I have a HETATM entry at the end of one of my protein chains. I have included the "env.io.hetatm = True" statement in my code. I have also included "." residues in my alignment file for each HETATM residue and formed a separate chain out of them using the "/" separator. I did this in both the template sequence and in the sequence to be modelled. However, I still get the following error: -- read_te_290E> Number of residues in the alignment and pdb files are different: 1566 1560 For alignment entry: 1 1GWP.pdb x (mismatch at alignment position 1561) Alignment KLFHIRTGNMDTYYWHRYT.. PDB KLFHIRTGNMDTYYWHRYT Match ******************** -- It appears that Modeller cannot read the HETATM entries in the PDB file. I wonder if anyone has a suggestion. Thanks.