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
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