[wwPDB] Prepare Depositions Using New pdb_extract Features

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 that been re-engineered (Python).

Coordinate Data

Uploaded coordinate files (PDBx/mmCIF or PDB) will be checked against the PDBx/mmCIF dictionary. Legacy PDB formatted files will be converted to a OneDep-compliant PDBx/mmCIF data file.

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.

Structure Determination Output Files

Upload the log file produced during data processing, and pdb_extract will parse the related diffraction metadata. Log files from various standalone packages and from CCP4 and autoPROC pipelines are supported, including:

• Aimless
• DIALS
• d*TREK
• HKL-2000
• HKL-3000
• Pointless
• Scala
• Scalepack
• XDS
• Xia2
• Xscale

[ wwPDB News ]