Using structures downloaded with the MMTF format break the QuatSymmetryDetector algorithm. It is related to the chemical component information. The tests explicitly set the format to MMCIF, so that is why the bug was not noticed when changing MMTF to default.

Here the stacktrace when the line cache.setUseMmCif(true); in TestQuatSymmetryDetection or DemoOrientBioAssembly is commented out (MMTF used):

java.lang.NullPointerException
    at org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory.getChemComp(ChemCompGroupFactory.java:47)
    at org.biojava.nbio.structure.HetatomImpl.getChemComp(HetatomImpl.java:429)
    at org.biojava.nbio.structure.ChainImpl.getSeqResSequence(ChainImpl.java:576)
    at org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor.extractProteinChains(ProteinChainExtractor.java:121)
    at org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor.run(ProteinChainExtractor.java:95)
    at org.biojava.nbio.structure.symmetry.core.ProteinChainExtractor.getCalphaTraces(ProteinChainExtractor.java:60)
    at org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer.extractProteinChains(ProteinSequenceClusterer.java:98)
    at org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer.run(ProteinSequenceClusterer.java:88)
    at org.biojava.nbio.structure.symmetry.core.ProteinSequenceClusterer.getSequenceAlignmentClusters(ProteinSequenceClusterer.java:56)
    at org.biojava.nbio.structure.symmetry.core.ClusterProteinChains.run(ClusterProteinChains.java:84)
    at org.biojava.nbio.structure.symmetry.core.ClusterProteinChains.(ClusterProteinChains.java:42)
    at org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector.run(QuatSymmetryDetector.java:104)
    at org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector.hasProteinSubunits(QuatSymmetryDetector.java:74)
    at org.biojava.nbio.structure.symmetry.analysis.CalcBioAssemblySymmetry.orient(CalcBioAssemblySymmetry.java:70)
    at demo.DemoOrientBioAssembly.runPDB(DemoOrientBioAssembly.java:108)
    at demo.DemoOrientBioAssembly.main(DemoOrientBioAssembly.java:81)