+ * <li>STRUCT_FROM_PDB (false) derive secondary structure annotation from PDB
+ * record</li>
+ * <li>USE_RNAVIEW (false) use RNAViewer to derive secondary structure</li>
+ * <li>ADD_SS_ANN (false) add secondary structure annotation to alignment
+ * display</li>
+ * <li>ADD_TEMPFACT_ANN (false) add Temperature Factor annotation to alignment
+ * display</li>
+ * <li>STRUCTURE_DISPLAY choose from JMOL (default) or CHIMERA for 3D structure
+ * display</li>
+ * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>