import jalview.structure.StructureSelectionManager
import jalview.structure.StructureMapping
import jalview.gui.Desktop

ssm = StructureSelectionManager
            .getStructureSelectionManager(Desktop.instance);
mapping1 = ssm.mappings.get(0)
mapping2 = new StructureMapping(mapping1.sequence, mapping1.pdbfile, 
  mapping1.pdbid, "B", mapping1.mapping, mapping1.mappingDetails)
mapping3 = new StructureMapping(mapping1.sequence, mapping1.pdbfile, 
  mapping1.pdbid, "C", mapping1.mapping, mapping1.mappingDetails)
mapping4 = new StructureMapping(mapping1.sequence, mapping1.pdbfile, 
  mapping1.pdbid, "D", mapping1.mapping, mapping1.mappingDetails)
ssm.addStructureMapping(mapping2)
ssm.addStructureMapping(mapping3)
ssm.addStructureMapping(mapping4)