[Biopython] Understanding pdb biopython

[João Rodrigues]

Hi there,

The numbering in your PDB file is not continuous and it matches to regions
in the structure that are missing residues. Open your PDB structure in
Pymol and you'll see. Alternatively, print the C-N distances (peptide bond)
for consecutive residues and you'll also notice when they are larger than
~3Å it corresponds to your break.

As for your discrepancy between the sequences in the FASTA file and the
PDB, that's just because not all residues are resolved in the crystal
structure.

Cheers,

João

2014-10-24 13:10 GMT-05:00 Sanjeev Sariya <s.sariya_work at ymail.com>:

> Hi All,
> I'm having a hard time using and understanding biopython pdb.
> ./read_pdb_file.py 3OE6.pdb
>
> I'm attaching python script, pdb file, fasta file and output with mail.
> I'have following doubts:
> - When I print the sequence I get in broken pieces. Why?
> - Also the sequence printed doesn't match with the fasta file (attached).
> - Am I doing making a silly mistake?
>
> I am running script as:
> python read_pdb_file.py 3OE6.pdb
>
> Kindly help and guide.
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20141024/d30ff6e8/attachment.html>