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.

News Index

• 07/22 Prepare Depositions Using pdb_extract

• 07/22 PDB-101 Focus: Peak Performance

• 07/18 Meet the RCSB PDB at ACA 75

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

• 07/15 Color the Diverse 3D Shapes Studied by Crystallographers

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