JSmol

JSmol is a JavaScript framework that allows web developers to create pages that utilize either Java or HTML5 (no Java), at will. This enables Jmol to display interactive 3D molecular structures on devices that do not have Java installed, or for which Java is not available (such as smart phones and some tablet computers, e.g. iPad) or has not been installed because of concerns for Java being a security threat.

JSmol/HTML5 (no Java) is virtually identical to JSmol/Java in terms of rendering. The Java mode gives faster performance and smoother rotation than the HTML5 mode by a factor of 6 to 10, typically. In many cases this is not noticeable. Where it is noticed is with rending structures involving 20,000+ atoms or with surface creation. Rendering in the HTML5 mode can be sped up substantially with judicial use of set platformSpeed.

More information about JSmol:

• Jmol JavaScript Object: A full discussion of what JSmol is and how it can be implemented on a web page. Technical information about the libraries used to implement both the Java and HTML5 modes and to interact with them via scripts and user interface controls such as buttons, links, and menus.

Maybe you want to go straight to

• Functions for Jmol JavaScript Object
• Detailed explanation of the parameters included in the Info variable

• JSmol pros and cons describes the problems JSmol has with large models and certain web browsers.

• Proteopedia page on using Java in relation to Jmol.

Installing Jmol / JSmol Get the files from SourceForge. Support and operating systems. Users: how to install Jmol application for local, standalone use. Web page authors: how to install Jmol objects (Jmol / JSmol) embedded within your web pages. Installing and Enabling Java (Proteopedia wiki). Has step by step instructions for both Windows and Mac OS X, and for the 5 most popular web browsers. Increasing java memory for the applet. Web site administrators: How to install the application on a web server to be delivered using Java Web Start. How to configure a wiki so that it uses the Jmol applet. Developers: compile the latest Jmol source code via subversion access.

Running Jmol / JSmol Jmol as a standalone application. J(S)mol as a web applet or HTML5 object. compatibility with JavaScript frameworks or libraries. J(S)mol embedded in wikis or blogs. Borrowed JSmol, or running JSmol without your own server. Running Jmol using Java Web Start. JSmol in a Jupyter notebook. Jmol in an Android tablet. Troubleshooting. Jmol / JSmol Tutorials A list of Jmol / JSmol Tutorials written by users. Using the mouse (English · Español · Français · Japanese). Scripting quickstart: rendering options · selecting atoms. How to create surfaces and isosurfaces, including cavities, pockets and tunnels. Displaying shapes, polyhedra, orbitals, dipoles, distances, forces and vibrations. Creating movies. Customizing Jmol: macros · menus. Web pages without writing code by using the Jmol "Export to Web" function.

Jmol + JSmol Documentation Description of files in Jmol+JSmol distribution File formats read or written by Jmol The Jmol scripting interface Scripting as a programming language Complete reference of scripting commands: at St Olaf (primary site) at Jena3D (mirror) Loading models directly from databases Mouse manual Default colors used by Jmol Atom sets predefined in Jmol Support for bond orders · isotopes · stereochemistry · hydrogen bonds Jmol as editor Multi-touch support Copying and pasting state scripts between applets. Backward compatibility (changes of behavior across versions) Features added since version 10 Users mailing list (and a mirror)

Contributors

AngelHerraez, EricMartz, Hansonr