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This is the primary home and download site for the Jmol Tutorial-Authoring Template (JTAT), which was released on September 8, 2008. Be sure to have a look at the JTAT Demonstration !

Please send any questions about this site to emartz AT microbio DOT umass DOT edu.

JTAT is one of several website-authoring tools for molecular views in the Jmol applet. Those known to me are listed below.

Unless otherwise indicated, comparisons are by Eric Martz. Please send suggestions for improvement to the email above.

  • Proteopedia.Org This is a wiki (as in Wikipedia), meaning that anyone can add text and molecular scenes in Jmol to this website. It already has a page for every published macromolecule (>50,000), to which custom molecular scenes may be added. Or you can create a new page on a molecular structure topic, and add new molecular scenes. Proteopedia's Scene Authoring Tools make this by far the easiest place to create rotatable, zoomable molecular scenes which are instantly viewable and searchable by anyone. No knowledge of Jmol scripting language (nor of javascript) is required. Editing wiki text is easier than HTML. The ease of creating molecular structure tutorials here, and their immediate accessibility online, are the great strengths of Proteopedia. Your tutorials can be protected from editing by others if you wish. Limitations (compared to JTAT) are: Jmol scrolls with the text, so the molecule may scroll out of view when the descriptions are long; Jmol is usually smaller; detail text cannot be hidden; no sliders for zoom/slab; no centering button; no synchronization of side-by-side comparisons. To understand this comparision better, take a look at the JTAT Demonstration vs. Proteopedia.Org.

  • JTAT Download a template for building tutorials that will display in a web browser. Insert molecular views with buttons and descriptions using a text editor. (Proteopedia's Scene Authoring Tools are recommended for creating molecular views to put into JTAT.) Supports multiple chapters and views comparing 2, 3, or 4 molecules side by side (with synchronization of mouse-directed rotations or zooms). Your tutorial will include a slider for zooming (or slabbing), spin toggle and centering buttons, details that display only when requested, and "How To" put views in Powerpoint slides, etc. Extensive help and documentation, including HTML quick-reference. Some knowledge of Jmol script language is helpful, and a little HTML (but no javascript) is involved. Considerably more challenging to use than Proteopedia, but you have more control and the product tutorial is more user friendly. The tutorial must be uploaded to a server to provide online access, or the tutorial can be shown offline. Example tutorial: JTAT Demonstration.

  • JmolShell Download a tutorial-development environment to create tutorials that will display in a web browser. Insert molecular views with buttons and descriptions using a text editor. Knowledge of Jmol script language, and a minimal amount of HTML, are required. Considerably more challenging to use than Proteopedia, but you have more control and the product tutorial is more user friendly. The tutorial must be uploaded to a server to provide online access, or the tutorial can be shown offline.

  • Jmol Application's Export to Web Page On the File menu of the Jmol application (as distinct from the applet) is Export to Web Page. Jonathan Gutow says: "No knowledge of html or java script is necessary. Some knowledge of Jmol scripting language is helpful, but anything you can do from menus requires no scripting. At present there are two page formats: a Jmol window with scrolling text and buttons on the left side; and a page with snapshots of Jmol images that can be converted to live Jmol by clicking on the images. After Jmol creates the page it can be edited in a standard WYSIWG web page editor to add text and other features."

  • SChiSM2 Use a web browser form to create a web page containing a series of molecular views with buttons and descriptions. Requires knowledge of Jmol script language, but neither HTML nor javascript. As of May, 2008, uses an old Jmol (version 10.2). You can save your project to a file and upload it later to continue development. Considerably more challenging to use than Proteopedia, but you have more control and the product tutorial is more user friendly. The tutorial must be uploaded to a server to provide online access, or the tutorial can be shown offline.

-Eric Martz, November 2007; JTAT Demo added December 10, 2007; JTAT Demo updated January 20, 2008 with Template. SChiSM2 and comparisons added February 15, 2008; Proteopedia, JmolShell, and Jmol's Export to Web Page added May 2008. JTAT released September 8, 2008.