Introduction to
Presentations in Protein Explorer (PiPE)

What are Molecular Structure Presentations?

Molecular structure presentations or tutorials generally consist of a series of author-chosen views of a molecule accompanied by explanatory text and color keys. Interactive presentations, in which the user can rotate each three-dimensional rendering of the molecule using free software, were pioneered by David Richardson with his kinemages in 1992, by Eric Martz using RasMol in 1995, and by Tim Maffett, Henry Rzepa and David Marcy using MDL Chime in 1996. (More is available on the History of Visualization of Biological Macromolecules including the history of Chime.)

More recently, bioinformatics databases or software may display results as an annotated molecular structure image. Examples include the National Center for Biotechnology Information's Macromolecular Structure Database (using Cn3D), the automated comparative modeling server SWISS-MODEL (using SwissPDB-Viewer also called DeepView), and XDomView (domain and exon visualization with Chime). None of the foregoing use Protein Explorer. Several structure or structure calculation databases use generic Protein Explorer (PE) to display results without any customized annotation within PE. The first to use a true Presentation in PE (PiPE) is ConSurf (identification of evolutionarily conserved patches).

Hundreds of educational presentations or tutorials on macromolecular structure are now available on the Internet, most indexed at the World Index of Molecular Visualization Resources. Most of these depend upon the RasMol-derived browser plug-in MDL Chime, first available in 1996. For presentations, Chime has several important advantages over RasMol. The Jmol java applet has all of Chime's advantages, and more.

Protein Explorer, like RasMol, was designed to facilitate self-directed exploration of macromolecular structure, rather than presentations. Protein Explorer was first released in 1998, with version 1.0 being offered in 1999. Several enhanced releases have been made available each subsequent year. In 1999 and 2000, Eric Martz taught classes in which he mentored students in constructing early Presentations in Protein Explorer (PiPEs), using unreleased versions of PE still under development. In 2002 Martz collaborated with Glaser, Pupko and Ben-Tal (Tel-Aviv) to enable the ConSurf Server to show evolutionarily conserved patches on protein surfaces as a PiPE. The first public release of a version that supports Presentations in Protein Explorer (PiPE) was in January 2005 (version 2.7 Alpha). Through personal communications prior to this release, Karl Oberholser developed PiPEs for use in his teaching and published an abstract at an ACS meeting entitled Visualizing protein structure and function with Presentations in Protein Explorer (PiPE). Also, Wayne Decatur developed PiPEs to explain aspects of ribosome structure, and to illustrate a paper in TiBS.
Why put presentations inside Protein Explorer?

Limitations of traditional presentations.

Nearly all of the molecular structure presentations authored prior to 2004 suffer from the limitation of being constrained to the the author's viewpoint. In order to visualize aspects of the molecule not explicitly addressed by the author, one must obtain the molecular structure data (atomic coordinate file or PDB identification code, too often not made evident by the author) and then start anew using a separate molecular visualization software package. Because of the extra time and specialized skills involved, few of those who could benefit actually do this. This effectively precludes, during a lecture, visualizing the answer to a question arising on a point not explicitly covered in the formal presentation.

Most presentations authored before 2004 cannot be downloaded for off-line use, or modification by users. Because many educators do not have convenient (or any) access to the Internet in their class rooms, this precludes them from using such tutorials to illustrate lectures.

Advantages of having presentations within Protein Explorer.

The first advantage of having a molecular structure presentation displayed within Protein Explorer (PE) is that this makes it much easier to explore beyond the views offered by the author of the presentation. Whenever an author-designed image raises a structural question not addressed explicitly in the presentation, tools are immediately at hand to answer the question. Simple questions may be answered using Protein Explorer's standard cluster of convenience buttons within the presentation control panel. These make it unnecessary to remember special tricks or commands to zoom, center a moiety of interest, start or stop spining, change the background from white to black, hide or display water or ligands, display secondary structure, or see inside a structure with a cross-sectional (slab) view. To address more challenging structural questions, the user can move seamlessly into QuickViews or other control panels in Protein Explorer in order to visualize the answers -- yet move back into the formal presentation when desired.

The second advantage of putting presentations within Protein Explorer is that this renders them downloadable by all, with no extra effort on the part of the author of the presentation or tutorial. This advantage depends on a new design for PiPEs, first released in 2005, in which the content for the presentation is put into the header(s) of the relevant PDB file(s).
How do you construct a Presentation in Protein Explorer (PiPE)?


First, be sure you are using the most recent version of Protein Explorer (PE). The most recent version of PE will always be available at In January 2005, it is an Alpha version linked to the top of the FrontDoor.

    Before you start:

  1. Familiarize yourself with the Design Guidelines. The PiPE Template automatically follows some of these (for example, dynamically adjustable font sizes).
  2. Download and install the most recent version of PE, available from In January 2005, it is an Alpha version linked to the top of the FrontDoor.

    A PiPE consists of a series of molecular views and explanations prepared by its author. Typically, there is a button that displays each view. Authoring each view involves the following steps:

  3. Using Protein Explorer, obtain the view desired.
  4. Save a command script to generate the desired view using Protein Explorer's Script Recorder.
      This is often best accomplished by starting a new session in which you achieve the desired view as directly as possible (to avoid including unnecessary digressions in the script that may slow performance).
  5. Install your command script in a button using the PiPE template.
  6. Provide a description and color key for your view.

    When the buttons and descriptions are completed:

  7. Place a copy of PE's standard cluster of convenience buttons between every few molecular view-buttons.
  8. Optionally, you may put your PiPE on a server to make it available through the Internet. This automatically makes it downloadable as well as viewable.

As you will see when you get to the details (below), all the code needed to generate the series of views in a PiPE (Chime command scripts, HTML, and javascript) is stored within the PDB file to which these views apply. This means that when you download this customized PiPE-containing PDB file, you get the presentation or tutorial as well as the molecule. Chime, and thus Protein Explorer, has a built-in mechanism for downloading any PDB file it is displaying. As shown schematically below, a published PDB file contains two sections with different kinds of content. A PiPE is constructed by adding a third section to the top.

PDB File As Published
PDB File Modified for PiPE
PiPE Block
Original Header
Original Header
Atomic Coordinates
Atomic Coordinates

Detailed, step-by-step instructions and a template are provided.