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Professor Emeritus, Chemistry and Biochemistry Department, Messiah College, Mechanicsburg, PA, USA
I used HyperChem in my first venture in biomolecular visualization and computation. I eventually made some tutorials in which information was passed between HyperChem and Toolbook. When I became aware of Chime, I focused most of my work on protein structure and function and used Protein Explorer (PE) and Presentations in PE (PiPEs) as they became available. When MolSlides became a feature of PE, I developed an assignment for biochemistry students to make MolSlides of a protein of their choice. In the early years of this work I received a variety of internal grants from Messiah College, and in more recent years I have been receiving release time from teaching. Realizing that Chime was on its death bed I got serious about learning Jmol during the Summer '07 , and during my Fall '07 sabbatical I ported most of the PiPEs to Jmol and converted the last of the HyperChem scripts to Jmol scripts. For most of this work I used α and β versions of Jmol Tutorial-Authoring Template being made by Eric Martz. My first exposure to Proteopedia was mentoring Emily Forschler as she developed Photosystem II.
- Carbohydrates - Series of pages that focus on aspects of the 3D structure of mono-, di-, and polysaccharides that are not easily illustrated with 2D figures in text books.
- Syn_and_anti_nucleosides - Illustrates the structural difference between the syn and anti configurations of nucleosides and the steric hindrance that is present in the syn configuration of pyrimidine nucleosides.
- Archaeal_Histones - Illustrates the structural features of two histones and the dimer of one of them.
- Collagen - Illustrates the structure of a collagen segment as well as the structure of a mutated tropocollagen.
- Complex III of Electron Transport Chain - After illustration of the structures and relative positions of the active peptides, the reactions of the Q cycle are illustrated and explained.
- User:Karl_Oberholser/PPDK_large - Large frame of a movie of the mechanism of pyruvate phosphate dikinase. The original page with a smaller movie frame and a description of the mechanism is here.
- User:Karl_Oberholser/Phosphoenolpyruvate:Sugar_Phosphotransferase - Large frame of a movie of the mechanism of Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System. The original page with a smaller movie frame and a description of the system and mechanism is here.
Other structures and tutorials available in Jmol
- Klotho Biochemicals in Jmol - A searchable list of common biochemicals whose structures can be displayed conveniently in Jmol.
- Biomodel-3 - 3D structures of carbohydrates, lipids, amino acids, nucleic acids.
- Small Molecules
- Files uploaded by Karl Obeerholser
- Jena3D Viewer