[Molvis-list] PE now makes MolSlides, even in Jmol

Eric Martz emartz at microbio.umass.edu
Thu Jun 16 08:04:26 EDT 2005

I have released Protein Explorer (PE) 2.75 Alpha, with a major new 
capability: MolSlides. I believe MolSlides will be the highest impact 
enhancement in PE's seven-year history. When you go to ProteinExplorer.Org 
you arrive at PE 2.45 Beta (no MolSlides) -- then click on the link at the 
FrontDoor to go to PE Alpha with MolSlides.

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 

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.

Developing and saving MolSlides in this release of PE can be done only in 
Windows, and only with Firefox, Netcape 7.2, or Mozilla (not in Internet 
Explorer, not on Macs), and only with a downloaded copy of PE. We expect to 
be able to support MolSlide creation on IE and Mac (Classic) and with 
on-line PE in a future release.

PE includes a MolSlide Manager that can add text to your molecular views by 
typing into a form, import previously saved sets of MolSlides, merge them 
with new ones, reorder them, and edit, copy, or delete them. You can 
preview the slides, and include authors' credits and copyright statements. 
It can also join two molecular views into a comparator-style slide.

MolSlides have three capabilities that go beyond being an interactive 
molecular slide show.

First, any MolSlide you have saved can be imported and applied to PE. This 
means you can save the state of a PE session very easily. After applying a 
MolSlide to PE, you can continue to explore and modify the applied view, 
perhaps saving additional MolSlides along the way.

Second, a set of MolSlides can be converted to a Presentation in PE (PiPE) 
automatically. Such PiPEs don't utilize the full range of PiPE capablities 
(e.g. animations), but this method of making a PiPE is much easier than by 
hand. And you could then enhance the PiPE manually.

Third, on Windows only, a MolSlide can be incorporated into a PowerPoint 
presentation, with a rotating, zoomable molecular view.

For more information and sample slides, please go to http://www.MolSlides.Org

This version of PE includes a new History dialog, where you can step back 
through the past views of your PE Session, applying any earlier view to the 
current Session.

Special thanks go to Tim Driscoll, who wrote and adapted the PE command 
script recorder, a large project without which MolSlides would not be 
possible. And thanks of course to the Jmol team, especially Miguel Howard, 
for implementing Chime's command language in Jmol. Thanks also to Frieda S. 
Reichsman, whose feedback improved the design of MolSlides, and to the 
National Science Foundation DUE for support.

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

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