Websites Using Jmol: M-Z

Jmol / JSmol Applications

• Websites Using J(S)mol
• J(S)mol in the Classroom
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  Course Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms
• Applications Embedding Jmol
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• Blue Obelisk

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

M N O P Q R S T U V W X Y Z

For Websites A-L, see Websites Using Jmol.

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• mmView Web-based viewer of the mmCIF files. - Lab. of Informatics and Chemistry, ICT Prague, Czech Republic.
• Modeome3D database - Homology 3D-models database with Jmol integrated tools.
• MOFomics: Metal-Organic Frameworks Characterization - Princeton University, Princeton, NJ, USA
• Mol4D - CMBI, Radboud University Nijmegen, The Netherlands Tutorials Organic Chemistry and Molecule editor/Mopac interface.
• Molecular Models Many models available sorted by functional group, name, or formula. A tutorial in organic nomenclature is also at this site.
• 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
• Molecular Symmetry Online - The Open University of Israel
• Moléculas Interativas Faculdade de Veterinária - Universidade Federal do Rio Grande do Sul - Porto Alegre - Brazil (in portuguese)
• 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 at Bristol University Interesting facts about molecules written by contributors from all over the world.
• Molecule of the Month at RCSB PDB Presenting short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. Same contents translated into Japanese also available from here
• The Molmodac Project - University of Illinois A biorganic chemistry project describing the molecular mechanisms of action of a variety of small organic molecules
• MolnQuiry Dept of Biology, Marietta College, Marietta Ohio. An educational site presenting the structural properties of biological molecules in an interactive, task-oriented learning environment
• Molevision Molevision, to rhyme with television, is a simple site designed to help students taking their first university modules in organic chemistry.
• MolVisions Custom physical models of molecules.
• MolviZ.Org offers tutorials on DNA Structure, Hemoglobin, Lipid Bilayers and Channels, Collagen, and other Jmol-based and cross-platform resources for education and research.
• MSD ligand chemistry - European Bioinformatics Institute, UK

• N₂ Molecular Orbitals Clickable MO energy level diagram for teaching, leading to JSmol/Jmol models showing surfaces and/or contours of MOs. Tables of coefficients etc. of Natural Atomic Orbitals, with optional stepwise LCAO explanation of s-p mixing - Newcastle University, England
• Nanocrystal Visualization Tool - Web interface for the visualization of semiconductor nanocrystals - University of Naples, Italy.
• Nano-Crystallography Open Access Database - The goal of this project is to provide 3D visualizations of crystal structures and morphologies in order to help educate future materials scientists and engineers worldwide. Portland State University
• 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.
• NeuroMouse - University of Toronto; Toronto, Canada. Neuromouse - is an interactive object-oriented database of information on the mouse nervous system. Jmol viewers are employed to allow users to visualize key proteins in important signal transduction pathways such as those which govern the process of programmed cell death (apoptosis).
• NH₃ phase diagram in 3D at Biomodel.UAH.es

• OCA - OCA, a browser/database for protein structure and function at the Weizmann Institute, Israel and several mirror sites around the world; offers a convenient interface for searching the Protein Databank (PDB) and uses Jmol to show results.
• 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.
• OrbiMol - Theoretical Chemistry Laboratory, Sorbonne Université, Faculté des Sciences et Ingénierie / CNRS UMR 7616, Paris, France. Molecular orbital database for teaching, vibrations and topological approach of small molecules. [in Multi-Languages].
• 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
• Organic Nomenclature - Learn how to name organic molecules using the IUPAC system; learn how to recognise, draw and name stereoisomers (E/Z, R/S, M,P).

• p53 Knowledgebase - Bioinformatics Institute (Singapore)
• PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins. A user-friendly application written entirely in Jmol command scripts.
• Pairwise Comparison of Corresponding MOs of PF3 and BF3 Clicking a line of an illustrated table gives side-by-side JSmol applets showing orbital surfaces for the two molecules - Newcastle University, England
• PatchFinderPlus is an automatic server to extract and display the largest positive electrostatic patch on a protein surface. Uses JmolApplet to display results.
• PDBsum - European Bioinformatics Institute, UK
• Periodic Table Live! www.chemeddl.org/collections/ptl/ - allows you to explore a broad range of information about the elements, their reactions, their properties, their structures and their histories. Hosted at the Chemical Education Digital Library.
• Peroxide Ion Molecular Orbitals Clickable MO energy level diagram for teaching, leading to JSmol/Jmol models showing surfaces and/or contours of MOs. Tables of coefficients etc. of Natural Atomic Orbitals and comparison of s-p mixing with the N2 case - Newcastle University, England
• PF3 Molecular Orbitals Clickable MO energy level diagram for teaching, leading to JSmol/Jmol models showing surfaces and/or contours of valence shell orbitals - Newcastle University, England
• PocketQuery - Protein-protein interaction (PPI) inhibitor starting points from PPI structure. University of Pittsburgh.
• Polyhedra structures Links to the five Platonic solids and to a truncated icosahedron, all with colored faces, and a link to the C60 buckminsterfullerene structure.
• POLYVIEW-3D - Automated annotation and visualization of macromolecular structures - University of Cincinnati and Cincinnati Children's Hospital Research Foundation, USA
• Pore Behaviour - Explore the world of microporous materials and even fly through some of them!
• PROPKA server PROPKA server for protein pKa predictions
• ProSAT⁺ is a tool to explore the relation between sequence and structural properties. It displays molecular structures from RCSB along with annotations from Uniprot, so it can be used to map and visualize sequence annotations onto a structure.
• 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.
• Protein Workbench STRAP Simultaneously displays sequence alignments and 3d-Structures.
• PROTEOPEDIA: The collaborative, 3D encyclopedia of proteins and other molecules

• 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.
• Química Orgánica en 3D – an undergoing project to illustrate different aspects of structure, stereochemistry and reactivity of Organic Molecules (in Spanish) by Carlos Valdés – Universidad de Oviedo (Spain)
• QUIRAL Site about chirality.

• RESP ESP charge DDataBase, R.E.DD.B. R.E.DD.B. is a database of RESP and ESP charges of high quality and reproducibility, and force field libraries for small molecules and molecular fragments: A database for computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies. Université de Picardie Jules Verne - Burnham Institute for Medical Research.
• RNA FRABASE 2.0 RNA FRAgments search engine & dataBASE - an engine with database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.
• Romanian Database of Raman Spectroscopy This database contains mineral species (natural and synthetic) with description of crystal structure, sample image, number of sample, origin, Raman spectrum and vibrations, Raman discussion and references. Also, this site contains artefacts sample with sample image and pigment spectrum; black, red, white or blue pigment. rdrs.uaic.ro
• Rome Center for Molecular Design RCMD - we use Jmol to view 3-D models of new potential drugs - Rino Ragno, Roma, ITA.
• RosettaBackrub RosettaBackrub - a webserver which allows users to perform flexible backbone protein structure modeling and design. We use Jmol to visualize the structures after a backrub or protein design.

• Reaction mechanisms in Inorganic Chemistry | Mecanismos de reacción en química inorgánica 3D-Mechanisms of Inorganic Reactions (in English and Spanish) - A site that presents Jmol animations of inorganic reaction mechanisms.- University of Valencia, Spain
• SChiSM2 Authoring tool: Use a web browser form to create a web page containing a series of molecular views in Jmol with buttons and descriptions. Requires knowledge of Jmol script language, but neither HTML nor javascript. You can save your project to a file and load it later.
• Science Stuff, Inc. - uses Jmol to present 3-d structures of chemical compounds in their chemicals catalog.
• SPPIDER - Analysis and prediction of protein-protein interaction sites - University of Cincinnati and Cincinnati Children's Hospital Research Foundation, USA
• SSFA-GPHR - SSFA-GPHR is a database for semi-quantitative Sequence- Structure- and Function- Analysis of GPHRs - Jmol is used for structure-based searches of mutation data, visualization of single, double and triple mutations and animations of structural morphings
• Stereochemistry - Learn how to name organic molecules using the IUPAC system; learn how to recognise, draw and name stereoisomers (E/Z, R/S, M,P).
• Stereomutation of Pentavalent Compounds Animations of the three principal mechanisms for the interconversion of stereoisomers with a trigonal bipyramidal atom - Dr. Erik P.A. Couzijn.
• Structure and reaction mechanism of RUBISCO A Rubisco tutorial with a Jmol version.
• Substitution Reactions in Metal Complexes Consecutive JSmol animations, to and from an intermediate, for dissociative substitution in octahedral, or associative substitution in square planar, complexes. Not calculated reaction paths, but interesting for teaching
• Sudoku Assistant Uses Jmol to visualize the three-dimensional logical chains of Sudoku puzzles.
• SuperLigands - an encyclopedia dedicated to a ligand oriented view of the protein structural space. The database contains small molecule structures occurring as ligands in the Protein Data Bank. SuperLigands integrates different information about drug-likeness or binding properties. A 3D superpositioning algorithm is implemented that allows to screen all ligands for possible scaffold hoppers as well as a 2D similarity screen for compounds based on fingerprints.
• SwarmDock Server A server for flexible protein-protein docking.
• Symmetry Resources at Otterbein - includes Symmetry Tutorial, an introduction to point group symmetry that uses Jmol to visualize symmetry elements and operations, and The Symmetry Gallery, an interactive collection of over 60 unique molecules with interactive display of all symmetry elements and animation of all operations. (Outstanding animated effects!)

• 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.
• Top Five 3D Molecular Visualization Technologies for the Rest of Us - Tutorials, a Tutorial-Authoring Template, a Self-Directed Molecular Exploration Tool (FirstGlance in Jmol), a tool for Seeing Protein Evolution (ConSurf), all in Jmol, plus an easy web form for generating publication-quality custom molecular views or powerpoint-ready animations (uses PyMol).
• TopMatch-web - Center of Applied Molecular Engineering, University of Salzburg, Austria. Public web service for the alignment and superposition of protein structures and the instant visualization of structural similiarities.
• Transition Metal Chemistry Courses for 1st and 2nd year University students - University of the West Indies, Mona, Jamaica. Includes; coordination chemistry, crystal field theory, spectroscopy and magnetism, Java applets for display of Tanabe-Sugano diagrams and JCAMP-DX files.
• 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
• Tutorial-Authoring Template (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.

• 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

• Vibrations of Phosphorus Chloride Species Page which reads output files from Gaussian freq jobs and allows selection of a vibration mode for display as a JSmol animated model. No tutorial content, but may be useful to teachers or learners as examples - Newcastle University, England
• VIrus Particle ExploreR - VIPERdb at The Scripps Research Institute. Enter the world of Icosahedral (isometric) Viral Capsids. We are interested in the study of capsid formation through the analysis of protein-protein interactions. Jmol helps visualize the symmetrical arrangements these proteins take when fully assembled into the viral capsid. It also serves as an educational tool to help understand concepts as the triangulation number (T), icosahedral symmetry, etc. To see it in action, access an entry info page for a particular virus (for example PDB-ID 2bbv) and open the IAU (Icosahedral Asymmetric Unit) tab.
• 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.
• Visualizations in Chemistry | Visualizaciones en química (in English and Spanish) - A site that uses Jmol to display selected chemical structures, inorganic reaction mechanisms, concept tests, simulations of processes and nomenclature.- University of Valencia, Spain

• Water phase diagram in 3D at Biomodel.UAH.es
• Water structure and science - Martin Chaplin reference website about water science. Jmol is used as the main viewer.
• World Wide Molecular Matrix - Unilever Centre at Cambridge, UK (2006/04/12 file not found)
• WebTB.org - Public resource for information on TB Structural genomics Jmol viewer in the structure gallery. Part of the TB Structural Genomics Consortium, WebTB.org is a public resource for information on TB proteins, published protein structures, protein homology, and structural genomics efforts and progress.

• XdomView - National University of Singapore

• Yeast snoRNA Database - University of Massachusetts, Amherst. A comprehensive database of S. cerevisiae H/ACA and C/D box small nucleolar RNAs.

• ZEOMICS: Zeolites and Microporous Structures Characterization - Princeton University, Princeton, NJ, USA
• 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
• ZincPharmer - Online interactive pharmacophore search software for screening the ZINC database. University of Pittsburgh.

A-L

Websites Using Jmol: A-L

Contributors

BruceTattershall, EricMartz, AngelHerraez, Ituvi, Fuster, Ceroni