[BiO BB] How to download Protein complexes from PDB ?

Mike Marchywka marchywka at hotmail.com
Thu Sep 13 11:40:58 EDT 2007

Thanks.  Can you point to something that just returns a single file 
all the matching PDB's as this was the feature at issue?   It looks like 
their java classes
anyway only return hit lists, not a single file containing all the relevant 
pdb entries.
They seem to have an applet but you need to enter a file list,

It looks like it is a bit more complicated than
it really needs to be for what I"m after. I don't have any SOAP code yet but 
I guess it would
be nice eventually. The eutils stuff is here and you can specify most stuff 
simple POST or GET and get back text as one option:


XML and SOAP may seem like universal alternatives to straight text download
but in many cases it is nice to just get text back.
With the straight text, I can more or grep it- may not make sense for many 
but if you've ever tried browsing XML you can appreciate the problem :)

>From: "Shameer Khadar" <skhadar at gmail.com>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] How to download Protein complexes from PDB ?
>Date: Thu, 13 Sep 2007 19:20:07 +0530
>Dear Mike
>I havent use efetch before. Anyway I will look in to that.
>Separately RCSB is providing WebServices and its clients in Java and Perl, 
>think here you will get a programmatic access to the database. But due to
>some strange security reasons my sysadmin people are not allowing me to
>access the webservices.
>http://www.rcsb.org/robohelp/webservices/summary.htm -> Exact URL
>I hope this will help.

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