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 in order to run PE because Classic/OS9 is not available for Intel Macs. Download PE for Windows HERE.

If you are using a Mac PPC you must have Classic/OS9 installed in order to use the downloads below.

  1. Print these instructions now!! The most common reason people have problems running downloaded PE is that they skip over the simple instructions below.

  2. If you do not have a recent version of 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.)

  3. 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

    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): 25 Megabytes. Download PE278.sitx.
      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 MolSlides. 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.

    • Older Versions of Protein Explorer for Mac PPC Classic

  4. If Stuffit Expander does not automatically decompress PE-Unstuffer.sit, 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, Stuffit Expander 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".

  5. 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.

  6. 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 alias to it (Finder's File menu, Make Alias, or Apple-m), and drag the alias to a convenient location, such as your Desktop. Do not drag the file itself -- this will render it useless!

  7. 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!   --------------------

  8. 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.

  9. 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.

  10. You may now delete PE-Unstuffer.sit (and PE-Unstuffer.hqx if present) if you wish.

  11. 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!

  12. 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 future version.

Thanks to Ilana Goldhaber-Gordon for helpful suggestions for this page.