Dear all,
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
<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).
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.
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.
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
Read this news online
<http://www.wwpdb.org/news/news?year=2023#6455391c1d621d75127a7a46>
Kind regards,
Deborah.
--
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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