Coordinate Data

    Metadata

    Structure Determination Output Files

Dear PDB-l, pdb_extract (pdb-extract.wwpdb.org) 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 <https://pdb-extract.wwpdb.org/> or the easily-installed command line interface <https://sw-tools.rcsb.org/apps/PDB_EXTRACT/source.html> 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 <https://pdbj.org/cif-editor/#filterErroneousData=false,url=https://pdb-extract.wwpdb.org/help/data_template_xray.cif>, 3DEM <https://pdbj.org/cif-editor/#filterErroneousData=false,url=https://pdb-extract.wwpdb.org/help/data_template_em.cif>, and NMR <https://pdbj.org/cif-editor/#filterErroneousData=false,url=https://pdb-extract.wwpdb.org/help/data_template_nmr.cif>. 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 -- Regards, Jasmine =========================================================== Jasmine Young, Ph.D. Biocuration Team Lead RCSB Protein Data Bank Research Professor Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway, NJ 08854-8087 Email:jasmine@rcsb.rutgers.edu Phone: (848)445-0103 ext 4920 Fax: (732)445-4320 ===========================================================