User:Karl Oberholser

From Proteopedia

Karl Oberholser

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.

Proteopedia Pages

Introductory Topics

• Intro._to_Protein_Structure
• 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.

Specific proteins

• Oxymyoglobin
• 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.
• Acetylcholinesterase
• Biomodel-3 - 3D structures of carbohydrates, lipids, amino acids, nucleic acids.

Helpful Pages

• Help:Editing
• Help:Color_Keys
• Help:Copying_FirstGlance_Scenes_into_Proteopedia
• Small Molecules
• Proteopedia:Wishlist
• Proteopedia:Problems
• What's_new
• Template:Button_Toggle_Animation
• Teaching_Strategies_Using_Proteopedia
• Files uploaded by Karl Obeerholser
• Jena3D Viewer
• Special:SandboxReservation

Other Useful sites

• Implementation of Jmol Contact; command
• Making a fake green link