pdb_extract

Version Release Notes

Mar 31, 2025: pdb_extract version V4.3 is now released

The improvements of this version compared to the previous version:

• Improve common metadata templates for better coverage of OneDep mandatory data;
• Check output file and generate a OneDep deposition readiness report;
• Allow users to download a metadata-only file as a template for related structures;
• For 3DEM structures, allow users to download a map-only-metadata file for related map-only deposition;
• Add summary of the uploaded model coordinates file;
• Deploy new Flask-based frontend web service with improved user interface.

Feb 23, 2024: pdb_extract version V4.2 is now released

The improvements of this version compared to the previous version:

• Parse XFEL data processing log from cctbx.xfel;
• Parse XFEL data processing log from CrystFEL;
• Repackage the source for simpler installation;
• Resolve the bug in dealing with direct method;

March 8, 2023: pdb_extract version V4.1 is now released

The improvements of this version compared to the previous version:

• Speed up mmCIF file parsing by switching from Python parser to C++ parser, except for dictionary check;
• Fix HKL-3000 log parsing error based on the latest template;
• Add Aimless log parsing from the latest autoPROC template, and combine Aimless log parsing on diffrent tempaltes into one module;
• Convert _software to _em_software for EM entries, and classify the software based on the dominant usage of the software on PDB entries;
• Convert _software to _pdbx_nmr_software for NMR entries, classify the software based on the dominant usage of the software on PDB entries, and add software authors based on OneDep DepUI NMR software author dictionary;
• Check duplicate diffraction id and provide warning;
• On pdb_extract server, add file upload exception handling for binary files or files with non-ASCII characters;
• On pdb_extract server, add _em_software and _pdbx_nmr_software example in mmCIF-formated templates;
• On pdb_extract server, allow author to update sequence if the uploaded mmCIF-formatted file already has sequence;

November 1, 2022: pdb_extract version V4.0 is now released

The improvements of this version compared to the previous version:

• Re-design under python framework;
• Remove dependency on outdated PDB-to-CIF converter by incorporating converter utilized by wwPDB OneDep system;
• Improve mmCIF format checking and dictionary compliance;
• Collaborate with PDBj to use CIF editor for author's template file to ensure future compliance;
• Clean up dependencies on old refinement software packages;
• Simplify the features to support modern refinement and data processing packages only;