[Bioperl-l] PDB Parser

neeti somaiya neetisomaiya at gmail.com
Fri Aug 17 02:23:08 EDT 2007


Hi,

My main concern is just the pdb id and title. PDB id I am able to fetch
easily, but is there a method which can give me the title of the PDB
structure?

Like for example from the following :-

HEADER    DNA/RNA                                 05-DEC-94   100D
TITLE     CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER
TITLE    2 R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO
TITLE    3 PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-
COMPND   3 R(*G)-3');
COMPND   4 CHAIN: A, B;
.
.
.
.

I just want "CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER
R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND
MINOR GROOVE TERTIARY BASE-PAIRING".

Thanks,
Neeti.

On 8/16/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Aug 16, 2007, at 4:59 AM, Sendu Bala wrote:
>
> > neeti somaiya wrote:
> >> I tried using Bio::Structure::IO::pdb with some code like :-
> >> use Bio::Structure::IO;
> >>
> >>     $in  = Bio::Structure::IO->new(-file => " pdb100d.ent",
> >>                                    -format => 'pdb');
> >>
> >>     while ( my $struc = $in->next_structure() ) {
> >>        print "Structure ", $struc->id,"\n";
> >>     }
> >>
> >> It works well. But I am not able to find documentation of other
> >> methods
> >> which will give me various specific details available in a pdb
> >> file, right
> >> from title, keywords, references to structure details, atoms,
> >> coordinates
> >> etc. There must be different methods to fetch and parse each of
> >> this data
> >> from a pdb file, right? Where can I find the details?
> >
> > $struct is a Bio::Structure::Entry, so look at the docs for that:
> > http://doc.bioperl.org/bioperl-live/Bio/Structure/Entry.html
> >
> > You'll probably want to look at the docs for the other Structure
> > modules
> > as well:
> > http://doc.bioperl.org/bioperl-live/Bio/Structure/modules.html
> >
> >
> > I agree, the documentation in this area could be improved.
> > Bio::Structure::StructureI could actually contain something, and
> > Bio::Structure should actually exist or not be referenced in the docs.
>
> There was a discussion a while back on refactoring the code within
> Bio::Structure to better deal with HETATM and other stuff.  As far as
> I'm concerned it's open for anyone wanted to tinker with it.
>
> chris
>



-- 
-Neeti
Even my blood says, B positive


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