[Molvis-list] Making MolSlides is easier in PE 2.76

[Eric Martz]

I have released Protein Explorer 2.76 Alpha, which supercedes version 2.75
Alpha. Most of the improvements in this release concern development of
MolSlides (http://www.MolSlides.Org). MolSlides can still be developed only
in Windows, and only in Firefox, Netscape 7.2, or Mozilla. However, they can
now be saved from an on-line session, and saved (or published) MolSlides can
be imported into an on-line session. Thus, it is no longer required to use a
downloaded copy of Protein Explorer in order to develop MolSlides.

Interactive quick-reference panels now make it easy to include HTML tags or
to color the text in your MolSlides. The text can be in any language,
including japanese
(http://www.umass.edu/microbio/chime/beta/molslides/japanese/).

The explanations of how to develop MolSlides, and how to use them to
save/restore the state of a PE session, have been improved. Many bugs were
fixed. Automated conversion of MolSlides to PiPEs
(http://www.umass.edu/microbio/chime/pe_alpha/protexpl/pipedoc/index.htm)
now works much more reliably.

Full details on the enhancements can be seen by clicking on the version
number at the FrontDoor, then on the link "Complete, Detailed Version
History", or going directly to
http://www.umass.edu/microbio/chime/pe_alpha/protexpl/vers_pe.htm#versionhistory

To get PE 2.76, go to proteinexplorer.org and click on the magenta link to
"2.7 Alpha" near the top of the FrontDoor.

PE 2.76 is downloadable for Windows.
Because MolSlide development is not yet supported on Macs, I have not made a
Mac download.

MolSlides are annotated molecular views saved from PE that display (or
project) like a series of slides. Pressing the spacebar advances to the
next slide. The molecular views can be rotated and zoomed. MolSlides are
made in PE, but can be displayed without PE. Examples are at
http://www.MolSlides.Org.

MolSlides will be useful for research presentations, for educational
tutorials, and because they are so easy to make, for student reports. The
hardest part of making a MolSlide is learning to use PE. Teachers can
assign students to watch the 30 min of Flash Movies that introduce
beginners to PE (the PE Demo). Once you get a useful molecular view in PE,
saving MolSlides from PE involves just a few mouse clicks. No text editing
is involved. You don't need to know anything about HTML or Chime/Jmol
command language or javascript.

PE can export a set of MolSlides in either Chime or Jmol. However, the Jmol
images are not yet faithful to those in Chime (and are sometimes blank).
Fixing this depends on discovering the Chime commands that Jmol doesn't
understand, and adapting PE or Jmol itself, which is a work still in
progress. MolSlides in Jmol can be viewed in Safari OSX, Mozilla on linux,
etc., as well as all common browsers on Windows. Some examples are at
MolSlides.Org.

Thanks to Timothy Driscoll (www.molvisions.com) who worked hard on the PE
Recorder that supports saving molecular views in MolSlides, and built
PE's first supporting CGI program.


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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz

Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
Biochem Structure Tutorials http://MolviZ.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://molvis.sdsc.edu/atlas/atlas.htm
PDB Lite Macromolecule Finder: http://pdblite.org
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       http://bioinformatics.org/mailman/listinfo/molvis-list
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