PiPE Specifications:
What PiPEs can and cannot (yet) do.
(PiPE = Presentation in Protein Explorer)

If you have not yet looked at an example of a PiPE, we recommend that you do so before reading further. Seeing and using a PiPE will give you a concrete basis for understanding what follows.

The list below describes what can (and sometimes cannot) be done with PiPEs. It does not explain how to do these things when constructing a PiPE -- that is covered in Constructing PiPEs and in the PiPEs Reference Manual.

The list of what PiPEs cannot yet do is in PiPE Limitations and Bugs.

  1. Presentations authored in the PiPE mechanism, if placed on server, can be downloaded without any special effort on the part of the author. Downloading involves saving the PDB file representing each Chapter, and also saving the main Contents page. The reason this works is given below.
  2. A presentation typically starts with an ordinary HTML page, the  PiPE Contents page (example), which has links to one or more Chapters. Clicking a link to a Chapter starts a Protein Explorer (PE) session. Instead of PE's FirstView, the initial control panel is the PiPE control panel, similar to the example shown at right.

  3. Each PE session (PiPE session, PiPE Chapter) can have only one PiPE control panel. Going to a different PiPE control panel involves returning to the Contents page and starting a different PiPE Chapter. Multiple PiPE Chapters can be run concurrently.

  4. A PiPE can be operated in any one of three modes (table of mode properties). Typically, the Contents page has radio buttons to select the mode. Alternatively, the link that runs a PiPE can specify the mode.

    1. Audience (for projection to illustrate a talk): large font, details do not pop up. The message box is closed; only presentation controls are initially visible at the lower left.
    2. Individual (for study by one or two people): small font, details pop up. The message box is closed; only presentation controls are initially visible at the lower left.
    3. Development (for testing during development of the PiPE by its author): small font, details pop up, and mode and PiPE block are accessible for display. The message box and associated controls start open. The command script, optional popup details name, and optional PDB filename attached to each molecular-view button are displayed.

  5. Each PiPE control panel can have one or more molecular-view buttons. There is no built-in limit on the number, but if it exceeds 10, consider separating the images into two or more PiPE Chapters.

  6. Each molecular-view button in a PiPE chapter may specify a different PDB file. There is one primary PDB file which contains all of the information (the PiPE block in the PDB file header) for the presentation Chapter control panel, but any number of secondary PDB files may optionally be used. PiPE blocks may be in secondary PDB files, but are ignored.

  7. Each molecular-view button displays a view designed by the author of the presentation to highlight appropriate features of the molecule. The view is generated by sending a command script to the Chime plugin that displays the molecular image. The easiest way to create a command script is to produce the desired view in PE, and then save the corresponding command script from the PE Recorder. The command script is recorded automatically while you are using PE.

  8. The contents of each PiPE Chapter are contained in the header of the PDB file utilized for that Chapter. These contents include HTML, javascript, and Chime command scripts. The layout of the control panel is under complete control of the author.
  9. Standard PE convenience buttons (Spin, Zoom, etc.) can be placed where desired between molecular-view buttons.

  10. The user can move seamlessly between the PiPE control panel and self-directed exploration in PE. Near each cluster of convenience buttons in the PiPE control panel are links to PE's QuickViews control panel, and to the PE Site Map, which enables access to any of PE's capabilities.

  11. If you move to QuickViews, the Title of the PiPE is displayed as a link for returning to the PiPE control panel. If you move to any control panel, the PE Site Map includes the Title of the PiPE as a link for returning to the PiPE control panel.

  12. Each PiPE Chapter can start with the background black or white. The [Bkg] convenience button can be used to change the background at will during the presentation.

  13. Each PiPE Chapter can start with PE's message box hidden or visible. Regardless of how the Chapter starts, the top boundary of the lower left frame can be dragged up or down to hide or show the message box. When visible, not only the message box, but also the command entry slot, PE Recorder controls, and links to Command Aliases, Preferences, etc. are accessible.

  14. Typically, PiPE Chapters start with the message box hidden. In this case, presentation controls appear in a small lower left frame, including access to Presentation Help. Presentation controls include changes to the font size in the control panel, and enabling/disabling display of popup details.

  15. Command scripts can call other command scripts. This permits structured programming of command scripts.

  16. Colors (RGB values) can be assigned a color name, and then used in command scripts and HTML by name.

  17. Details (additional information beyond that provided by the molecular-view button in the control panel) may be attached to each molecular-view button. Except in "Audience" mode, these appear automatically in a small popup window at the lower left when the molecular-view button is pushed. Popping up of details can be disabled/enabled at any time with a button in the presentation controls.