pdb_extract is a resource which assembles specific details about your experiment and
experimental model from your coordinate and structure determination output files in
preparation for PDB deposition.
Use this online tool (tutorials available)
or download the standalone program to run on your local machine. This tool will:
- provide an author information form for Xray,
, which can be saved/updated for multiple related entry depositions.
- assemble coordinate and log files pertaining to your specific experimental methods.
- allow you to fix the primary sequence of your protein/nucleotide chains to account for unresolved residues.
How to Run:
Note: If the input file is in PDB format, the TER card must be used to separate each complete polymer.
- Select your experimental method and upload your fully refined coordinate file
- Select the file type and refinement program utilized
- Press the RUN button to start pdb_extract
- The mmCIF files that you obtain can be used as input for
If the file size is large, it is recommended to upload gzipped (*.gz
) or compressed (*.Z
) file for faster loading.
Reference: Huanwang Yang, Vladimir Guranovic, Shuchismita Dutta, Zukang Feng, Helen M. Berman and John D. Westbrook (2004), Acta Cryst. D60, 1833-18399
Questions, comments, and suggestions should be sent to firstname.lastname@example.org.