[Bioperl-l] PDB Parser

Chris Fields cjfields at uiuc.edu
Mon Aug 20 14:51:14 EDT 2007


Just curious, but what kind of query were you trying?  It might be  
worth trying to work through it to add as an example to the cookbook  
page.

chris

On Aug 20, 2007, at 11:57 AM, Bernd Mueller 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
>
> _______________________________________________
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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