[Bioperl-l] PDB Parser

Oliver Wafzig Oliver.Wafzig at sygnis.de
Mon Aug 20 08:42:55 UTC 2007

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 

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. 


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