See also the Classpath wiki. I justed the Jmol version from SVN branches/v10_9, compiled with 'ant jar' using the build.xml. I ran Jmol with: java -Dawt.toolkit=gnu.java.awt.peer.qt.QtToolkit -jar Jmol.jar $ java -version: java version "1.4.2" CACAO version 0.96 ... During the splashscreen I get a lot of: QFont: It is not safe to use text and fonts outside the gui thread But that seems harmless. However, after the following stacktrace it hangs: setting color scheme to:jmol uncaught exception: java.lang.UnsupportedOperationException java.lang.UnsupportedOperationException at gnu.java.awt.peer.qt.QtFontPeer.getLineMetrics(QtFontPeer.java:188) at java.awt.Font.getLineMetrics(Font.java:967) at java.awt.Font.getLineMetrics(Font.java:1361) at java.awt.font.TextLayout.<init>(TextLayout.java:103) at javax.swing.plaf.basic.BasicButtonListener.propertyChange(BasicButtonListener.java:87) at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:388) at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:332) at java.awt.Component.firePropertyChange(Component.java:4916) at javax.swing.AbstractButton.setText(AbstractButton.java:1616) at javax.swing.AbstractButton.init(AbstractButton.java:926) at javax.swing.JToggleButton.<init>(JToggleButton.java:294) at javax.swing.JCheckBox.<init>(JCheckBox.java:135) at javax.swing.JCheckBox.<init>(JCheckBox.java:125) at org.openscience.jmol.app.GuiMap$KeyJCheckBox.<init>(GuiMap.java:328) at org.openscience.jmol.app.GuiMap.newJCheckBox(GuiMap.java:215) at org.openscience.jmol.app.PreferencesDialog.buildDispPanel(PreferencesDialog.java:194) at org.openscience.jmol.app.PreferencesDialog.<init>(PreferencesDialog.java:142) at org.openscience.jmol.app.Jmol.<init>(Jmol.java:180) at org.openscience.jmol.app.Jmol.getJmol(Jmol.java:344) at org.openscience.jmol.app.Jmol.main(Jmol.java:433) Without setting the awt.toolkit is boots normally.