Hello,
I am trying to use the modeler comparative tool in Chimera to model the structure of a protein (in fasta format) by another similar protein’s 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, I’m getting this error: _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb :
From the log window, I didn’t get any other details beyond the above error. Does anyone know how I can figure out what is going wrong?
Thank you! I really appreciate it!
Best, Zoey
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 > protein’s 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, I’m 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
Thank you, Ben! The problem is solved!
From: Modeller Caretaker modeller-care@salilab.org Date: Monday, November 27, 2023 at 6:23 PM To: Yang, Li-Yen zoeyxyang@gatech.edu, modeller_usage@salilab.org modeller_usage@salilab.org 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 > protein’s 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, I’m 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 -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
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Modeller Caretaker -
Yang, Li-Yen