PDB Extract is a pre-deposition service for assembling structure files for wwPDB OneDep deposition .
Use this online tool (tutorials available) or download the standalone program to run on your local machine. This tool will:

How to Run:

  1. Select your experimental method and upload your fully refined coordinate file
  2. Select the file type and refinement program utilized
  3. Press the RUN button to start pdb_extract
  4. The mmCIF files that you obtain can be used as input for OneDep deposition and validation.
Note: If your input file is in PDB format, TER card must be present at the end of each complete polymer chain.




Note: 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 deposit@deposit.rcsb.org.