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