G'day,
A slighlty, unrelated question - would it be more feasible to do this with the CDK 2D renderer?
If you don't require all of the functionality of the JMol viewer then a CDK viewer makes sense. We do exactly what you describe with a Renderer2D <http://cdk.sourceforge.net/api/org/openscience/cdk/renderer/Renderer2D.html> viewer in a JTable and have had it handle a few thousand 2D structures without any problems.
Regards, Chris.
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