Sometimes chain designations miss from the pdb files, although the TER tokens should reliably signal to the programs the end/beginning of chains. Try to fix the file with Mol2mol (http://web.interware.hu/frenzy/mol2mol/ ): input the file and save it immediately in PDB format. It will add chain identifiers, maybe it helps. Dr. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tgunda (AT) puma.unideb.hu