Rapid command-line access to the PDB

This is hardly earth-shattering stuff, but just for reference.

There are multiple ways to grab PDB files from the RCSB PDB servers. If you know the accession code of a structure, the simplest way is wget (or similar) straight off the FTP or HTTP server:

FTP
wget ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdbXXXX.ent.gz

HTTP
wget http://www.rcsb.org/pdb/files/XXXX.pdb.gz

where XXXX is the 4-character PDB accession code.

Note the recent change of URL for the PDB archive: ftp://ftp.wwpdb.org. Note also the confusing 2, not 3 “w” in the URL.

5 thoughts on “Rapid command-line access to the PDB

  1. freesci

    Thanks! That actually inspired me to put this command into a bash script I called getpdb:


    #!/bin/bash
    wget ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdb$1.ent.gz

    so I can type “getpdb 1hio” and have the file downloaded to the current directory. Again, nothing groundbreaking, although I have never thought about simplifying process of getting PDB files.

  2. nsaunders Post author

    This is what I love about using the command line in Linux. There are all these small, self-contained unassuming tools which come together to create an ultra-efficient way of working. I still get a buzz from it after all these years.

    By the way, this list of HTML character codes will help you enter things like the dollar sign in the comments.

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  5. Dominik

    If you like Unix style of command-line work, you may try BioShell:
    http://bioshell.chem.uw.edu.pl/

    which helps you manipulating various files, for example:
    java Strc -ip=4mba.pdb -selection=A.34:108 -op=out.pdb
    to get residues from 34 to 108 from chain A

    The package is written in java and formally you have to start each command with “java”. This may be avoided by an alias (e.g. in your .bashrc file)

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