[Bioperl-l] PDB Parser

neeti somaiya neetisomaiya at gmail.com
Tue Aug 21 05:41:22 EDT 2007


Hi,

I wanted to automate my pdb script, right from downloading of data. As per
the solution given by RCSB about custom report for pdb ids and titles only,
I was trying something like the code below, but it doesnt seem to work :-

my $url = '
http://www.pdb.org/pdb/results/tabularReport.do?reportTitle=CustomReport&customReportColumns=
VStructureSummary.structureId~VCitation.title&format=csv';
use LWP::Simple;
my $content = get $url;
die "Couldn't get $url" unless defined $content;

Can anyone tell how I can do it, if there is any other way to do it, or if I
am going wrong somewhere, or if it is't possible for this case at all.

Please help.

On 8/20/07, neeti somaiya <neetisomaiya at gmail.com> wrote:
>
> Hi,
>
> Thanks for all the responses.
> I got the solution from RCBS people :-
>
> Dear Dr. Somaiya,
>
> Thank you for your email message.
>
> Please try the following:
> 1) Go to http://www.pdb.org/pdb/statistics/holdings.do and select the
> number in the bottom right corner of the table (currently 45213).
> 2) From the menu on the left select 'Tabulate'>>'Custom Report' and
> under 'Primary Citation' select 'Title'
> 3) At the bottom, select 'Create Report' and then one of the 'Download'
> options.
>
> Please let us know if we can be of additional assistance.
>
> Sincerely,
> Rachel Green
>
> On 8/20/07, Bernd Mueller <bernd at kirx.de> wrote:
> >
> > Hello,
> >
> > Maybe you wanna try the Database-EUtilities module from bioperl. They
> > are described on http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
> >
> > I tried them for a similar search on pubmed but without any reasonable
> > results because my target was too focused.
> >
> > From EUtilities documentation on
> >
> > http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpentrez.section.EntrezHelp.The_Databases
> >
> > "Protein Database
> >
> > The Protein database contains sequence data from the translated coding
> > regions from DNA sequences in GenBank, EMBL, and DDBJ as well as protein
> >
> > sequences submitted to Protein Information Resource (PIR), SWISS-PROT,
> > Protein Research Foundation (PRF), and Protein Data Bank (PDB)
> > (sequences from solved structures). "
> >
> > So PDB is included in eutilities from NCBI.
> >
> > Regards,
> > Bernd
> >
> > neeti somaiya wrote:
> > > Thanks for your response.
> > > Actually I am looking for something standalone and not on the web, as
> > in
> > > something which I can download onto my machine and parse later to get
> > id and
> > > title.
> > >
> > > On 8/20/07, Oliver Wafzig <Oliver.Wafzig at sygnis.de> wrote:
> > >> On Monday 20 August 2007 06:33, neeti somaiya wrote:
> > >>> Another question I had was, I am interested only in pdb id and
> > title,
> > >> and
> > >>> for this I am downloading and unzipping each of the full pdb
> > structure
> > >>> files, parsing to get just id and title. Is there any other data
> > source
> > >> Hi Neeti,
> > >> this is a non bioperl way to download the data.
> > >> Use the SRS server on the EBI page to download only id and title
> > lines
> > >> from
> > >> pdb.
> > >>
> > >> 1) Point your browser to the SRS page (http://srs.ebi.ac.uk ).
> > >> 2) Search for 'PDB' on the 'library page' and select it.
> > >> 3) Use the standard query form. Select 'id' in the dropdown list and
> > >> insert '*' (wildcard).
> > >> 4) Create a view by selecting 'ID' and 'Title', then click the search
> > >> button.
> > >> 5) Click the save results button.
> > >> 6) Select 'file' in the 'output to' area and 'ALL' in the 'Number of
> > >> entries
> > >> to download' field. Press 'save'.
> > >>
> > >> If the download is slow, read the 'download tips' on the download
> > page and
> > >> split the results in chunks.
> > >>
> > >> --
> > >> Oliver
> > >> _______________________________________________
> > >> Bioperl-l mailing list
> > >> Bioperl-l at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > >>
> > >
> > >
> > >
> >
> > --
> > Dipl.-Inform.(FH)
> > Bernd Mueller
> > phone: +49 179 2336692
> > email: bernd at kirx.de
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> -Neeti
> Even my blood says, B positive
>



-- 
-Neeti
Even my blood says, B positive


More information about the Bioperl-l mailing list