Hi Tamas,
I faced the same problems you raised last year with respect to molecular visualization displays in my virtual text of organic chemistry. After comparing the two displays, I decided to offer the user a choice and at the cost of considerable effort, and with Miguel's help, two versions of the text were made available at: http://www.cem.msu.edu/~reusch/vtxtindex.htm
Each version has a test page that allows the user to examine the compatibility of his/her system with the viewer as well as with Peter Ertl's molecular editor applet. Because I started this conversion early, I did not use the Jmol.js library, electing to use applet generated buttons exclusively.
I believe that Jmol is the superior viewer for all the reasons cited by Eric, and as a Mac user I make use of it. However, I am informed by the supervisors of our servers that our site receives over 90% more hits on the Chime version than on the Jmol version. This undoubtedly reflects the overwhelming dominance of Wintel platforms and the good behavior of Chime with their I.E. browser.
Bill
  

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