[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: Fred Pontes <>
Date: Tue, 01 Apr 2025 10:21:51 +0100
Fixed! Thank you so much for the explanations.
On Mon, Mar 31, 2025 at 9:18 PM Modeller Caretaker <
> wrote:
> 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
> --
> https://salilab.org/modeller/
> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
>
>
--
Frederico José de S. Pontes
PDRA at LICAMM
University of Leeds
Fixed! Thank you so much for the explanations.
On Mon, Mar 31, 2025 at 9:18â?¯PM Modeller Caretaker <">> wrote:
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(Â Â Â Â
> 1) = Â 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).