pdb_extract is an online tool which assembles specific details about your experiment and experimental model from your coordinate and structure determination output files in preparation for PDB deposition. This tool will:

  • provide you with an author information form, which can be saved/updated for multiple related entries
  • 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
  • output the coordinate (and structure factor files, if applicable) in mmCIF format for Validation and for deposition at RCSB ADIT or PDBj ADIT.

  1. Select your experimental method (X-ray or NMR)
  2. Upload your fully refined coordinate file
  3. Select the file type and refinement program utilized
  4. Press the RUN button to start pdb_extract
  5. The mmCIF file(s) that you obtain should then be used as input for validation or deposition

Coordinate File File type
Select Program for Structure Refinement If Other:


  • If the refinement program you used is not listed, select OTHER and write the name in the box provided.
  • If the file size is large, it is recommended to upload gzipped (*.gz) or compressed (*.Z) file for faster loading.

Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.

   · Latest Release Notes (New V3.11)
                                    (Aug. 2011)
   · pdb_extract Online
   · X-ray Tutorial   
   · NMR Tutorial   
   · Manual HTML
   · Manual PDF
   · Template Files HTML