a collaboration among several universities from Spain and Chile.
• Bioquímica e Biologia Molecular - Centro de Biotecnologia e Faculdade de Veterinária - Universidade Federal do Rio Grande do Sul - Porto Alegre - Brazil (in portuguese)
• Biotopics 3-D structures of simple Biological molecules - carbohydrates, lipids, nucleic acids, other compounds of Biological interest.
• Browser-linked Chemkin-style thermodynamic database Demo for linking chemical nicknames & structures without altering a legacy database.
• ChemExper Chemical Directory A database containing over 500000 molecules, 10000 IR and 70000 3D models that can be visualize using Jmol.
• CDK Web Show case for functionality in the Chemistry Development Kit. The website uses Jmol for generated rendering 3D structures. [2006/04/12 -- file not found]
• Conformational Epitope Prediction Server - Bioinformatics Centre, University of Pune, India. Shows predicted surface antigenic epitopes in Jmol.
• CoolMolecules - St. Olaf College, USA
• Dr. Gutow's VSEPR Tutorial - Hosted by the University of Wisconsin Oshkosh this is a tutorial on the VSEPR (Valence Shell Electron Pair Repulsion) model for determining molecular shapes. Example molecules viewed using Jmol.
• Dutch Dictionary on Organic Chemistry - Radboud University Nijmegen, The Netherlands
• EDinformatics -- Explain it With Molecules This is an interactive site designed for K-12 students.
• Evolution of Knowledge Uses scripts to color conserved amino acids in proteins like insulin and G3PD. Attention: this is an "intelligent design" website that links to non-peer reviewed material. The arguments for intelligent design of macromolecules and of life in general are very weak and have been refuted in many venues. Note that the chapters of the book that this site links to have not been subject to legitimate peer review.
• FirstGlance in Jmol is a simple, browser-based tool for molecular visualization. Buttons show informative views of any macromolecule available on-line. Help, including color keys, appears automatically and is always in view. Hyperlinks show a molecule in one click. It is designed to be useful both to novices and to specialists.
• FlexWeb - FIRST Online - Arizona State University, Tempe, Arizona, USA; FIRST / FRODA Software for rigidity analysis and geometric rigidity simulation. Registration Required but free for non-commercial users
• FXI Deficiency Mutation Database - UCL, UK
• GRIS: Glycoprotein-hormone Receptors Information System - GRIS gathers and presents heterogenous data on glycoprotein-hormone receptors (GpHRs) such as mutational data, homology models and allows the users to employ several structural analysis tools. Jmol is used to visualize the models.
• Jena Library of Biological Macromolecules (JenaLib) - Jena, Germany
• Librairie de molécules - Molecular model library for science secondary teachers in french, France
• Modeome3D database - Homology 3D-models database with Jmol integrated tools.
• Mol4D - CMBI, Radboud University Nijmegen, The Netherlands Tutorials Organic Chemistry and Molecule editor/Mopac interface.
• Molecular Origami Precision Scale Models from Paper. View the model using Jmol or make it out of paper yourself. - St. Olaf College]
• Molecular Structure of Hormones in the Human Body (Medical Computing .Net) - Irvine, USA
• Moleculen in Beweging - CMBI, Radboud University Nijmegen, The Netherlands Very nice Dutch website for high school students on several aspects of chemistry. I especially liked the IR section which links peaks to actual vibrations.
• Molécules en 3D dossiers profitant des fonctionnalités de l'applet Jmol et utilisables par les élèves de second cycle (seconde, première, terminale) de l'enseignement français (dossiers adaptés aux programmes français en vigueur).
• Molecules In Motion molecular animations - Interactive Molecular Structures
• Molecule of the Month Interesting facts about molecules written by contributors from all over the world.
• MolVisions Custom physical models of molecules.
• MSD ligand chemistry - European Bioinformatics Institute, UK
• NASIM/VPL - University of Technology, Bratislava, Slovakia NASIM/VPL - Nanotechnology Simulator / Virtual Physician Laboratory is a opensource initiative of CCMS laboratory built on top of Jmol and other projects that provides to construct simple molecules with interactive editor and compute problems from chemistry on computer clusters.
• OCA - OCA, a browser/database for protein structure and function at the Weizmann Institute, Israel and several mirror sites around the world.
• Orbitron - The Orbitron: a gallery of atomic orbitals and molecular orbitals on the WWW by Mark Winter at the University of Sheffield, UK: includes dot-density plots rendered in Jmol for the display of atomic, hybrid, and a few molecular orbitals
• Online Macromolecular Museum - CLU, Thousand Oaks, CA, USA The OMM contains exhibits of a variety of macromolecules. New exhibits use Jmol. Older, Chime-based exhibits are being converted to Jmol. One exhibit is an interactive Jmol scripting tutorial.
• p53 Knowledgebase - Bioinformatics Institute (Singapore)
• PDBsum - European Bioinformatics Institute, UK
• Protein Data Bank Research Collaboratory for Structural Bioinformatics Protein Data Bank now uses Jmol as one of its primary viewers
• Protein Dipole Moment Server - Weizmann Institute, Rehovot Israel With this server you can discover if your protein might have an unusally large net charge or dipole moment, and how this might relate to specific structural features of the protein, and thereby its function.
• ProteinExplorer.Org - A powerful software package to help explore and understand macromolecular 3D structure, with levels for beginners and experts. Although it works primarily with Chime, molecular views can be exported to MolSlides that use Jmol.
• Protein Structure Annotation Database A database of protein structure annotation that uses the Jmol applet as really nice tool for displaying the structure of proteins.
• QCRNA The DFT Database for RNA Catalysis is a large collection of high-level density-functional electronic structure calculations of molecules, complexes and reactions relevent to RNA catalysis.
• RESP ESP charge DDataBase, R.E.DD.B. - Université de Picardie Jules Verne - Burnham Institute for Medical Research
• Structure and reaction mechanism of RUBISCO A Rubisco tutorial with a Jmol version.
• Sudoku Assistant Uses Jmol to visualize the three-dimensional logical chains of Sudoku puzzles.
• The Virtual Museum of Minerals and Molecules - Previously implemented on Chime, the VMMM is now fully converted to Jmol (applet + JavaScript), with over 100 molecules and minerals in its galleries.
• TLS Motion Determination - University of Washington, USA Analyzes a protein crystal structure for evidence of flexibility. Animations of the predicted flexibility are presented using Jmol.
• Transporter Library The Transporter Ligand Library, created by Dept. of Neurochemistry, CRC, HAS collects biological and structural information about ligands for neurotransmitter transporters. - Budapest, Hungary
• Undergraduate Education - Ohio State University, USA A collection of online educational material for Chemistry. The main focus is on Organic Chemistry but there are also materials for General Chemistry. Many areas use Chime, but I am converting to Jmol.
• U Penn X-ray Facility - The X-ray Facility in the Department of Chemistry at the University of Pennsylvania uses Jmol to archive completed structure determinations
• Virtual Textbook of Organic Chemistry - Michigan State University, USA Because this is a large site the Jmol references may be difficult to find ... but they are in there.
• World Wide Molecular Matrix - Unilever Centre at Cambridge, UK (2006/04/12 file not found)
• XdomView - National University of Singapore
• Zinc is not Commercial - University of California, San Francisco, USA Database with more than 3.3 million 3D small molecules free for download and online viewable with Jmol

Contributors

AngelHerraez, EricMartz, NicolasVervelle, Kschroeder, Cjacoboni, Fuster, Zizzzl, Ceroni, Yves.noel, Linucks, Fyd, Thurmond, EPAC, Dkoes, Biofisikx, Pierocanepa, Cudo29, Wade, Mevans86, JimHu, Gutow, MarkII, Ngreeves, Livekoor, Sspilatro, Ppillot, Aloctavodia, Tzontonel, Xavier, Iobataya, Vchest, Dwoodcock, Bishoptc, Johannespernaa, Einarabelc5, Mykc, Mieczyslaw, Rancidbear, Jhjensen, Rhuehne, BrianMcMahon, Elf, Symplus, Jls043, Cvaldes, Oconchus, Gfucile, Wandasia, Stephanruehl, Contactoquiral, Tholton, Zhah, AntonyWilliams, Trani, Rod, Walterse, Immel, Deanjohnston, Starsnooop, Liisa, Jjunker, Spiderino, Eoc21, Rjlanc, Rlight, Sciencestuff, Pimpim, Yhonma, Christoph.gille, Henderson, Alan Hewat, Quentinkaas