Websites Using Jmol: A-L - Revision history

Ituvi at 21:47, 15 February 2023

2023-02-15T21:47:27Z

BruceTattershall: Change of address of page

2022-07-29T17:19:50Z

Change of address of page

BruceTattershall: Change of address of page

2022-07-29T16:55:10Z

Change of address of page

BruceTattershall: Change of address of page

2022-07-29T16:50:29Z

Change of address of page

BruceTattershall: Change of address of page

2022-07-29T16:44:27Z

Change of address of page

BruceTattershall: Change of address of page

2022-07-28T18:10:14Z

Change of address of page

BruceTattershall: Change of address of page

2022-07-28T17:56:32Z

Change of address of page

Perrim: Add ChemCompute

2022-03-23T01:48:24Z

Add ChemCompute

BruceTattershall: New website for Bruce Tattershall

2022-03-21T19:47:48Z

New website for Bruce Tattershall

Ceroni at 13:50, 25 June 2021

2021-06-25T13:50:17Z

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 * [http://cocon.nmr.de Cocon on the Web] - Generation of constitutions based on NMR correlation data, uses Jmol to visualize the results.
 * [http://www.stolaf.edu/depts/chemistry/mo/struc/ CoolMolecules] - St. Olaf College, USA.
 * [http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/webvib/index.html Crystal Tutorial Project: Vibration modes on a web page using Jmol] - Y. Noel, Università di Torino, Italy.
 * [http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/nanotube/nanotube.html Crystal Tutorial Project: Nanotube systems ] - Y. Noel and R. Demichelis, Università di Torino, Italy.

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 * [http://ekhidna.biocenter.helsinki.fi/dali/ Dali] - Protein structure comparison and database searching. Resulting structural superimpositions viewed using Jmol.
 * [http://www.ecosci.jp/ec.html Data Book of Molecules] - Home Page for Learning Environmental Chemistry, Japan
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/maingrps/b2h6mo/b2h6.php 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/maingrps/b2h6mo/b2h6.php 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''
 * [http://biomodel.uah.es/en/model4/dna/ DNA Structure Tutorial] - a classic by [[User:EricMartz|Eric Martz]], converted to Jmol/JSmol by [[User:AngelHerraez|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.
 * [http://www.uwosh.edu/faculty_staff/gutow/VSEPR_TUTORIAL/VSEPR.html 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.

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 * [http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/webvib/index.html Crystal Tutorial Project: Vibration modes on a web page using Jmol] - Y. Noel, Università di Torino, Italy.
 * [http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/nanotube/nanotube.html Crystal Tutorial Project: Nanotube systems ] - Y. Noel and R. Demichelis, Università di Torino, Italy.
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/structural/cc6/cc6anim.php Cyclohexane Ring Flipping] ''Clickable activation energy diagram for teaching, leading to Jmol/JSmol animated models. Includes twist-boat conformer interconversion - Newcastle University, England''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/structural/cc6/cc6anim.php Cyclohexane Ring Flipping] ''Clickable activation energy diagram for teaching, leading to Jmol/JSmol animated models. Includes twist-boat conformer interconversion - Newcastle University, England''

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 * [http://www.chemtube3d.com/ ChemTube3D] "Interactive 3D Organic Reaction Mechanisms and supporting information on reactivity and spectroscopy. By Nick Greeves  at the University of Liverpool, UK."
 * [http://www.cheshift.com/ CheShift] "A quantum mechanics database of <sup>13</sup>C<sup>α</sup> chemical shifts for protein structure validation."
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/maingrps/como/co.php 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/maingrps/como/co.php 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''
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/orbitals/co2mo/co2.php CO<sub>2</sub> 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/orbitals/co2mo/co2.php CO<sub>2</sub> 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''
 * [http://biomodel.uah.es/Jmol/plots/phase-diagrams/inicio.htm?mol=co2 CO<sub>2</sub> phase diagram in 3D] at Biomodel.UAH.es
 * [http://bioinfo.ernet.in/cep.htm Conformational Epitope Prediction Server] - Bioinformatics Centre, University of Pune, India. Shows predicted surface antigenic epitopes in Jmol.

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 *[http://fenix.cecalc.ula.ve/moleculas/ 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 [[User:einarabelc5| Einar Coutin]], Universidad de Los Andes (Venezuela).
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/maingrps/bf3mo/bf3.php 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/maingrps/bf3mo/bf3.php 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''
 * [http://www.rosalindfranklin.edu/cms/biochem/Walters/psf.html 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).
 * [http://biomodel.uah.es/ 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 [[User:AngelHerraez|Angel Herráez]], Universidad de Alcalá (Spain). Also some sections duplicated in English. -- User may choose Jmol or JSmol.

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 * [http://imgt.cines.fr IMGT/3Dstructure-DB]: IMGT&reg; (http://[http://imgt.cines.fr 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.
 * [http://icsd.fiz-karlsruhe.de/icsd/ 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.
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/ringsandcages/models.php 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/ringsandcages/models.php 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''
 * [http://dna.ccs.tulane.edu/icm Interactive Chromatin Modeling] - ICM (I see 'em) Web is the Interactive Chromatin Modeling Webserver at [http://dna.ccs.tulane.edu Bishop's Theoretical Molecular Biology Lab] that allows users to fold a sequence of DNA into an array of nucleosomes or chromatin.
 * [http://techcenter.mbi.ucla.edu/Gallery/jmol.php 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.

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 * [http://anchorquery.ccbb.pitt.edu/ AnchorQuery] Specialized pharmacophore search for targeting protein-protein interactions with MCR chemistry.  University of Pittsburgh.
-* [https://www.staff.ncl.ac.uk/bruce.tattershall/teaching/ugmodels/modellist.html 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''
+* [https://teaching.ncl.ac.uk/chemmodels/teaching/ugmodels/modellist.html 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''
 * [http://www.aptanomics.com/ Aptanomics Intranet] ''The Jmol applet is used to explore the structure of molecules in our database.'' - Aptanomics SA, Lyon, France.
 * [http://av.bmbq.uma.es/bma/apuntes/index.htm Apuntes de Biología Molecular] ''by M. Gonzalo Claros'' - Universidad de Málaga, Málaga (Spain).

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 * ChemEd DL's [http://chemdata.r.umn.edu/models360 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.''
 * [http://www.chemexper.com/ ChemExper Chemical Directory] ''A database containing over 500000 molecules, 10000 IR and 70000 3D models that can be visualized using Jmol.''

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 * [http://chemistry-development-kit.org/ CDK Web] ''Show case for functionality in the Chemistry Development Kit. The website uses Jmol for generated rendering 3D structures.''
 * [http://wwwchem.uwimona.edu.jm/lectures Chemistry of Things Jamaica] - University of the West Indies, Mona, JAMAICA, Includes; ''Coffee, sugar and rum, fruit and vegetables, spices, bauxite, etc.''
 * [http://chemoinformatician.co.uk/main/ChemoinformaticsSoftware.html Chemoinformatics software], Ed Cannon, PhD student, University of Cambridge. The website uses Jmol to illustrate Open Software and 3D molecule visualization.
 * [http://www.chemspider.com/ ChemSpider] ''Building a structure centric community for chemists. Almost 20 million molecules and using Jmol to display them.''

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 * [http://www.hiv.lanl.gov/content/sequence/PROTVIS/html/protvis.html 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.
 * [http://www.librairiedemolecules.education.fr/ Librairie de molécules] - Molecular model library for science secondary teachers in french, France