Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file.
So it could probably be '2AHNA' or '2AHNB'.
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
------------------------------
Message: 2
Date: Mon, 9 Apr 2012 17:21:12 +0530
From: Sumedha Roy <>
To: modeller usage <>
Subject: [modeller_usage] Error in ALIGN_CODES(i)
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Hello all,
When I try to model my protein-DNA complex, I get the error:
_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i)
was not found in the alignment file; ALIGN_CODES( 2) = 2AHN
But I see no mistake either in the alignment or the format. I've attached
both the ALI file and model-ligand.py. Please help!!!
--
Sumedha Roy
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Message: 3
Date: Mon, 09 Apr 2012 11:44:11 -0700
From: Modeller Caretaker <>
To: Sumedha Roy <>
Cc: modeller usage <>
Subject: Re: [modeller_usage] Error in ALIGN_CODES(i)
Message-ID: <>
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On 04/09/2012 04:51 AM, Sumedha Roy wrote:
> When I try to model my protein-DNA complex, I get the error:
> _modeller.ModellerError: read_al_373E> Protein specified in
> ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(
> 2) = 2AHN
>
> But I see no mistake either in the alignment or the format. I've
> attached both the ALI file and model-ligand.py. Please help!!!
Your alignment file is in incorrect format. Each sequence must start
with a >P1; header. Your second sequence starts with >P2; instead.
Ben Webb, Modeller Caretaker
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