User:Eric Martz/Molecular Playground/Authoring

From Proteopedia

Revision as of 20:11, 7 December 2009

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

Components 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.

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

Jmol Scripting Options

A Single Molecular Scene, Spinning

The simplest option is a single customized molecular scene, or perhaps a series of scenes, with the molecule spinning slowly in each scene. Such scenes, lacking animation, can be created in Proteopedia, without learning any Jmol scripting language. Proteopedia offers Molecular Scene-Authoring Tools that make this relatively easy. If you are planning to put your web page in Proteopedia, you can create your molecular scenes on that web page. Alternatively, you can create your molecular scenes in a Sandbox page. If you use a sandbox, then, once your scene is ready, you can move it to a permanent article page (see #Web Pages below).

• Proteopedia:Video_Guide which includes
  • A Video on Adding Molecular Scenes.
• Help:Editing which includes
  • How To Create A New Page
• Instructions for creating a molecular scene with Proteopedia's Scene Authoring Tools.

Examples

At right is an example of a customized molecular scene^[1] (), created with Proteopedia's Scene Authoring Tools. (A black background works better in general for MP's projection, but in this case a white background worked better to make the translucent white protein trace less intrusive.)

Web 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].

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Dimensions of Projected Jmol

The UMass ISB^[2] 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:

Notes 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. ↑ MolecularPlayground.Org