[EMBOSS] extracting sequence from a pdb file

Mehta, Perdeep Perdeep.Mehta at STJUDE.ORG
Tue Nov 4 20:42:40 UTC 2008

Thanks Peter.

The file is standard ATOM record straight from PDB. I will check on that.

Best regards,

-----Original Message-----
From: Peter Rice [mailto:pmr at ebi.ac.uk]
Sent: Tuesday, November 04, 2008 12:04 PM
To: emboss at emboss.open-bio.org
Cc: Mehta, Perdeep
Subject: Re: [EMBOSS] extracting sequence from a pdb file

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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