[EMBOSS] extracting sequence from a pdb file

[Peter Rice]

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).

regards,

Peter Rice