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.
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.
As with any general purpose molecular visualization software, it takes some time to learn how to use Protein Explorer -- but having done so, one can begin personalized exploration immediately, starting with any view in the presentation. And at any time, one can return to the presentation.
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.
Overview
First, be sure you are using the most recent version of
Protein Explorer.
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.
The first version that supports Presentations
in Protein Explorer (PiPE)
was released in 2003 (version 2.3 alpha).
The most recent version will always be available
at
Before you start:
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:
When the buttons and descriptions are completed:
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.
Details
Detailed, step-by-step instructions and a template are provided
in a separate document,
How do you construct a
Presentation in Protein Explorer (PiPE)?
This is often best accomplished by recording a new session
in which you achieve the desired view more directly.
Contruction of Presentations in Protein Explorer (PiPE).