wwPDB 2022 News

Contents

01/18/2022 Improved support for extended PDBx/mmCIF structure factor files
01/05/2022 Time-stamped Copies of PDB and EMDB Archives

01/18/2022

Improved support for extended PDBx/mmCIF structure factor files

Extensions to the PDBx/mmCIF dictionary for reflection data with anisotropic diffraction limits, for unmerged reflection data, and for quality metrics of anomalous diffraction data are now supported in OneDep.

In October 2020, a subgroup of the wwPDB PDBx/mmCIF Working Group was convened to develop a richer description of experimental data and associated data quality metrics. Members of this Data Collection and Processing Subgroup are all actively engaged in development and support of diffraction data processing software. The Subgroup met virtually for several months discussing, reviewing, and finalizing a new set dictionary content extension that were incorporated into the PDBx/mmCIF dictionary on February 16, 2021. A reference implementation of the new content extensions has been developed by Global Phasing Ltd.

These extensions facilitate the deposition and archiving of a broader range of diffraction data, as well as new quality metrics pertaining to these data. These extensions cover three main areas:

  1. scaled and merged reflection data that have been processed to take account of diffraction anisotropy, by providing descriptors for that anisotropy, in terms of (1) a parameter-free definition of a cut-off surface by means of a per-reflection “signal” and a threshold value for that signal, and (2) the ellipsoid providing the best fit to the resulting cut-off surface;
  2. scaled and unmerged reflection data, by providing extra item definitions aimed at ensuring that such data can be meaningfully re-analysed, and their quality assessed independently from the associated model, after retrieval from the archive;
  3. anomalous diffraction data, by adding descriptors for numerous relevant, but previously missing, statistics.

The new mmCIF data extensions describing anisotropic diffraction now enable archiving of the results of Global Phasing’s STARANISO program. Developers of other software can make use of them or extend the present definitions to suit their applications. Example files created by autoPROC, BUSTER (version 20210224) and Gemmi that are compliant with the new dictionary extensions are provided in a GitHub repository.

These example files, and similarly compliant files produced by other data processing and/or refinement programs, are suitable for direct uploading to the wwPDB OneDep system. Automatic recognition of that compliance, implemented by means of explicit dictionary versioning using the new pdbx_audit_conform record, will avoid unnecessary pre-processing at the time of deposition. This improved OneDep support will ensure a lossless round trip between data processing/refinement in the lab and deposition at the PDB.

wwPDB strongly encourages structural biologists to always use the latest versions of structure determination software packages to produce data files for PDB deposition. wwPDB also encourages crystallographers wishing to deposit new structures together with their associated diffraction data to use the software which guarantees consistency between data and final model. This consistency is difficult to achieve when separate diffraction data files and model coordinate files are pieced together a posteriori by ad hoc means.

wwPDB also encourages depositors to make their raw diffraction images available from one of the public repositories to allow direct access to the original diffraction image data.

01/05/2022

Time-stamped Copies of PDB and EMDB Archives

<I>A snapshot of the PDB Core Archive (ftp://ftp.wwpdb.org) as of January 3rd, 2022 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. </I>A snapshot of the PDB Core Archive (ftp://ftp.wwpdb.org) as of January 3rd, 2022 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org.

A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org) as of January 3, 2022 has been added to ftp://snapshots.wwpdb.org and ftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.

The directory 20220103 includes the 185541 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core Archive is 923 GB.

A snapshot of the EMDB Core archive (ftp://ftp.ebi.ac.uk/pub/databases/emdb/) as of January 3, 2022 can be found in ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20220103/ and ftp://snapshots.pdbj.org/20220103/. The snapshot of EMDB Core Archive contains map files and their metadata within XML files for both released and obsoleted entries (18059 and 254, respectively) and is 4.5 TB in size.