as it is a local alignment, there are multiple positions in the pdb
file that have been skipped in the alignment so I have to remove those
atoms from the pdb file one by one. Additionally, there are missing
positions in the crystal template so I have to remake the alignment
(deleting from the template fasta file these residues) each time I find
missing atoms in the pdb
Right, the sequence in your alignment has to match that in the PDB file
exactly, as that's what Modeller uses to map template structural
information onto your model. If you don't want to use a template residue
in your model, align it with a gap residue "-" in the model sequence.