Thank you, Ben! The problem is solved!


From: Modeller Caretaker <>
Date: Monday, November 27, 2023 at 6:23 PM
To: Yang, Li-Yen <>, <>
Subject: Re: [modeller_usage] [modeller] sequence mismatch error

On 11/27/23 2:50 PM, Yang, Li-Yen via modeller_usage wrote:
> I am trying to use the modeler comparative tool in *Chimera* to model
> the structure of a protein (in fasta format) by another similar
> proteinís structure (in pdb format).
> I first associated this sequence (in fasta) with the corresponding chain
> in the pdb, and I used the modeller comparative tool to model the structure.
> However, Iím getting this error: _modeller.SequenceMismatchError:
> read_te_291E> Sequence difference between alignment and pdb :

You would need to see the full error message to be sure what the problem
is, and that's presumably inside Chimera somewhere. I see you asked a
similar question on the Chimera mailing list, so hopefully they can help
you. My guess would be that you have at least one non-standard residue
in your protein, and Chimera is handling it differently from Modeller.

        Ben Webb, Modeller Caretaker
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