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
and
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,
Cheers,
Cedric
Hi,
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
Thanks,Liliana--
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