Hi Francois What you need is to deactivate autobonding.
On a previos post http://sourceforge.net/mailarchive/message.php?msg_id=12416924 Miguel sayed: Jmol prerelease 10.00.21 is now available It includes support for: 2. "set autobond off" can be used before loading any file type to prevent auto-bonding. Explicit bonds with the file are retained This should fix your problem (I have not tested it) Good luck
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