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.
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.
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.
Each molecular-view button
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
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.
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.
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.
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.
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.
Command scripts can call other command scripts. This permits structured programming of command scripts.
Colors (RGB values) can be assigned a color name, and then used in command scripts and HTML by name.
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.