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

[Peter Cock]

Dear Haun,

Regarding R-value and R-free,

http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/r-value-and-r-free

These seem to be in the REMARK header lines, but I don't work with structures
nowadays so hopefully someone else can help with a working example.

Regarding the tutorial, the first inconsistency was fixed fairly recently,
https://github.com/biopython/biopython/commit/eb947f3d2e496f282bcf5b3e697b2a0b5d676b2c

I've fixed the missing import now:
https://github.com/biopython/biopython/commit/a7be23691656d6663fa5796e7cf1255b1c57654f

These changes will appear on the website copy of the Tutorial as part of the
Biopython 1.70 release (which I expect to happen this week).

Thank you for getting in touch,

Peter

On Mon, Jul 10, 2017 at 10:28 AM, Huan Wang <huan.wang at mail.huji.ac.il> wrote:
> 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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