Alternatives to the Jmol "export
to web..." function
A list of alternatives to the built-in "export to web..." function with
a few comments about them (more complete discussions of some of these
may be found at the JTAT wiki):
- Server Based
- Protopedia.org : This is a wiki
designed for people to contribute annotated and animated views of
macromolecules in Jmol. The functionality is produced inside
the wiki.
- SChiSM2: This is a
server based templating system that allows you to have a Jmol applet
controlled by buttons, with associated explanatory text.
Result looks very similar to what is produced by the
"Scriptbutton" template in the Jmol "export to web..." function.
- International Union of Crystallography authoring kit:
This is a server based application that produces Jmol pages
to be published in on line versions of their journals. B.
McMahon and R. M. Hanson "A toolkit for publishing enhanced figures", Journal
of Applied Crystallography (2008). 41, 811-814.
- Separate Software Packages or Templates
- JTAT: This is a template very
similar to the "Scriptbutton" template in the Jmol "export to web..."
function. You will need to edit some html, plus some text in
javascript files to access all of the template's functionality.
You also have to do all the bookkeeping necessary to keep
track of files.
- Molecular Workbench:
generates tutorials in the form of java applications that can
be started from a web page although they are not contained within the
web page. Molecular Workbench uses Jmol for 3-D rendering of
molecules. Some reference articles on Molecular Workbench are
Q. Xie and R. Tinker, "Molecular Dynamics Simulations of Chemical
Reactions for Use in Education", Journal
of Chemical Education, 83, 77-83 (2006); A.
Pallant and R. Tinker, "Reasoning with Atomic-Scale Molecular Dynamic
Models", Journal
of Science Education and Technology, 13, 51-66 (2004).
- JmolShell: Is a set of tools
(javascript, html and Jmol script templates) one can use to build
consistent Jmol tutorials.
- Legacy tools by J. Gutow:
These are perl scripts and java applications that are no longer
maintained. Most of their functionality has been incorporated
into Jmol in one way or another. These legacy tools might serve
as useful starting places for someone writing code to build web pages
using Jmol.
Last Update:
August 14, 2009
Expires: --
by J. Gutow