[Bioperl-l] PDB Parser

neeti somaiya neetisomaiya at gmail.com
Mon Aug 20 13:39:01 EDT 2007


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


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