Downloading and Installation of Protein Explorer
for the Macintosh PPC
If you are using an Intel Mac, the downloads below will not work.
You will need Windows (see parallels.com)
in order to run PE because Classic/OS9 is not available for Intel Macs.
Download PE for Windows
If you are using a Mac PPC you must have Classic/OS9 installed
in order to use the downloads below.
Print these instructions now!! The most common reason people
have problems running downloaded PE is that they
skip over the simple instructions below.
If you do not have a recent version
Aladdin Stuffit Expander freeware,
update your version now.
A recent version is required in order to process the .sitx file below.
(We know that version 7 or later works; version 6 does not.)
Download one or more PE Unstuffer components.
It works fine to download it to your Desktop; or you may download
it to another location if you prefer. For current Protein Explorer
version numbers and release
dates, please consult proteinexplorer.org.
Hold down the Option key
before clicking an Unstuffer link
to force it to download.
Your download options are:
PE 2.78 Beta (June 20, 2006):
This includes all components, including the Demo and the Atlas.
This includes the folder "my_molecules", a required component,
which contains the Presentation Template and Example PiPEs and
PE 2.79 was not packed for download to Mac because the important changes
affect MolSlide development, which cannot be done on the Mac PPC.
If Stuffit Expander does not automatically decompress
drop it onto Stuffit Expander.
Possibly nothing will appear to happen for about fifteen seconds (and your
computer may appear to freeze) -- be patient -- Stuffit Expander is
scanning the hundreds of files stuffed into the .sit file. After this pause,
will create a folder named "Protein Explorer N.NN"
(where "N.NN" is the current version number).
PE versions 2.71 or later will also create a folder named "my_molecules".
You may leave "Protein Explorer N.NN" on your Desktop, or drag it to another permanent location of
your choosing (such as your Macintosh HD).
If you move "Protein Explorer N.NN", you must also move the folder
"my_molecules" to the same location, so these two folders remain
side by side.
Double-click the new "Protein Explorer N.NN" folder to open it.
Inside you will find, among other things, a file named "How to Start PE.htm".
Select this file, make an
to it (Finder's File menu, Make Alias, or
Apple-m), and drag the
alias to a convenient location, such as
Do not drag the file itself -- this will render it useless!
Open the new alias to How to Start PE.htm
and follow the instructions there.
(This should display the
downloaded instructions in your browser. If it doesn't, please
re-do the previous instructions carefully.)
-------------------- Now you can run your downloaded Protein Explorer!
If you created PiPEs with an earlier version of PE, copy
your PiPEs files into my_molecules\pipes of the new version.
This ensures that your PiPEs will work with the new version of PE.
If you wish, you may duplicate the alias to How to Start PE.htm
or drag it to another location. The alias will work from any location
as long as the original file How to Start PE.htm
remains in the "Protein Explorer N.NN" folder.
You may now delete PE-Unstuffer.sit (and PE-Unstuffer.hqx
if present) if you wish.
If you are updating from a previous version of Protein Explorer,
optionally, you may delete the folders and aliases for the old version, along
with your old bookmarks.
(If you keep the old files, you can use either the
old or the new version as you wish.)
Do not delete the folder my_molecules which may contain
your own personal PiPEs and/or MolSlides!
Never put any files containing your personal work in
the "Protein Explorer N.NN" folder, of any of its
sub-folders, since they will be deleted when you update to a
Thanks to Ilana Goldhaber-Gordon for helpful suggestions for this page.