Examples
Using Proteopedia to make interactive 3D molecular scenes for projection in lectures
- Teaching Strategies Using Proteopedia includes help on how to get started making your own molecular scenes.
- Quick and simple: Nucleosomes
- More developed: Gramicidin Channel in Lipid Bilayer / Canal de gramicidina en bicapa lipídica.
- A sample lesson for High School students
Preparing molecular structure tutorials for use by students
Examples in Proteopedia.Org:
- Tamiflu and Relenza
- Lac Repressor includes Challenge Questions for Students.
Examples in traditional tutorial format:
- Carbohydrates, lipids, vitamins, amino acids, proteins, nucleic acids, and more: BioModel in English, en español.
- DNA, Hemoglobin, Antibody, Lipid Bilayers & Channels, Collagen, Water, and others: MolviZ.Org. Many en español.
- World Index: MolVisIndex.Org.
Questions for students
- Sample questions that students must answer about any molecule. These questions are from a 5-day (20 hour) course Protein 3D Structure Visualization and Structural Bioinformatics for M.S. graduate students taught at Osaka University by Eric Martz and Keiichi Namba.
- See also the list of tutorials with questions about specific molecules, in the Eric's Strategies section on the Topics page.
Examples of recent or powerful uses of Jmol
- Electron Density Maps
- Morphs: lac repressor, cyclohexane.
- Noncovalent interactions with any designated moiety are easily visualized in FirstGlance in Jmol using its Contacts dialog.
- Side by side comparision with synchronization of mouse rotation/zoom.
- Pockets (View 2).
- Translucency (View 3).
- Interactive minimization and modeling: #145, #146, #149 in Jmol 11 examples.
- Fog metal-ligand polyhedron or #52 at Jmol 11 examples.
- Symmetry operations: Jmol can generate and display the biomolecule, the unit cell, and crystal contacts to the asymmetric unit. Demonstration.
Glossaries of Structural Bioinformatics Terminology
- About Macromolecular Structure in Proteopedia links explanations of topics such as Asymmetric Unit, Biological Unit, Cation-pi internactions, Evolutionary Conservation & ConSurf Server, Intrinsically disordered protein, Molecular Morphing, Protein Data Bank, R factor, Resolution, R-free, Quality assessment for molecular models, and Temperature Factor.
Molecular Workbench ready-to-use materials
page revision: 33, last edited: 14 Sep 2010 14:20