[modeller_usage] Re: Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1)

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 -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage