[EMBOSS] extracting sequence from a pdb file

Peter Rice pmr at ebi.ac.uk
Tue Nov 4 18:03:31 UTC 2008

Mehta, Perdeep wrote:
> Hi,
> Does anyone know if there is a program in EMBOSS that can extract protein sequence from a pdb format file?

It depends on the pdb file format.

There is a "pdb" sequence format that reads from the ATOM records, but 
fails on some pdb entries.

There is also a "pdbseq" sequence format (-sf pdbseq on the command line) 
that reads the SEQRES records.

If you find a PDB file that fails to read, please let us know. I just 
tested on an old 2ins entry file and it found zero sequences and failed (it 
  was designed for a cleaned up PDB format).


Peter Rice

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