[Biopython] How to get Free R value and Report mistakes in the documents

[Huan Wang]

Dear all,

I am a newbie to Biopython and I would like to extract the Free R values
from PDB files.
After asking Google and browsing the Biopython document, I did not find the
solution yet.

It seems that Biopython only can read and get the resolution and journal
information etc. from the header of the PDB file.
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc150

My question is does the Biopython able to fetch the Free R values from PDB
file? Or I need to write my own script to get those values.


*In addition,* I found two mistakes in the section 11.1.1 Readin a PDB
file.

(1)

>>> from Bio.PDB.PDBParser import PDBParser
>>> p = PDBParser(PERMISSIVE=1)

>>> structure_id = "1fat"
>>> filename = "pdb1fat.ent"
>>> s = p.get_structure(structure_id, filename)

However, the following codes do not work,

>>> resolution = structure.header['resolution']
>>> keywords = structure.header['keywords']

Actually, they should be

>>> resolution = s.header['resolution']
>>> keywords = s.header['keywords']

Because the variable, s, has been defined, however, structure did not.


(2) just below the above-mentioned example,

The dictionary can also be created without creating a Structure object, ie.
directly from the PDB file:

>>> with open(filename, 'r') as handle:
...     header_dict = parse_pdb_header(handle)
...


However, it does not work. The error message is "name
'parse_pdb_header' is not defined ".

*Actually, one need to import the module parse_pdb_header **first*, as
shown below,

*>>> from Bio.PDB import parse_pdb_header*

>>> with open(filename, 'r') as handle:

...     header_dict = parse_pdb_header(handle)
...

Then, header_dict will get the information from the PDB file.


I hope the developers will correct those mistakes in the document. Thank
you very much.

Best wishes,
Huan
.
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