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PDBX

pdbx is a current rewrite of an internal PDBx/mmCIF toolkit for use with other lab projects. The new tools seek to be compatible with current local data and usable with the V4.0 and V5.0 editions with official specification changes provided by wwPDB. The preferred format of the live PDB, to current knowledge, is V3.30 where possible and PDBx/mmCIF otherwise (see wwPDB FAQ). Additionally, related structure pipelines in the wild (incl. the AMBER molecular dynamics suite) may produce PDB files that do not strictly adhere to any specific version, so it is necessary to consider flexibility in the format specification.

General syntax examples of the format can be found here. wwPDB provides the legacy PDB specification here. A comparative source of implementation can be found on the OpenStructure documentation here.

Contributing

Project documentation is provided in English. Please contact the author(s) if you have any questions.