I have a problem when I am realising my model with multiple templates,
in the step to align the alignment of pdb's versus my sequence I obtain
the following problem…
...
_modeller.ModellerError: read_al_373E> Protein specified in
ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 13) =
giAAR00925
Your alignment file is not valid PIR format: see
http://salilab.org/modeller/9v7/manual/node445.html for the correct
format. Otherwise, your scripts look OK. If you still can't figure out
the problem, please put your input files into an archive (e.g. tar.gz
file or zip file) and send them to me, and I'll take a look.