Main»Home Page

Home Page

This is the primary home and download site for the Jmol Tutorial-Authoring Template (JTAT), which was released in 2008, and updated in 2010 and 2018. 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 Jmol/JSmol . 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 machine-generated page for every published macromolecule (>100,000). Here you can create customized molecular scenes, which will be online immediately. 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 is smaller by default (but can easily be enlarged); detail text cannot be hidden; no sliders for zoom/slab; no centering button; synchronization of side-by-side comparisons is iffy. Advantages (compared to JTAT): Creating a molecular structure tutorial in Proteopedia is much easier than doing so in JTAT. 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 web browser mode) 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."

-Eric Martz, August, 2018. This page was started November 2007; JTAT Demo first added December 10, 2007; JTAT Demo updated January 20, 2008 with Template. Proteopedia, JmolShell, and Jmol's Export to Web Page added May 2008. JTAT Version History.