[EMBOSS] extracting sequence from a pdb file
pmr at ebi.ac.uk
Tue Nov 4 18:03:31 UTC 2008
Mehta, Perdeep wrote:
> 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).
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