Extracting Proteins from the PDB: getpdb

The getpdb utility extracts entire proteins or single chains from the PDB database, either as installed locally, or from the RCSB web site. The syntax is:

$SCHRODINGER/utilities/getpdb [options] id1 [id2 ...] 

The id is in the form PDB-code[:Chain-ID]. Multiple proteins or chains can be specified in a space-separated list. For information on command options, see getpdb Command Help.

The database is located by searching the following list of locations, in order:

• $SCHRODINGER_PDB
• $SCHRODINGER_THIRDPARTY
• $SCHRODINGER/thirdparty
• The RCSB web site

The -l option restricts the search to local copies of the PDB, and does not look on the web. The -r option bypasses the local copies and downloads directly from the web.

If you are using a web proxy server, see Access to the Web via a Proxy for Schrödinger Applications for instructions on setting up access.

To extract an entire protein from the PDB database, enter:

$SCHRODINGER/utilities/getpdb PDB-code

For example, the following command retrieves the PDB file for the structure 1AAA:

$SCHRODINGER/utilities/getpdb 1aaa

To extract a single chain, enter:

$SCHRODINGER/utilities/getpdb PDB-code:Chain-ID

For example, the following command extracts all residues (including HETATMs) in chain A and HETATMs with no chain name:

$SCHRODINGER/utilities/getpdb 1ems:A 

Note: The Chain-ID variable is case sensitive, though the PDB-code variable is not. In this example, 1EmS:A would also work, but 1ems:a would produce errors. A chain ID can only be specified for PDB and FASTA formats.