[modeller_usage] HETATM reading

[Seth Tanner <cryoexp AT gmail.com>]

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.