Websites Using Jmol: A-L

Jmol / JSmol Applications

• Websites Using J(S)mol
• J(S)mol in the Classroom
• Journals Using J(S)mol
• J(S)mol Literature
• Articles Using J(S)mol
• Books Using J(S)mol
• Wikis Using J(S)mol
• Blogs Using J(S)mol
• CMS Using J(S)mol (Moodle and others)
  Course Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms
• Applications Embedding Jmol
• Distributions Including Jmol
• Blue Obelisk

Jmol users, please add your (X)HTML website, name beginning A-L, here.

A B C D E F G H I J K L

For Websites M-Z, see Websites Using Jmol.

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• 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.
• 3D Electron Microscopy Data Navigator at Osaka University offers the Yorodumi Viewer, which uses Jmol for electron density maps. Click on the Structure Viewer links to see examples. Note that Jmol can be resized within the page.
• 3D-Structures in Organic Chemistry Models and structures related to teaching basic organic chemistry (DE) - PD Dr. Stefan Immel
• 3D-Structures of Achiral and Chiral Molecules Structures visualizing different types of chirality (DE) - PD Dr. Stefan Immel
• 3D-Structures and Animations in Vibrational Spectroscopy Structures and animations used to visualize vibrational frequencies in IR spectroscopy (DE) - PD Dr. Stefan Immel

• AnchorQuery Specialized pharmacophore search for targeting protein-protein interactions with MCR chemistry. University of Pittsburgh.
• Annotated List of Links to Models Combined list of BWT's web pages of models for teaching or learning undergraduate Inorganic or Structural Chemistry, with notes on possible use - Newcastle University, England
• 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).
• Arduengo Research Group X-ray Structures The Jmol applet is used to depict X-ray structures obtained by the research group of Prof. A.J. Arduengo (Structures entry under Structures Link. - University of Alabama - Tuscaloosa, U.S.A.
• Atlas of Macromolecules is a browsable list of over 150 3D protein or nucleic acid structures, many with snapshots, and each with links for viewing in FirstGlance in JSmol.
• Authoring Template for Tutorials using JSmol (JTAT), updated August 2018 to use JSmol. Download a template into which you can insert molecular views and text. Requires use of a plain-text editor. Detailed instructions provided.

• Banco de Datos de Moleculas Interactivas is an undergoing project to provide High School and Higher Education Students and Teachers with tools to develop a throughly chemistry teaching experience.-in Spanish, by Einar Coutin, Universidad de Los Andes (Venezuela).
• BF3 Molecular Orbitals Clickable MO energy level diagram for teaching, leading to Jmol/JSmol models showing surfaces and/or contours of valence shell orbitals - Newcastle University, England
• Biochemistry for Medical Students--Protein Structure and Function Examples of protein structures relevant to medicine. --Eric Walters, Rosalind Franklin University of Medicine and Science (USA).
• 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 Herráez, Universidad de Alcalá (Spain). Also some sections duplicated in English. -- User may choose Jmol or JSmol.
• Biomolecular Explorer 3D designed to give high school biology teachers easy access to interactive 3D structures of biologically significant molecules. Website and CD-ROM.
• Biomolecules at Kenyon Jmol tutorials created by Kenyon College undergraduates.
• BioROM Ayudas para el aprendizaje de bioquímica, biotecnología y biología molecular - Material in Spanish, a collaboration among several universities from Spain and Chile. Website and CD-ROM.
• Biotopics 3-D structures of simple Biological molecules - carbohydrates, lipids, nucleic acids, other compounds of Biological interest.
• BioWiki DokuWiki with Jmol applet - users can place 3D-molecular models anywhere in this wiki easily.
• Browser-linked Chemkin-style thermodynamic database Demo for linking chemical nicknames & structures without altering a legacy database.

• ChemCompute Free Computational Chemistry for Education. Run computational jobs using GAMESS, TINKER, NAMD, and Psi4 for free.
• ChemEd DL's Molecules 360 (formerly at www.chemeddl.org/collections/molecules/) A collection of small inorganic molecules and their properties. Hosted at the Chemical Education Digital Library.
• ChemExper Chemical Directory A database containing over 500000 molecules, 10000 IR and 70000 3D models that can be visualized using Jmol.
• ChemgaPedia Comprehensive free e-learning platform for chemistry and related sciences. FIZ CHEMIE (Chemistry Information Center), Berlin, Germany.
• CDK Web Show case for functionality in the Chemistry Development Kit. The website uses Jmol for generated rendering 3D structures.
• Chemistry of Things Jamaica - University of the West Indies, Mona, JAMAICA, Includes; Coffee, sugar and rum, fruit and vegetables, spices, bauxite, etc.
• Chem Models New website to access all of BWT's JSmol models, e.g. MOs of N2, CO, CO2, BF3, B2H6; inorganic ring molecules; inversion of cyclohexane - Newcastle University, England
• Chemoinformatics software, Ed Cannon, PhD student, University of Cambridge. The website uses Jmol to illustrate Open Software and 3D molecule visualization.
• ChemSpider Building a structure centric community for chemists. Almost 20 million molecules and using Jmol to display them.
• ChemTube3D "Interactive 3D Organic Reaction Mechanisms and supporting information on reactivity and spectroscopy. By Nick Greeves at the University of Liverpool, UK."
• CheShift "A quantum mechanics database of ¹³C^α chemical shifts for protein structure validation."
• CO Molecular Orbitals Clickable MO energy level diagram for teaching, leading to JSmol/Jmol models showing surfaces and/or contours of MOs. Discussion in terms NAOs from NBO analysis - Newcastle University, England
• CO₂ Molecular Orbitals Clickable MO energy level diagram for teaching, leading to Jmol/JSmol models showing surfaces and/or contours of valence shell orbitals - Newcastle University, England
• CO₂ phase diagram in 3D at Biomodel.UAH.es
• Conformational Epitope Prediction Server - Bioinformatics Centre, University of Pune, India. Shows predicted surface antigenic epitopes in Jmol.
• Cocon on the Web - Generation of constitutions based on NMR correlation data, uses Jmol to visualize the results.
• CoolMolecules - St. Olaf College, USA.
• CoSyM - Continuous Symmetry Measures, The Open University of Israel.
• Crystal Tutorial Project: Vibration modes on a web page using Jmol - Y. Noel, Università di Torino, Italy.
• Crystal Tutorial Project: Nanotube systems - Y. Noel and R. Demichelis, Università di Torino, Italy.
• Cyclohexane Ring Flipping Clickable activation energy diagram for teaching, leading to Jmol/JSmol animated models. Includes twist-boat conformer interconversion - Newcastle University, England

• Dali - Protein structure comparison and database searching. Resulting structural superimpositions viewed using Jmol.
• Data Book of Molecules - Home Page for Learning Environmental Chemistry, Japan
• Diborane Molecular Orbitals Web page for teaching, with discussion of Jmol/JSmol models of molecular orbitals in terms of group theory symmetry representations- Newcastle University, England
• DNA Structure Tutorial - a classic by Eric Martz, converted to Jmol/JSmol by Angel Herráez. Available in 10 languages! Disponible también en español. Também disponível em português. Disponible aussi en français. Auch verfügbar auf Deutsch. Disponibil i în limba română. Anche disponibile in italiano. Również dostępne w języku polskim. Türkçe çevirisi mevcuttur. 进入 中文版. ยังมีอยู่ในไทย. Επίσης διαθέσιμο στα Ελληνικά.
• 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.
• Dr. Gutow's Atomic Orbital Page - Hosted by the University of Wisconsin Oshkosh this site uses Jmol to allow the user to choose and compare atomic orbitals (1s, 2s, 2p, 3s, 3p, 4s, 3d and 4p orbitals).
• Dr. Gutow's Hybrid Atomic Orbital Site - Hosted by the University of Wisconsin Oshkosh this site uses Jmol to allow the user to choose and and compare hybrid atomic orbitals. A general chemistry level explanation is also provided.
• DCU CHIME and Jmol Pages - Dublin City University visitor access page to Molecular Viewing Galleries and organic chemistry tutorials.
• Dutch Dictionary on Organic Chemistry - Radboud University Nijmegen, The Netherlands

• EcoliWiki Wiki-based community annotation of E. coli, its bacteriophages, plasmids, and mobile genetic elements. Jmol used for visualizing proteins with available structures.
• EDinformatics -- Explain it With Molecules This is an interactive site designed for K-12 students.
• Edumol is a JSmol-JSme-based molecular modelling site. It's chemistry and educational functions are optimized for basic and secondary level chemistry education.
• Electron Density Maps shows in JSmol how isomeshes are derived from the one-sigma electron density data, and how temperature (B value) is related to electron density.
• ePlant is a suite of 3D data display modules for integrative systems biology of the model plant Arabidopsis thaliana. Jmol is used to render annotated protein structures and protein-protein interaction networks.
• Erowid chem compare 3d side-by-side comparison of two molecules for many, many psychoactive compounds. Features: dynamic loading of applet without page reload based on user preferences; synchronization of mouse control for both molecules; Highlighting of elements with drop-down menu.
• 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 JSmol 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. Used over 500,000 times. 3D buttons in Nature show newly published structures in FirstGlance.
• 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

• Gallixa skin cream - Gallixa is a skin product that contains gallium maltolate. A molecule of gallium maltolate is visualized in this interactive Jmol presentation.
• GANGSTA+ - GANGSTA+ non-sequential 3D-structure alignment tool
• 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.

• hBar Lab: Computer-aided Chemistry On Demand - First web application for performing molecular modeling calculations including quantum chemistry calculations online. registration required.
• Hemoglobin - A tutorial covering the alpha-2,beta-2 tetramer, heme, binding of molecular oxygen to heme, roles of histidines, secondary structure, amphipathic alpha helices, T<-->R transition morph animations, and polymerization of sickle hemoglobin. Built with the 2018 update of the Jmol Tutorial-Authoring Template.

• IMGT/3Dstructure-DB: IMGT® (http://imgt.cines.fr) is the international ImMunoGeneTics information system, an integrated knowledge resource specialized in the immunoglobulins, T cell receptors, major histocompatibility complex and related proteins of the immune system.
• Inorganic Crystal Structure Database (ICSD) is the world's most extensive database of fully evaluated inorganic crystal structure data. It is produced by the Fachinformationszentrum FIZ Karlsruhe in Germany and the U.S. National Institute of Standards and Technology NIST, with the Jmol interface developed at the Institute Laue-Langevin ILL in France.
• Inorganic Ring and Cage Molecules JSmol/Jmol models of molecular structures to support an undergraduate course about synthesis, structure, symmetry and chirality in non-metal ring and cage chemistry. Each structure has an Answers and Comments button giving points of interest to an inorganic chemist and often discussion of point group symmetry - Newcastle University, England
• Interactive Chromatin Modeling - ICM (I see 'em) Web is the Interactive Chromatin Modeling Webserver at Bishop's Theoretical Molecular Biology Lab that allows users to fold a sequence of DNA into an array of nucleosomes or chromatin.
• ISFI - Integrated Structure Function Innovation Website Jmol viewer in the structure gallery. The Integrated Center for Structure and Function Innovation (ISFI) is an NIH Protein Structure Initiative Specialized Center focused on developing and applying a set of synergistic technologies organized to overcome recognized bottlenecks in structure determination at the key steps of production of soluble protein and protein crystallization.

• J-ICE J-ICE is a web-based Jmol interface forCrystallographic and Electronic Properties. J-ICE can deal with CASTEP, CRYSTAL09 (as well as 06, 03 and 98), GROMOS, QUANTUM ESPRESSO, VASP, Wien2k, FHI-aim, CIF, PDB and many others formats.
• Jena3D Viewer (Jena3D) - Jena3D is a web-based interactive viewer for three-dimensional biopolymer structures, based on Jmol. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, local structure files can be viewed. Jena3D visualizes not only information included in the PDB files but also SCOP, CATH and Pfam domains, SAPs(SNPs), PROSITE motifs and the exon structure mapped onto proteins. It is closely linked to the Jena Library of Biological Macromolecules (JenaLib).
• Jena Library of Biological Macromolecules (JenaLib) - Integrated database on all 3D structures available at the Protein Data Bank (PDB) and the Nucleic Acid Database (NDB). Information from other databases like UniProt, PROSITE and ENSEMBL is mapped onto protein structures. For visualization the closely related Jmol based Jena3D Viewer is used. Jena, Germany
• JnetPlus - Interactive Java viewer for visualization of network structures in form of two- or tree-dimensional graphs.

• k-turn motifs in RNA - The Lilley lab have created a database of known and postulated k-turn sequences and three-dimensional structures. This site provides 1) a database of sequence and structure, as a resource for the RNA community, and 2) a tool to enable the manipulation and comparison of 3D structures where known.

• LANL Protein Feature Accent tool - The HIV database team at Los Alamos National Laboratory website now features a tool for examining the structural placement of sequence features using Jmol. Protein sequences or alignments can be submitted and will be aligned to sequences from selected HIV protein structures; sequence features in the alignment may then be selected with the mouse and corresponding residues will be highlighted on the protein graphic in the Jmol window.
• Librairie de molécules - Molecular model library for science secondary teachers in french, France
• La Chimie par le Web - Public courses for chemistry students - Université du Maine - France

M-Z

Websites Using Jmol: M-Z

Contributors

BruceTattershall, EricMartz, AngelHerraez, Perrim, Ceroni, Ituvi