dm.getDataVector().removeAllElements();
dm.fireTableDataChanged();
dm = (DefaultTableModel) pdbChainsJTable.getModel();
dm.getDataVector().removeAllElements();
dm.fireTableDataChanged();
// clear the peptide to pdb mappings in the peptide table
for (int i = 0; i < peptideTable.getRowCount() && !progressDialog.isRunCanceled(); i++) {
peptideTable.setValueAt(false, i, peptideTable.getColumn("PDB").getModelIndex());
}