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.
Without seeing your actual input files it is impossible to be sure what
your problem is, but perhaps you have a range set up in your alignment
header: see
instructs Modeller to read residues 1:A through 106:A from the PDB file.
So if "106:A" is before your HETATM, Modeller won't read it. Simply
update the end of the range to match the residue number (or remove the
range entirely to have Modeller read the whole file).