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JSmol is a JavaScript framework that allows Jmol to work within a web browser using either Java or HTML5. 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). Not installing Java avoids possible security risks.

JSmol/HTML5 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. 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. In addition, the HTML5 mode has been reported to work very slowly in some versions of Internet Explorer, rotation is slow and jerky in Opera when not using set platformSpeed. Safari, Firefox, and Chrome appear to have much better JavaScript engines, and performance is much better using these browsers. In contrast, JSmol/Java works equally well in all of those browsers.

More information about JSmol:

  • JSmol pros and cons describes the problems JSmol has with large models and certain web browsers.
  • Jmol JavaScript Object: Technical information about the libraries used to implement both the JSmol and Jmol objects in a web page -- and to interact with them via scripts and UI controls such as buttons etc.