User:Eric Martz/Molecular Playground/Authoring

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This page is under development. It is presently very incomplete!

This page makes recommendations and offers shortcuts for authoring effective presentation modules for Molecular Playground (MP; see MolecularPlayground.Org).

Components of a Module for MPComponents of a Module for MP

Each module in MP will ideally include the following components:

  1. A Jmol script that
    1. Displays a molecule, optionally with animations, labels, and color keys.
    2. Displays a one-line text banner stating the name of the molecule and why it is important, plus a second line with the invitation "More at MolecularPlayground.Org".
  2. A web page that plays the above Jmol script, and also provides more information about the molecule for a general audience, with links to information in greater depth. The author of the module can choose to put the web page in Proteopedia, or elsewhere.

For examples, see "The Molecules" web pages linked to MolecularPlayground.Org.

Jmol Scripting OptionsJmol Scripting Options

A Single Molecular Scene, SpinningA Single Molecular Scene, Spinning

The simplest option is a single customized molecular scene, with the molecule spinning slowly. Such a scene, lacking complicated animations, can be created in Proteopedia -- without learning any Jmol scripting language. Proteopedia offers Molecular Scene-Authoring Tools that make this relatively easy. Details will be found below under Procedure, but first, let's look at a concrete example.

Relenza binding to influenza neuraminidase N1 mutant H274Y (3ckz).

Drag the structure with the mouse to rotate

ExampleExample

At right is an example of a customized molecular scene[1] (), created with Proteopedia's Scene Authoring Tools.

Now we'll use the MP support script (explained in the procedure linked below) to put a banner at the top of Jmol[2]. (MP_relenza01.spt)

Next, we'll use the MP support script (explained below) to add a color key[2]. (MP_relenza02.spt)

Finally, it is very easy to jazz up the entrance with a zoom animation[2]. (MP_example03.spt)

ProcedureProcedure

The step-by-step procedure for constructing scripts, similar to those exemplified above, will be found at Molecular Playground/Procedures#Installing a state script from Proteopedia. This procedure includes an explanation of how to use the MP Support script that will be required (File:MPSupportVersion01.spt).

Web PagesWeb Pages

Your MP web page need not be in Proteopedia. You can put it on another server, and it can be linked to the name of your module at [Molecular Playground].

Displays to AvoidDisplays to Avoid

The following displays cause spinning or rotation to become slow and jerky in the full-sized (1024 x 768 pixels) MP projection. Your displays will be more satisfying if these can be avoided. A good way to test this is to try your scripts in the Jmol application at 1024 x 768 pixels.

  • Large numbers of spacefilled atoms, such as spacefilling all atoms in a protein. The higher the zoom, the jerkier the spinning.
  • Translucency.
  • High-Quality Display, namely set antialiasdisplay true. The MPSupportVersion01.spt actually uses high-quality when the script is displayed in the applet, because at the typical applet size (450 x 350 pixels) the speed penalty is acceptable.
  • Trace is slower than backbone. Thick traces are slower than thin traces. High zoom levels are even slower. You can get away with a thin trace at low zoom for a moderate-sized protein.

Dimensions of Projected JmolDimensions of Projected Jmol

The UMass ISB[3] projector projects a rectangle 1024 pixels wide by 768 pixels high. Zoom values, in particular, differ for square vs. rectangular Jmols. (Proteopedia uses a square Jmol by default, but a rectangular Jmol can be specified.) When you are running Jmol to develop and test a script, it should have the same width/height ratio, 1.333. The Jmol application displays the pixel size of the molecular display area at the bottom of its window. Molecular Playground pages in Proteopedia should also use rectangular Jmol's (size='[450,338]'). For convenience, here are some pixel dimensions with width/height = 1.333:

Pixels for 1.333 width/height ratio
1024 x 768 800 x 600
640 x 480 600 x 450
450 x 338 400 x 300


Notes and ReferencesNotes and References

  1. ↑ This scene shows the anti-influenza drug Relenza binding to mutant neuraminidase H274Y (3ckz). This mutant is resistant to Tamiflu. For more information, see Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza#Resistance_to_Tamiflu_and_Relenza.
  2. ↑ 2.0 2.1 2.2 The font sizes in the banner and color key will be proportionally larger when projected in MP, but they will not be larger in the Popup window in Proteopedia. Using the MP support script in Proteopedia requires that we upload our main script. Uploaded scripts can be played with buttons, as demonstrated above, but are not played with green links.
  3. ↑ MolecularPlayground.Org
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