Re: TCoffee Newsgroup: 3D-Coffeenot recognising PDB sequences

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Cedric Notredame

Mar 17, 2022, 1:10:59 PM3/17/22

Dear Liliana,

I suspect an issue in your ATOM field., The way it works is that when providing a PDB *sequence*, T-Coffee starts by checking that the PDB SEQRES matches the PDB *sequence*, if not, it extracts a new SEQRES from ATOM.

The best way to check this is to run

t_coffee -other_pg extract_from_pdb <pdbfile> -seq_field SEQRES -fasta


t_coffee -other_pg extract_from_pdb <PDBFILE> -seq_field ATOM -fasta

My expectation would be that the second CL does not return a usable sequence

Please let me know if this helps,



On 17/3/22 15:00, 'Liliana Oliveira' via Tcoffee wrote:

I'm using T-Coffee locally on Ubuntu. I'm trying to align protein sequences that I have the individual structures/models of in pdb format, however for some reason 3D-coffee does not seem to recognise the sequences within the files and defaults to using proba_pair to look for similar sequences within the PDB database. Has anyone had the same issue or have any idea how to fix it?

At first I thought it was just an issue with reading ATOM but even after I manually added the SEQRES to the pdb files, it still showed the same errors (see below).   

58176 -- WARNING: Could not use SEQRES field in PE-H.pdb -- used ATOM instead [T-COFFEE:WARNING]

pid 59000 -- Method  cannot be applied to [PE-H vs Can_403], proba_pair will be used instead


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