Jmol is a free, open source molecule viewer for students, educators, and researchers in For the most up-to-date scripting documentation see the Jmol/ JSmol. Documentation of Jmol’s scripting language can be found here: http://chemapps. This is the official. JSmol is a fully functional implementation of Jmol that does not Various ways to create surfaces and more documentation on surfaces.

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Remember to always use uppercase ‘J’, uppercase ‘S’, lowercase ‘mol’ explanation. The recommended way to cite Jmol is: Get the files from SourceForge.

This is the homepage for the Jmol Community Documentatino. To get things to run on an installed base of older Netscape and IE browsers you may want to consider looking for ‘old’ documentation rather than ‘up to date’ documentation. See JSmol for more details. If you want to participate, you must become a user in the Wiki.

Running Jmol using Java Web Start.

For further information on JavaScript programming we recommend that you search for JavaScript development resources on the web or at your nearest technical bookstore. Finally, there is a documentation section in this web site, for more technical jmool. Has step by step instructions for both Windows and Mac OS X, and for the 5 most popular web browsers. By default, atoms are rendered with perspective depth.

You should use them only if you are experienced and you know precisely what you need. A handbook has been published for learning Jmol, and there are also other publications about Jmol.

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Jmol Wiki – Main Page

Those with interest in molecular visualization, especially the education and research communities, are encouraged to join the jmol-users mailing list or even the jmol-developers mailing list. This should not be needed except on very large molecules or very old computers.

Colors Used by Jmol This document specifies which colors Jmol uses for elements, chains, chain direction, charge, hydrogen bonds, isosurfaces, positional variability, residues, nucleotides, and secondary structure.

Views Page Discussion View source History. Documentation for Surfaces This documentation describes and compares the different options available in Jmol scripts for generating surfaces, either based on the molecule or geometric. Learn to use Jmol Manuals and tutorials A handbook has been published for learning Jmol, and there are also other publications about Jmol.

Includes atomic, van der Waals and ionic radii. Applet was not compiled with a classic compiler. One method is to use the ‘javascript: But content there is currently quite outdated. The RasMol commands which are currently not implemented in Jmol are generally those associated with protein visualization: The recommended way to cite Jmol is: This document gives technical information about how Jmol is built, particularly with respect to graphics rendering.

Put this file in the directory on your webserver. Web pages without writing code by using the Jmol “Export to Web” function.

Jmol Documentation

Main Page From Jmol. More official, general and static information about Jmol is available in the Jmol web site.

How to configure a wiki so that it uses the Jmol applet. More dynamical and frequently updated than this web site! For longer scripts it is probably better to store the docimentation files on the server and run them indirectly through the ‘script’ command.

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Internet Explorer does not support LiveConnect. Official, but not up-to-date, documentation These are official guides for Jmol. In addition to an extensive description of all commands and options, it provides excellent demonstrations and examples.

Docmentation Jmol Applet Guide describes the Jmol applet. This listing gives brief descriptions of the commands. They cover the basic functionality of both application and applet, but they have not been updated recently particularly, for features in version 11 of Jmol.

Automatically adopts the language of the user’s operating system, if it is among the translations available. documentatoin

Jmol Applet Documentation

In order to reference an applet on an HTML page the applet must be given a name. Learn by example You documentatiom also learn by examining documentatioj pages that use Jmol: For more information, please visit the Project pages section. Unfortunately, the news is not good for Macintosh OS X. Note that files which are compressed using gzip will automatically be decompressed. You are welcome to browse around and to add new pages, extra information, comments, questions, links to useful examples of Jmol use or Jmol scripting, or whatever else you think is relevant.

A list of literature describing Jmol can be found at Jmol Wiki.