[Molvis-list] Protein Explorer: Undo, Script Recorder, Presentations

[Eric Martz]

Protein Explorer 2.7 Alpha is now released and freely downloadable from 
http://www.proteinexplorer.org. You must click on the magenta link at the 
top of the PE 2.45 Beta FrontDoor to reach PE 2.7 Alpha. Registration is no 
longer asked of downloaders. This version adds three major capablities:

1. An Undo button. Up to 25 actions can be undone at the click of a button.

2. An automatic Chime command script recorder. You can save any "molecular 
view" and restore it later in PE. The saved scripts are superior in several 
important ways to the scripts automatically generated by RasMol or Chime 
(fewer bugs, much faster, know about surfaces). Scripts saved from PE's 
recorder should also work in Chime, RasMol, and Jmol (minor adjustments 
will probably be required for RasMol and Jmol).

3. Support for Presentations in Protein Explorer (PiPEs). Such 
presentations or tutorials have a series of molecular-view buttons to 
display views chosen by the author. You can move seamlessly from the formal 
presentation to self-directed exploration with PE's tools (e.g. 
QuickViews), and then back to the presentation. This has proven useful in 
answering unanticipated structural questions from the audience during a 
seminar. Complete instructions are provided for using the Script Recorder 
to attach your own views to buttons and constructing tutorials or PiPEs. A 
working template is included, ready for insertion of your content.

A notable feature of PiPEs is that if placed on a server, any person 
viewing them can download each chapter (PDB file) as a single file -- and 
thus the entire presentation or tutorial. All presentation content (html, 
command scripts, javascript) is placed in the header of the PDB file. Since 
Chime's menu makes it easy to save to disk any PDB file it displays, you 
get the entire presentation with the PDB file. This easy downloading 
requires no additional effort from the author. It is my hope that this will 
help to change the present situation in which the vast majority of 
Chime-based tutorials are not downloadable.

These enhancements have literally been years in the making. The Script 
Recorder and Undo button were implemented by Timothy Driscoll, and designed 
by Tim, Frieda Reichsman, and myself. The PiPE mechanism was designed and 
implemented by myself (with feedback gratefully received from dozens of 
students who took my MolVis classes at UMass), and has gone through several 
incarnations before reaching the present design.

These new features are in a preliminary state and do not yet work perfectly 
(hence the "Alpha" designation). The limitations and bugs we have noticed 
and not yet been able to fix are listed. Please give us feedback!

Sincerely, -Eric Martz

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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
Molecular Visualization EMail List (molvis-list):
       http://bioinformatics.org/mailman/listinfo/molvis-list

Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
               http://www.umass.edu/molvis/martz
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