User:Karl Oberholser: Difference between revisions

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''It is with great sadness that we report the death of [[Karl Oberholser]] on July 25, 2013. Karl was an innovator in educational molecular visualization, and a member of the [[Proteopedia:Team|Editorial Board of Proteopedia.Org]]. He will be greatly missed.'' [[User:Eric Martz|Eric Martz]] 01:55, 28 July 2013 (IDT)
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==Karl Oberholser==
==Karl Oberholser==
[[Image:Karl 6-08_2.jpg|right|150px]]
[[Image:Karl 6-08_2.jpg|right|150px]]
Professor of Chemistry, Chemistry and Biochemistry Department, Messiah College, Grantham, PA, USA
Professor Emeritus, Chemistry and Biochemistry Department, Messiah College, Mechanicsburg, PA, USA
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''<email>oberhols@messiah.edu</email>''<p>
''<email>oberhols@messiah.edu</email>''<p>
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 and 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 &alpha; and &beta;  versions of Jmol Tutorial-Authoring Template being made by Eric Martz. My first exposure to Proteopedia was mentoring [[User:Emily_Forschler|Emily Forschler]] as she developed [[Photosystem II]].
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 &alpha; and &beta;  versions of Jmol Tutorial-Authoring Template being made by Eric Martz. My first exposure to Proteopedia was mentoring [[User:Emily_Forschler|Emily Forschler]] as she developed [[Photosystem II]].


==Proteopedia Pages==
==Proteopedia Pages==
*[[Fibroins]]  
Introductory Topics
*[[Alpha-helical coiled-coil]]
* [[Intro._to_Protein_Structure]]
*[[Class of globular proteins]]
* [[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.
*[[Myoglobin]]
* [[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.
*[[User:Karl_Oberholser/Ramachandran_Plots]]
Specific proteins
*[[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 [[Pyruvate_phosphate_dikinase|here]].
*[[Oxymyoglobin]]
*[[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 [[Enzyme_I_of_the_Phosphoenolpyruvate:Sugar_Phosphotransferase_System|here]].  
*[[Archaeal_Histones]] - Illustrates the structural features of two histones and the dimer of one of them.
*[[Complex III of Electron Transport Chain]] - under construction
*[[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 [[Pyruvate_phosphate_dikinase|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 [[Enzyme_I_of_the_Phosphoenolpyruvate:Sugar_Phosphotransferase_System|here]].
 


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==Other tutorials running in Jmol==
==Other structures and tutorials available in Jmol==
*[http://www.messiah.edu/molscilab/Jmol/collagen/collagen_index.htm Collagen]
*[http://chemapps.stolaf.edu/klotho Klotho Biochemicals in Jmol] - A searchable list of common biochemicals whose structures can be displayed conveniently in Jmol.
*[http://www.messiah.edu/molscilab/jtat_080120/acetylcholinesterase/contents/contents.htm Acetylcholinesterase]
*[http://www.messiah.edu/molscilab/jtat_080120/acetylcholinesterase/contents/contents.htm Acetylcholinesterase]
*[http://www.messiah.edu/molscilab/index_sub_carbo.htm Carbohydrates] - Series of tutorials that focus on aspects of the 3D structure of mono-, di-, and polysaccharides that are not easily illustrated with 2D figures in text books.
*[http://biomodel.uah.es/en/model3/index.htm Biomodel-3] - 3D structures of carbohydrates, lipids, amino acids, nucleic acids.
 
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== Helpful Pages ==
*[[Help:Editing]]
*[[Help:Color_Keys]]
*[[Help:Copying_FirstGlance_Scenes_into_Proteopedia]]
*[http://proteopedia.org/tools.html Small Molecules]
*[[Proteopedia:Wishlist]]
*[[Proteopedia:Problems]]
*[[What's_new]]
*[[Template:Button_Toggle_Animation]]
*[[Teaching_Strategies_Using_Proteopedia]]
*[http://proteopedia.org/wiki/index.php?limit=100&title=Special%3AContributions&contribs=user&target=Karl+Oberholser&namespace=6&year=&month=-1 Files uploaded by Karl Obeerholser]
*[http://jena3d.fli-leibniz.de/ Jena3D Viewer]
*[[Special:SandboxReservation]]


== Useful Proteopedia Pages ==
== Other Useful sites ==
*[[Help:Editing]]
* [http://stolaf.edu/people/hansonr/jmol/contact/ligand.htm Implementation of Jmol '''Contact;''' command]
* [http://proteopedia.org/wiki/index.php/User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring Making a fake green link]

Latest revision as of 01:55, 28 July 2013

It is with great sadness that we report the death of Karl Oberholser on July 25, 2013. Karl was an innovator in educational molecular visualization, and a member of the Editorial Board of Proteopedia.Org. He will be greatly missed. Eric Martz 01:55, 28 July 2013 (IDT)


Karl OberholserKarl Oberholser

Professor Emeritus, Chemistry and Biochemistry Department, Messiah College, Mechanicsburg, PA, USA

oberhols@messiah.edu

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 PagesProteopedia 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



Other structures and tutorials available in JmolOther structures and tutorials available in Jmol


Helpful PagesHelpful Pages

Other Useful sitesOther Useful sites

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