[Bioperl-l] PDB Parser

neeti somaiya neetisomaiya at gmail.com
Mon Aug 20 09:05:01 EDT 2007


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
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>



-- 
-Neeti
Even my blood says, B positive


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