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:

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 validation.
Note: If the input file is in PDB format, the TER card must be used to separate each complete polymer.




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.