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 or the easily-installed 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: , , and . 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:
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Aimless
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DIALS
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d*TREK
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HKL-2000
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HKL-3000
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Pointless
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Scala
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Scalepack
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XDS
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Xia2
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Xscale
