[Molvis-list] Proteopedia published / fall class prep!

Eric Martz emartz at microbio.umass.edu
Mon Aug 4 17:26:06 EDT 2008

Dear molvis-list,

I announced http://Proteopedia.Org here on May 3, "Proteopedia.Org: A 
Jmol wiki with scene-authoring tools". (See that announcement:
http://www.bioinformatics.org/pipermail/molvis-list/2008q2/000501.html )

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
     * Ligand
     * Non-Standard Residues (see also Standard Residues)
     * Personal favorites
     * PDB file format
     * Protein Data Bank
     * Quality assessment for molecular models
     * R value
     * Resolution
     * 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
Workshops: http://workshops.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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