http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.16.zip
I tested that with
java -Djava.awt.headless=true -Xmx512m -jar "JmolData.jar" -ionj "load
mycif.cif;write t.png"
and it worked fine. Pretty sure that's truly headless. No Swing, no AWT.
http://www.oracle.com/technetwork/articles/javase/headless-136834.html
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