Glossary for PiPEs

Glossary of PiPE Terms
for Protein Explorer.

See elsewhere Rationale, Examples, Instructions, Reference Manual, etc..

Block, PiPE: See PiPE Block.
Chapter of a PiPE: Each Chapter of a PiPE is contained in a single session of PE, and consists of one PE control panel with a series of molecular-view buttons with descriptions or explanations, and color keys.
Contents: A web page with an overview of the contents of a PiPE. Typically this page lists a series of Chapters, and may include a general introduction, references, and acknowledgements.
Details: The description or explanation of each molecular view provided next to the molecular-view button in the PiPE control panel is typically kept short. Additional information can be provided in smaller text in a popup window for details. Generally, the description within the control panel is intended to be projected when illustrating a lecture, while the details, if any, are not. The details are intended for when the PiPE is viewed by an individual. (See also Modes of PiPEs.)
Modes of PiPEs: PiPEs can be run in one of three modes, depending on the intended viewer(s): Audience (for projection to illustrate a talk), Individual (for one or two people), or Development (for the author of the PiPEs, during their development). Typically, the mode is selected with radio buttons at the top of the Contents page.
PiPE, PiPEs: Presentations in Protein Explorer. A series of views (renderings, perspectives, color schemes) of a macromolecule chosen by the author to convey selected 3D structural features. Each view can be produced by pressing a button, and is accompanied by a description or explanation, and optionally, a color key. Here is full documentation on PiPEs.
PiPE block: The portion of the header of the primary PDB file that specifies the content for a PiPE Chapter. The format of the PiPE block is detailed in the PiPE Reference Manual. Here is a schematic diagram of the PiPE block.
Presentation, see PiPE.
Primary PDB file: The PDB file which contains, in its header, the PiPE block that specifies the content for a PiPE control panel, including molecular-view command scripts and buttons (in javascript), descriptions and explanations of the molecular views (in HTML), layout, atomic coordinates for one molecule, and names of PDB files for optional secondary PDB files. See also how to use secondary PDB files.
Template: A brief PiPE with minimal content provided to facilitate construction of a new PiPE by example. The template can be copied, and the new content inserted.
Secondary PDB file(s): PDB files ("molecules") named in the PiPE block of the primary PDB file for use in one or more of the molecular views, in addition to the molecule whose coordinates are specified in the primary PDB file. Secondary PDB files may contain PiPE blocks, but they are ignored in chapters where these PDB files are secondary. See also how to use secondary PDB files.

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