Compared to Protein Explorer 1 (or RasMol, see
chronology below):
- You don't need to learn any
hand-typed commands to achieve a very high
level of visualization power. The
menus and buttons in
PE's QuickViews
will do nearly everything you need.
But if you have already learned some commands,
or wish to learn them,
you can enter them at will, and use
aliases that greatly simplify typing them!
However,
you will not experience the full power of PE 2 unless
you first try to do everything without typing commands.
- There is a clickable amino acid (or nucleotide) sequence
display that selects and highlights residues or ranges you click,
called Seq3D.
- There is a 1 Hour Tour to get you started,
a FAQ,
and a Help/Index/Glossary with over 200 entries
to help you figure out how to do what you need.
- Educators will find lesson plans and
help with assessment, as well as an extensive
illustrated
Atlas of Macromolecules.
- PE has become an "impressive, integrated
knowledge base".
- Extensive help is displayed automatically for every menu
operation. For example, if you COLOR +/- Charge,
you are told how and where to calculate the charge or pI of your protein on-line.
If you SELECT Nucleic, there is a button to help you
distinguish DNA from RNA.
- PE has molecule-specific links to external
resources, for example to visualize specific oligomers or virus capsids,
or to color by evolutionary conservation or mutation.
- There are new, very powerful "one-click" routines for
visualizing
noncovalent interactions
(DISPLAY Contacts),
cation-pi interactions
(DISPLAY Cation-pi),
salt bridges
(DISPLAY Salt Br.),
and rolling-probe, solvent accessible surfaces
(DISPLAY Surface).
Evolutionarily conserved or hypervariable residues can be identified
with ConSurf, which is integrated with PE.
- These and other features make PE 2 much easier to use, and much
more powerful than PE 1 or RasMol. The beta-releases of PE 2 were
used thousands of times per week and downloaded dozens of times per
day consistently throughout 2000-2002.
Here is a detailed
comparision with RasMol.
- PE 2 works in either Internet Explorer or Netscape, on Windows
or Macintosh. It can also be coaxed to work in
linux or other unix systems.
- Here is the
detailed history of changes
in each beta release.
PE 2 comprises over 60,000 lines of html, javascript, and RasMol script,
making it three times the size of PE 1.
In amount of program code, it now rivals the size of RasMol.
(Chime has well over 100,000 lines of C++.)
Chronology.
Protein Explorer is built upon and depends wholly upon MDL Chime,
which in turn was built upon the open-source code of RasMol.
Feedback to Eric Martz.