Downloading PDB Files

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The following lists a sample of Internet sites from which you can download PDB files

1) The Protein Data Bank (PDB) at Brookhaven National Laboratories, U.S.

The PDB can be accessed via the WWW at:

http://www.pdb.bnl.gov/cgi-bin/browse

The URL for a PDB file is:

http://www.pdb.bnl.gov/cgi-bin/get-pdb-entry?id=****&type=text&encoding=none

where **** is the 4-letter code.

The Brookhaven PDB anonymous ftp and gopher servers are at pdb.pdb.bnl.gov

ie. if accessed with a WWW browser the URLs are ftp://pdb.pdb.bnl.gov- the directory /current_release/ contains directories compressed_files/ and uncompressed_files/, each of which contains directories named after the 2nd and 3rd letters of the PDB files they contain- (as in EMBL site, see below);

and gopher://pdb.pdb.bnl.gov- the URL is currently of the form gopher://pdb.pdb.bnl.gov:70/11/PDB/Entries/.****

The Brookhaven PDB WWW home page is at http://www.pdb.bnl.gov

2) PDB Browser at ExPASy (Experimental Protein Analysis System, University of Geneva)

The URL for a PDB file with code **** is

http://expasy.hcuge.ch/cgi-bin/get-pdb-entry?****

3) The anonymous ftp server of EMBL, Heidelberg, Germany

ftp.embl-heidelberg.de

in directory /pub/databases/pdb/current/

Please read the text in this directory

(Access via WWW by clicking on ftp://ftp.embl-heidelberg.de/pub/databases/pdb/current/

The subdirectory compressed/ contains many sub-directories, all of which have 2-character names- they correspond to the 2nd and 3rd characters of the code of the PDB files they contain, e.g. 1abc would be stored in directory /pub/databases/pdb/current/compressed/ab/ The filenames are of the form pdb****.ent and can also be obtained in Unix-compressed format.

The EMBL WWW home page is at http://www.embl-heidelberg.de/

4) The PDB Browser at the Martin Luther University, Halle-Wittenberg, Germany

The URL is of the form:

http://www.biochemtech.uni-halle.de/cgi-bin/send-text?filename=****

5) The PDB Browser at the Institute of Biochemistry and Biophysics, Warsaw (The Polish National EMBnet Node)

Use http://www.ibb.waw.pl/WWWBrowse/send-image?filename=**** where **** is the 4-character code.

6) Birkbeck College Crystallography Department also has a PDB mirror.

A PDB file can be obtained from the URL http://www.cryst.bbk.ac.uk/PDB/pdb****.pdb where **** is the 4-character code. Note that if you have your browser configured for chemical-MIME, the structure will be fed straight into Rasmol! Alternatively, proceed to the URL http://www.cryst.bbk.ac.uk/PDBtop/current/** where ** are the 2nd and 3rd characters of the 4-character code; you will receive a menu of PDB files. You can retrieve any one of them by using the "Save Link As" option of your WWW browser, e.g. with some versions of Netscape and Mosaic, hold down the Shift key while clicking on the link. With later versions of Netscape clicking on a link with the right mouse button has the same effect.

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