[Bioperl-l] how to download PDB files using Bioperl script

Christopher Bottoms maizemu at gmail.com
Wed Oct 27 12:53:26 EDT 2010


Ashwani,

Do you need to download the files once or does this need to be automated?

If you just need to do it once, check out
http://www.rcsb.org/pdb/download/download.do for downloading multiple
files.

If you need to automate the process, let me know and I'll help you
figure it out. The easiest way I can think of, which I used to do, is
downloading them from the ftp site.

Sincerely,

Christopher Bottoms

On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
> Hi, Ashwani,
>
> I havenot found any module in BioPerl for downloading PDB files, though
> Bio::Structure::IO::pdb can parse PDB files.
>
> However, PDB provides RESTful service
> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
> batch downloading the proteins.
>
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
>
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
> Sent: Thursday, October 21, 2010 9:39 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>
> Hi All,
>
>
> I have around 150 pdb file names and I need to download them from Protein
> Data Bank. I wonder if someone could tell me how to do it by using Bioperl.
>
> Thanks in advance.
>
> Regards,
> Ashwani
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