On 3/31/25 6:21 AM, Fred Pontes via modeller_usage wrote:
> "/_modeller.ModellerError: read_al_373E> Protein specified in
> ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(       
> 1) =  6KG7.pdb/"

Jed is correct here. The align code is the thing after ">P1;" in your
alignment file (in this case you called it 'template1') not the thing
after "structure:" (that's the name of the PDB file). You can call an
alignment sequence anything you want (including the name of the PDB if
you like).

        Ben Webb, Modeller Caretaker
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