NAME

getPdbStructures.pl

SYNOPSIS

A Perl utility for downloading a list of files from the Protein Data Bank FTP archive.

USAGE 

  getPdbStructures.pl -l <list of PDB IDs> [-d <location for downloaded files> -s -n -c]

OVERVIEW

getPdbStructures.pl is a Perl program for downloading all Protein Data Bank (PDB) structure files listed in a text file from the PDB FTP archive.

REQUIREMENTS

getPdbStructures.pl requires either one of the following common download utilities. On most systems where Perl is installed, one or both of these utilities should already be present.

1) LWP::UserAgent, a Perl module for downloading files from the World Wide Web. LWP::UserAgent is part of the libwww-perl module, which is available from CPAN. Please see the link in the SEE ALSO section.

2) wget, a common Unix utility for downloading files from the World Wide Web. wget is also available for most Windows operating systems. Please see the link in the SEE ALSO section.

ARGUMENTS

-l <list of PDB IDs> = path to text file listing the PDB IDs you wish to download. This file should contain one four-character PDB ID code per line. Do not separate the lines with commas. See the example in the NOTES section.

-d <location for downloaded files> = path to where you want the directory of downloaded files to be placed (optional)

-s = include structure factor files (optional)

-n = include NMR restraint files (optional)

-c = include mmCIF files (optional)

NOTES

1) Please note that this program will write a file titled ``ls-lR'' in your current working directory.

2) This program will download PDB-format files by default. All downloaded files will be in UNIX-compressed (``.Z'') format.

3) Be aware that only LWP::UserAgent::mirror, but not wget, preserves the original time stamps of the files being downloaded. getPdbStructures.pl is intended only for your personal use, and hence this limitation may be of little consequence to you. Please note that files downloaded by getPdbStructures.pl should not be served to the public through any kind of mirror site.

4) The text file listing of PDB IDs should list the ID codes one per line as follows: 

        100d
        1fjk
        4hhb

The characters can be in either upper or lower case.

EXAMPLES

Example 1: Download only PDB-format files into the same directory that the program is located in. 

        % getPdbStructures.pl -l list.txt

Example 2: Download all four file types (PDB, mmCIF, structure factors, NMR restraints) into another directory. 

        % getPdbStructures.pl -l list.txt -d ./interesting_structures/pdb/download -s -n -c

VERSION

This documentation refers to version 1.0 of getPdbStructures.pl.

Version history: 

  Version  Date        Comments
  1.0      2003-05-09  First release

AUTHOR

David J. Padilla for the Protein Data Bank ( info@rcsb.org )

BUGS

1) Not really a bug, but if your perl location happens to be different from /usr/local/bin/perl, simply run the program as 

  perl getPdbStructures

SEE ALSO 

  http://www.rcsb.org/pdb/ -- Protein Data Bank (PDB) home page
  ftp://ftp.rcsb.org/pub/pdb -- PDB FTP site
  ftp://ftp.rcsb.org/pub/pdb/software -- download page for this script and documentation
  http://www.cpan.org/modules/by-module/LWP/ -- libwww-perl download page
  http://www.gnu.org/software/wget/wget.html -- wget home page

COPYRIGHT 

                            Copyright 2003
               The Regents of the University of California
                          All Rights Reserved


 Permission to use, copy, modify and distribute any part of this PDB
 software for educational, research and non-profit purposes, without fee,
 and without a written agreement is hereby granted, provided that the above
 copyright notice, this paragraph and the following three paragraphs appear
 in all copies.


 Those desiring to incorporate this PDB Software into commercial products
 or use for commercial purposes should contact the Technology Transfer
 Office, University of California, San Diego, 9500 Gilman Drive, La Jolla,
 CA 92093-0910, Ph: (858) 534-5815, FAX: (858) 534-7345.


 In no event shall the University of California be liable to any party for
 direct, indirect, special, incidental, or consequential damages, including
 lost profits, arising out of the use of this PDB software, even if the
 University of California has been advised of the possibility of such
 damage.


 The PDB software provided herein is on an "as is" basis, and the
 University of California has no obligation to provide maintenance,
 support, updates, enhancements, or modifications.  The University of
 California makes no representations and extends no warranties of any kind,
 either implied or express, including, but not limited to, the implied
 warranties of merchantability or fitness for a particular purpose, or that
 the use of the pdb software will not infringe any patent, trademark or
 other rights.