JMol 16.3.55 bundles uk.ac.ebi.beam 1.3.4 internally, which conflicts with CDK 2.12 that relies on uk.ac.ebi.beam 1.3.10. I now manually remove the outdated version of uk.ac.ebi.beam from the Jmol JAR, but it would be much easier if simply the Maven dependency mechanism could be used (or the bundled library updated to 1.3.10).