[Bioperl-l] downlaoding pdb files

Jurgen Pletinckx jurgen.pletinckx at algonomics.com
Thu Jun 3 10:47:29 EDT 2004

I don't think such a beast currently exists.

Fortunately, it's fairly easy to get a specific file from the
RCSB web site:

GET "http://www.rcsb.org/pdb/cgi/export.cgi?format=PDB;pdbId=1LRA" >

where 'GET' (also known as lwp-request) is part of the LWP package,
which is a prerequisite of bioperl. In other words, you probably
have this in working order. (I can find E:\Perl\bin\GET and
/usr/local/bin/GET, respectively, on my machines)

Alternatively, there's the RCSB ftp site:

GET ftp.rcsb.org/pub/pdb/data/structures/divided/pdb/lr/pdb1lra.ent.Z >

or the bio-mirror site (which seems slightly faster):

GET bio-mirror.net/biomirror/pdb/data/structures/divided/pdb/lr/pdb1lra.ent.Z >

Take care with the directory paths for the ftp sites - the typical
pdb organisation into two-letter subdirectories is in effect.

I've just taken a look at the disk usage of our copy of the
database - 3.8 gigabytes for the compressed files; 15 gigabytes
for the uncompressed files. If you can spare 20 gigabytes, it's
worthwhile to have a local copy ...

I hope this helps!
Jurgen Pletinckx
AlgoNomics NV

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