nucleic acid structures retrieved from PDB do not import correctly

Structures such as PDB 3i8f do not import successfully in Jalview. Protein chains are extracted but the ribosomal RNA sequence is not extracted correctly, and any attempt to open the structure fails with an exception:

Trace message truncated for length over 10K
Exception in thread "Thread-31" java.lang.NullPointerException
at jalview.analysis.AlignSeq.calcScoreMatrix(AlignSeq.java:695)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:138)
at jalview.gui.AppJmol.notifyFileLoaded(AppJmol.java:804)
at org.jmol.viewer.StatusManager.setStatusFileLoaded(StatusManager.java:152)
at org.jmol.viewer.Viewer.setStatusFileLoaded(Viewer.java:2944)
at org.jmol.viewer.Viewer.openClientFile(Viewer.java:1300)
at org.jmol.viewer.Viewer.getOpenFileError(Viewer.java:1284)
at org.jmol.viewer.Eval.load(Eval.java:2771)
at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:574)
at org.jmol.viewer.Eval.runEval(Eval.java:110)
at org.jmol.viewer.Viewer.evalStringWaitStatus(Viewer.java:2573)
at org.jmol.viewer.ScriptManager.runScript(ScriptManager.java:130)
at org.jmol.viewer.ScriptManager.runNextScript(ScriptManager.java:119)
at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(ScriptManager.java:147)
at java.lang.Thread.run(Unknown Source)