[Molvis-list] Proteopedia published / fall class prep!
emartz at microbio.umass.edu
Mon Aug 4 17:26:06 EDT 2008
I announced http://Proteopedia.Org here on May 3, "Proteopedia.Org: A
Jmol wiki with scene-authoring tools". (See that announcement:
Proteopedia has now been published online at http://genomebiology.com
(it is currently the first paper at the main page), and is in press.
I remain very enthusiastic about Proteopedia. In my short courses, I
teach researchers and students to use it as the website of first
resort for exploring a macromolecular structure. One of several
convenience links at Proteopedia will display the molecule in
question in FirstGlance in Jmol for further exploration.
Proteopedia is the quickest and easiest place to prepare interactive
molecular scenes for projection in classes, or for use by students.
You can protect such scenes from editing by others if you wish. Any
scenes you create are immediately viewable by anyone, and searchable.
Karl Oberholser had authored a great interactive page on Ramachandran
Plots for students. See
Biochem majors can author pages in Proteopedia as class or research
projects. An outstanding page on Photosystem II was authored by Emily
Forschler in the spring, while a senior at Messiah College.
Her Professor, Karl Oberholser, reported:
"I think that Emily's work on Photosystem II shows that Proteopedia
is a system that a Jmol novice can use with good effect. Emily had no
experience with using Jmol. The other students in the class ...
[made] PowerPoint presentations of their chosen proteins, and after
seeing Emily's Proteopedia presentation one student's response was
all of us should have used Proteopedia."
Recently I have drafted a series of pages in Proteopedia introducing
topics such as
* Asymmetric Unit
* Atomic Coordinate File
* Biological Unit
* Conservation, Evolutionary
* Free R
* Highest impact structures
* Non-Standard Residues (see also Standard Residues)
* Personal favorites
* PDB file format
* Protein Data Bank
* Quality assessment for molecular models
* R value
* Sites, Functional
* Standard Residues (see also Non-Standard Residues)
* Temperature value
You can find links to these and others here:
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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz
Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
Biochem 3D Education Resources http://MolviZ.org
See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
Protein Explorer - 3D Visualization: http://proteinexplorer.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.proteinexplorer.org
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
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