Downloading and Installation of Protein Explorer for Windows

  1. Print these instructions now!! The most common reason people have problems installing Protein Explorer is that they skip over the instructions below.
      Protein Explorer is a browser-based application. It does not have an automatic installer like most programs have. After PE is downloaded and unpacked (into over 900 separate files), "installing" it consists of opening the correct file in a compatible browser, and then creating a shortcut or bookmark that makes future use a one-click operation.

  2. Download one or more PE Unzipper 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 Your download options are:

    • PE 2.80 (May 14, 2007): (Not available in smaller pieces.)

      • Download PE-280-All-Unzipper.exe 27 Megabytes (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. Installing it will automatically redirect your existing PiPEs to the new version of PE, but otherwise will not affect PiPEs or MolSlides you have made.

    • Older Versions of Protein Explorer

  3. Protein Explorer 2.72 or later included a folder my_molecules, in the same folder as "Protein_Explorer_N.NN". If you are upgrading from PE 2.72 or later, it is crucial that you now move your freshly downloaded PE-N.NN-Unzipper.exe file to the folder that contains my_molecules and the folder Protein_Explorer_N.NN. This ensures that when you unzip (next step), any PiPEs you have made in the folder my_molecules\pipes will henceforth run in the new version of PE.
      If this is the first time you have installed a downloaded copy of PE, you can leave the Unzipper file on your desktop.

  4. Double-click the PE-Unzipper.exe file. A WinZip Self-Extractor dialog will open. Click the Unzip button (leaving all other settings unchanged). When extraction has finished, click the Close button in the WinZip dialog.

  5. The previous step creates two folders named "Protein Explorer N.NN" (where "N.NN" is the current version number), and "my_molecules".
      If this is the first time you have installed a downloaded copy of PE, Drag these two folders to a permanent location of your choosing (we recommend the C: drive, for example, C:\ProteinExplorer). It is best if you drag them to a permanent location now -- this may avoid future complications. The folder my_molecules MUST be in the same directory as the folder Protein Explorer N.NN -- it is required for the operation of Protein Explorer.

  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".

  7. Right-click "How to Start PE.htm" and select Send To, then Desktop (create shortcut). Do not drag it and drop it on the Desktop. This will not work!

  8. Click the Desktop Icon in your taskbar to minimize all open applications and reveal your Desktop (or hold down the Windows key and press m).

  9. Double-click the new Shortcut to How to Start PE.htm on your Desktop 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!   --------------------

  10. If you wish, you may copy the Shortcut to How to Start PE.htm and paste it into other locations, or drag it and drop it into another location. If you wish, you can drag it and drop it onto your main Start menu.

  11. You may now delete the file PE-Unzipper.exe if you wish.

  12. If you are updating from a previous version of Protein Explorer, optionally, you may delete the folder Protein_Explorer_N.NN for the old version (deleting all of its contents, notably the folders atlas, protexpl, pe_demo, and shared, and their contents), along with your bookmarks/favorites to the OLD version. (If you keep the old files and bookmarks/favorites, 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! This folder is automatically updated whenever you download and install a new version of PE.

  13. 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.