[modeller_usage] Re: Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1)
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Subject: [modeller_usage] Re: Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1)
From: Modeller Caretaker <>
Date: Mon, 31 Mar 2025 13:18:36 -0700
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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