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This can also happen due to mismatched java version number. The java version expected by sage is declared in "~/.local/lib/python2.7/site-packages/sage/interfaces/jmoldata.py" There, in the "JmolData" class at "is_jvm_available" function you'll find the code responsible for java version check.

java_version = re.search("version.*[11][.][06]", version)

See, I've changed the version number to 11.06, it previously was 1.78(=[1][.][78]). Then voila, JMol started working normally.