Prepare Depositions Using pdb_extract

07/22

pdb_extract is used to extract information from the output files produced by many software for structure determination and to generate a complete PDBx/mmCIF data file ready for PDB deposition

pdb_extract is a pre-deposition service for preparing reusable metadata file and/or structure model files in PDBx/mmCIF format for efficient multiple depositions via wwPDB OneDep deposition.

pdb_extract merges coordinate data, author-provided metadata, and data processing information from output files produced by structure determination programs into a complete PDBx/mmCIF file that can used for easy deposition with OneDep. Use the pdb_extract online form or the easily-installed command line interface (Python).

Depositors are encouraged to use method-specific metadata templates (X-Ray, EM, NMR) to prepare a re-usable common metadata file in PDBx/mmCIF format. This metadata file can then be uploaded to OneDep directly for map-only 3DEM depositions or be merged with coordinate file using pdb_extract for OneDep deposition.

Recent Improvements

• Log parsing from major XFEL programs CrystFEL and cctbx.xfel
• Log parsing from refinement programs Phenix and Refmac
• Generation of a OneDep deposition readiness report
• Option to download a metadata-only file as a template for related structures
• Option to download a map-only-metadata file for related 3DEM map-only depositions

Easily Prepare Common Metadata

Depositors are encouraged to use the PDBj CIF editor to easily edit a template file to include corresponding metadata (sequence, crystallization condition, etc.). Method-specific templates have been pre-loaded into the PDBj CIF editor (X-ray, 3DEM, and NMR). Click on the top-left menu (light gray widget icon) to save the edited metadata file in PDBx/mmCIF. Upload this completed file in pdb_extract to prepare single or multiple related structures for submission.

New Features Index

• 07/22 Prepare Depositions Using pdb_extract

• 07/15 wwPDB News: Transitioning to PDBx/mmCIF and Extended PDB IDs

• 07/03 Register for the Aug 11 Virtual Office Hour on Pairwise Alignment

• 07/01 Watch the Webinar: Python For Cheminformatics-Driven Molecular Docking

• 06/25 wwPDB News: Extension to EMDB Accession Codes

• 06/16 Register for the ACA Workshop on PDB Deposition

• 06/09 Watch the Sequence Annotations Viewer Office Hour

• 05/28 Explore Integrative Structures at RCSB.org

• 05/22 Register Now for Tutorial: Introduction to Molecular Animation

• 05/19 Announcement: Ligand Expo To Be Retired in 2025

• 05/06 Watch the Webinar: Seeing Bird Flu in 3D

• 04/28 Watch the Webinar: Streamlining Access to RCSB PDB APIs with Python

• 04/22 wwPDB Validation Reports Accessible via API

• 04/16 wwPDB News: Download Snapshots of the PDB Core Archive via HTTPS, SYNC, RSYNC, or FTP

• 04/15 Introducing Extended PDB IDs at RCSB.org

• 04/08 Sequence Annotations Viewer: Geometry Validation

• 03/27 Register Now for Crash Course: Python For Cheminformatics-Driven Molecular Docking

• 03/24 Developers: Switch to Sequence Coordinates Service by May 31, 2025

• 03/06 Register for the April 10 Virtual Office Hour on Sequence Annotations Viewer

• 03/04 Take the User Survey on Statistics and Win

• 03/03 Register for the May 8 Workshop on PDB Deposition

• 03/03 Register for March Training Events

• 02/25 Register for the April 7 Virtual Office Hour on Depositing IHM Data

• 02/17 Register Now for Webinar on API Access with Python

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• 02/02 Register Now for Webinar on Seeing Bird Flu in 3D

• 01/28 Frontiers in Data Panel Webinar: Preparing Structural Science Data for 2085

• 01/23 Developers: Collaborate with RCSB PDB at Rutgers

• 01/21 Watch the Webinar: Unlock Rapid Analyses Across the Whole PDB Using BinaryCIF

• 01/16 wwPDB News: PDB-Dev now PDB-IHM

• 01/12 Paper Published: Updated resources for exploring PDB structures and Computed Structure Models

• 01/05 wwPDB News: Time-stamped Copies of PDB and EMDB Archives