Procedure for Downloading PiPEs for Off-Line Use


    Why download PiPEs?

    When a fast Internet connection is not always convenient or available, you will be able to view your downloaded and saved PiPEs quickly and easily. This may be especially desirable when you wish to project PiPEs to an audience in a seminar, lecture, or presentation.

    Respect Copyrights ©!

    If the PiPE you wish to download states that authors retain the Copyright ©, you are legally required to ask their permission for the use(s) you plan for their work. Many Universities and Colleges now enforce the copyrights of materials authored by their faculty. Aside from the law, please do the authors the courtesy of asking their permission. Faculty may be happy to give permission to use their PiPEs for non-profit educational use, but they will be doubly happy to know that others are using the PiPEs they worked so hard to create. Documenting such use may have value in their promotion and tenure files.

    How to download a PiPE:

  1. Running downloaded PiPEs requires that you first download Protein Explorer (PE). Downloading PE creates a directory tree with a place for your downloaded PiPEs, enabling them to display with the downloaded PE.

    To download PE, go to and look for the Download PE link. The downloaded PE must be version 2.72 or later. Versions available for download will be stated on the download page.

      Although it is technically feasible to display downloaded PiPEs in PE on-line (coming from a server) in some browsers, we don't recommend it. After all, if you are downloading the PiPEs you probably prefer to be able to display them off-line.

  2. Create a folder (directory) to receive the downloaded PiPE files. In order to work properly, this folder must be within my_molecules/pipes/, a folder created automatically when you downloaded and installed PE. Furthermore, it is strongly recommended that your downloaded PiPEs be placed in my_molecules/pipes/downloaded/.

      Example: We'll use Karl Oberholser's Collagen Structure PiPE as an example, from his Molecular Science Laboratory at Messiah College. Since Oberholser offers tutorials on several molecules, it makes sense to make two levels of subdirectories such as my_molecules/pipes/downloaded/oberholser/collagen/.

      Downloaded PiPEs will work in subdirectories up to four levels below pipes. All of these possibilities would work:
      (2 subdirectories below pipes) my_molecules/pipes/downloaded/collagen/
      (3 subdirectories below pipes) my_molecules/pipes/downloaded/oberholser/collagen/
      (4 subdirectories below pipes) my_molecules/pipes/downloaded/oberholser/fibrous/collagen/

      Note: in April 2005, Oberholser's tutorials work in all PE-compatible browsers except Netscape 4! (This problem can be avoided by using directory and filenames without spaces embedded in their names.)

  3. Download the PiPE PDB files. Each chapter of a PiPE utilizes at least one customized PDB file (the primary PDB file), and may also utilize one or more secondary PDB files. You need to download all the PDB files needed in each chapter of the PiPE.

      Example: Display Chapter 1 of Oberholser's Collagen Structure PiPE. Scroll down in the control panel to the very bottom, and click on the link Download this presentation for off-line use. This will display a list of the PDB files needed with instructions for downloading. Save them all in the directory you made for this PiPE, e.g. my_molecules/pipes/downloaded/oberholser/collagen/.

      Now do the same for Chapter 2 (and, in PiPEs with more than two chapters, for each additional chapter).

  4. Test a downloaded PDB file.

    If you want to download the main/contents page of the PiPE (next step below) you may skip this step. However, the Empty Explorer method may be useful for you to know about! It enables you to stop here and use your PiPE chapters, whereas downloading the main/contents page requires configuring some files with a text editor or HTML editor.

    Go to the FrontDoor of your downloaded PE. Click on the link to open Empty Explorer. After PE starts up, you will be at the Load Molecule control panel. Use the Browse button there to load one of your downloaded PiPE PDB files. (In the File Upload dialog, you may have to change the Files of Type: to All Files (*.*).) PE should automatically display it as a PiPE Chapter.

    The last 10 PDB file you have loaded will appear on the menu Select Previously Loaded PDB File at the Load Molecule control panel of Empty Explorer. Therefore you could load chapters from this menu without continuing to any steps below. Be aware that this menu is specific to each computer -- if you use a different computer to deliver a lecture than you did preparing the lecture, the menu will not be populated with your PiPE chapters.

  5. Download the Main/Contents Page of the PiPE. If you want the complete PiPE, with its convenient links to Chapters, and introductory text and literature citations, you will need to download the main (contents) page.

      Example: Go to Oberholser's Collagen Structure PiPE. Without starting any chapter, open your browser's File menu (usually at the very top left of the browser window), and select Save (Page) As. Save the HTML file into the same folder as the PiPE PDB files that go with it. (Some elaborate PiPEs may have additional graphics files or HTML pages that you will want to save using the same method. Right-clicking on a static graphic image opens a menu that includes Save Image As.)

      Your contents page most likely won't work until you complete the steps below.

  6. Make a link from My PiPEs to your downloaded PiPE.

    • Click on my_molecules/downloaded/index.htm. If this link does not display a page entitled Downloaded Presentations ..., copy the file
      Now the above link should work.

    • Open the file my_molecules/pipes/downloaded/index.htm in a text editor or an HTML editor as you prefer. Make a link that goes to the main/contents page of your downloaded PiPE,

        Example: Since the link is in my_molecules/pipes/downloaded/index.htm, it should go to "oberholser/collagen/collagen_index.htm". (Pay attention to whether your downloaded HTML file ends ".htm" or ".html".)

    Now, you should be able to access your downloaded PiPE from the FrontDoor of your downloaded PE. Click on Presentations in PE, then Downloaded PiPEs. But the links to PiPE chapters probably won't work until you complete the step below.

  7. Connect your Main/Contents Page to your downloaded PE. Use a text editor to customize the two lines near the top of the main HTML file that refer to the files pe_path.js and pstart.js. The file paths in these two lines must correctly lead to your template directory.

      Example: The directory
      is 3 levels down from the directory "pipes" that contains "template". Therefore, the correct paths require 3 steps back, namely

      These two lines tell the PiPE main/contents page where to find your downloaded copy of PE. By having all your downloaded PiPEs us the common path specified in template/pe_path.js, you can redirect them all to a new version of Protein Explorer by changing the definition of pe_path in that file (in just one place).

    Each link to a chapter in your downloaded PiPE should now start PE and display the chapter.

Feedback to Eric Martz.