A few comments:

1. JCP has the advantage of accepting SMILES; which I think is more 
widespread and feature-loaded than JME. I also allows more variety 
when drawing structures. I have set quizzes that use SMILES to match 
user-drawn structures against correct answers. I doubt that JME 
string would be capable of not too simple structures. 
(I may be wrong in my appreciation of JME capabilities)

2. I think that MOL is a better choice for inter-app transfer than 
JME

3.  Re. JME specification: some hints at
http://wiki.jmol.org/index.php/File_formats/Coordinates#JME




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