Websites Using Jmol: M-Z - Revision history

Ituvi at 21:41, 15 February 2023

2023-02-15T21:41:53Z

Fuster at 08:10, 14 October 2022

2022-10-14T08:10:50Z

BruceTattershall: Change of address of page

2022-07-29T17:34:43Z

Change of address of page

BruceTattershall: Change of address of page

2022-07-29T17:05:38Z

Change of address of page

BruceTattershall: Change of address of page

2022-07-29T17:00:41Z

Change of address of page

BruceTattershall: Change of address of page

2022-07-28T18:20:26Z

Change of address of page

BruceTattershall: New website for Bruce Tattershall

2022-06-18T19:00:47Z

New website for Bruce Tattershall

Ceroni at 13:54, 25 June 2021

2021-06-25T13:54:07Z

AngelHerraez: 3D phase diagrams

2021-06-18T22:57:16Z

3D phase diagrams

EricMartz: Move 'Reaction mechanisms ...' from the very top to the R section.

2021-01-03T22:17:25Z

Move 'Reaction mechanisms ...' from the very top to the R section.

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 * [http://www.stolaf.edu/people/hansonr/mo/acs2001/models.htm Molecular Origami] ''Precision Scale Models from Paper. View the model using Jmol or make it out of paper yourself. - St. Olaf College]
 * [http://www.medicalcomputing.net/endocrine.html Molecular Structure of Hormones in the Human Body (Medical Computing .Net)] - Irvine, USA
 * [http://www.ufrgs.br/bioquimica Moléculas Interativas] Faculdade de Veterinária - Universidade Federal do Rio Grande do Sul - Porto Alegre - Brazil (in portuguese)
 * [http://cheminf.cmbi.ru.nl/wetche/vwo/cdrom05/jmol/ 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.''

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 * [http://bip.weizmann.ac.il/oca 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.
 * [http://www.clunet.edu/BioDev/omm/gallery.htm 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.''
-* [http://www.lct.jussieu.fr/pagesperso/orbimol OrbiMol] - Theoretical Chemistry Laboratory, Pierre and Marie Curie University, UPMC Paris VI / CNRS UMR 7616. ''Molecular orbital database for teaching, vibrations and topological approach of small molecules.'' [in Multi-Languages].
+* [http://www.lct.jussieu.fr/pagesperso/orbimol 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].
 * [http://winter.group.shef.ac.uk/orbitron/ 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
 * [http://molecularmodels.ca/nomenclature/nom1.htm 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).

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 * 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.
 * [https://teaching.ncl.ac.uk/chemmodels/teaching/orbitals/peroxidemo/perox.php 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''
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/maingrps/pf3mo/pf3.php 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/maingrps/pf3mo/pf3.php 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''
 * [http://pocketquery.csb.pitt.edu PocketQuery] - Protein-protein interaction (PPI) inhibitor starting points from PPI structure. University of Pittsburgh.
 * [http://chemweb.chem.fsu.edu/editors/rlight/polyhedra/index.html 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.

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 * [http://p53.bii.a-star.edu.sg/ p53 Knowledgebase] - Bioinformatics Institute (Singapore)
 * [http://molviz.org/pacupp PACUPP]: Pockets And Cavities Using Pseudoatoms in Proteins. A user-friendly application written entirely in Jmol command scripts.
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/maingrps/pf3mo/pf3bf3/pf3bf3.php 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/maingrps/pf3mo/pf3bf3/pf3bf3.php 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''
 * [http://pfp.technion.ac.il/ PatchFinderPlus] is an automatic server to extract and display the largest positive electrostatic patch on a protein surface. Uses JmolApplet to display results.
 * [http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ 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.
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/orbitals/peroxidemo/perox.php 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/orbitals/peroxidemo/perox.php 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''
 * [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/maingrps/pf3mo/pf3.php 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''
 * [http://pocketquery.csb.pitt.edu PocketQuery] - Protein-protein interaction (PPI) inhibitor starting points from PPI structure. University of Pittsburgh.

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-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/orbitals/n2mo/n2.php N<sub>2</sub> 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/orbitals/n2mo/n2.php N<sub>2</sub> 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''
 * [http://www1.na.infn.it/cmg/Ninno/index.php?n=Software.Vis Nanocrystal Visualization Tool] - Web interface for the visualization of semiconductor nanocrystals - University of Naples, Italy.
 * [http://nanocrystallography.research.pdx.edu/ 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

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 * [http://www.scheikundeolympiade.nl/Stereo.html 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.
 * [http://www.scicom.demon.co.uk Structure and reaction mechanism of RUBISCO] ''A Rubisco tutorial with a Jmol version.''
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/tm/tmsubst/inorgsubst.php 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/tm/tmsubst/inorgsubst.php 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''
 * [http://www.stolaf.edu/people/hansonr/sudoku Sudoku Assistant] ''Uses Jmol to visualize the three-dimensional logical chains of Sudoku puzzles.''
 * [http://bioinf-tomcat.charite.de/superligands/ 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.

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 {{Anchor|V}}
 * [http://viperdb.scripps.edu/ 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.
 * [http://www.cem.msu.edu/~reusch/vtxtindex.htm 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.

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-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/orbitals/n2mo/n2.php 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''
+* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/orbitals/n2mo/n2.php N<sub>2</sub> 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''
 * [http://www1.na.infn.it/cmg/Ninno/index.php?n=Software.Vis Nanocrystal Visualization Tool] - Web interface for the visualization of semiconductor nanocrystals - University of Naples, Italy.
 * [http://nanocrystallography.research.pdx.edu/ 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
 * [http://nasim.ccms.elf.stuba.sk/redirectors/2nasim.html 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.''
-* [http://phm.utoronto.ca/~jeffh/neuromouse.htm 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). ''
+* [http://phm.utoronto.ca/~jeffh/neuromouse.htm 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).''
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 * [http://www.lsbu.ac.uk/water/index.html Water structure and science] - Martin Chaplin reference website about water science. Jmol is used as the main viewer.
 * [http://wwmm.ch.cam.ac.uk/Bob World Wide Molecular Matrix] - Unilever Centre at Cambridge, UK (2006/04/12 file not found)

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 {{Anchor|M}}
 * [http://ich.vscht.cz/projects/mmview/ mmView] ''Web-based viewer of the mmCIF files''. - Lab. of Informatics and Chemistry, ICT Prague, Czech Republic.
 * [http://modeome3d-pbil.ibcp.fr/ Modeome3D database] - Homology 3D-models database with Jmol integrated tools.
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 * [http://ci.vbi.vt.edu/cammer/schism2.html 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.
 * [http://www.sciencestuff.com Science Stuff, Inc.] - ''uses Jmol to present 3-d structures of chemical compounds in their chemicals catalog.''