Jmol Documentation

Jmol Literature

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

Jmol Technical Notes

This document gives technical information about how Jmol is built, particularly with respect to graphics rendering.

Translating Jmol

Jmol can be translated into your laguage. Please, read instructions in this Wiki page and, if you need help, contact the developers team.

Scripting for Jmol

Scripting Documentation

This interactive online documentation is the reference guide for all commands that form the Jmol scripting language. In addition to an extensive description of all commands and options, it provides excellent demonstrations and examples.

Documentation for the JavaScript Library

Jmol.js (included in Jmol standard distribution) is a library, written in JavaScript, that can be used to simplify development of web pages that include the JmolApplet. Here is its description and documentation.

Scripting JmolApplet Without Using the JavaScript Library

Please, note that these methods are not recommended. You should use them only if you are experienced and you know precisely what you need. Particularly, if you are learning how to use JmolApplet and scripting, you are encouraged to only use the JavaScript library.

Do not insert the JmolApplet using the <applet> tag. With older browsers it was possible to put an <applet> tag into the page, so creating an instance of the Jmol applet. With newer browsers, particularly those implementing HTML5, the <applet> tag is deprecated and should not be used. Use the <object> tag instead.

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. It also provides a testing and demonstration page.

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. Also, it describes standard color names in JavaScript and the Netscape 8-bit color palette.

Atomic and Ionic Radii Used by Jmol

This document demonstrates, using a 3D periodic table, which radii Jmol uses for elements. Includes atomic, van der Waals and ionic radii.

The Jmol Developers Guide

The Jmol Developers Guide describes Jmol development procedures.

Official, but not up-to-date, documentation

These are official guides for Jmol. 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).

The Jmol Guide

The Jmol Guide describes the Jmol application.

The Jmol Applet Guide

The Jmol Applet Guide describes the Jmol applet.

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