Dear Bob,
I know you'll have way too much but here are some ideas.
At 2/15/08, you wrote:
>Q: What new features would you include?
Maybe not the newest, but dramatic in a presention:
Surfaces, cavities, and molecular orbitals.
Animations.
You might mention that Nature now links every new macromolecular 3D
structure report to FirstGlance in Jmol ("3D View" links). This
started with the Nov 30 2007 issue. Nature Structural and Molecular
Biology started almost 2 years earlier.
Protein Science (the journal) was the first to provide rotatable 3D
visualization and animations with research articles, in the form of
Kinemages by David and Jane Richardson, in volume 1, issue 1, 1992.
(This was pre-Internet! Floppy diskettes were mailed out with
issues!) A few years later, this journal (not the Richardsons!)
regrettably abandoned their leadership in this area.
( http://www.umass.edu/microbio/rasmol/history.htm#mage )
Frieda Reichsman's recent work has brought an end to the 15-year
hiatus in this technology:
"Journal Figures Come to Life as 3D Replicas" -- so far, in
Biochemical Journal and ACS Chemical Biology
(http://moleculesinmotion.com/#figures ).
Note that Frieda's work involves hand-crafting, on a figure-by-figure
basis, for a few high-impact figures, rotatable/zoomable 3D
renderings in Jmol of the author's structure figures in the journal.
In contrast, Nature has links to show every new PDB file in
FirstGlance in Jmol, where it is up to the viewer to explore in a
self-directed manner.
>Q: Do you have a URL that might be highlighted? (Don't be shy!)
http://www.bioinformatics.org/jmol-tutorials/jtat/jtatdemo/ch_view2/chapter.htm
View 2 shows both a surface (as a mesh) and a cavity (opaque surface)
for a molecule of current broad interest: tamiflu binding to the N1
neuraminidase of bird flu (of possible pandemic fame). The cavity was
a surprise and the authors propose it could be a target for a better
anti-flu drug.
http://www.umass.edu/molvis/martz/lectures/labmolgen07/mj3.htm
animates the binding of tamiflu to bird flu N1, showing how the fit
is induced during binding.
Background on this story for a quick brush up:
http://www.umass.edu/molvis/martz/lectures/labmolgen07/n1tami.htm
>Q: Do you want to say something about how Jmol solved some particular
>problem in molecular visualization that you have had?
1. Yeah .... it has single-handedly given rebirth to my (second) career!
2. Jmol provided a great solution for Alexey Porollo to make it easy
for users to specify an orientation and center in his website that
uses a simple form to generate publication-quality images (and
animations) with PyMol (http://polyview.cchmc.org/polyview3d.html )
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz
Top Five 3D MolVis Technologies http://Top5.MolviZ.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):
http://bioinformatics.org/mailman/listinfo/molvis-list
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