Atomic coordinate file: Difference between revisions
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In response to the inadequacies of the PDB data format, the International Union of Crystallographers and the | In response to the inadequacies of the PDB data format, the International Union of Crystallographers and the | ||
[[Protein Data Bank | World Wide Protein Data Bank]] have adopted the ''macromolecular crystallographic information format'' (mmCIF) as their primary data format for macromolecules. mmCIF is also sometimes referred to as PDBx (not to be confused with the PDB format). While the mmCIF/PDBx format has considerable merit from the perspective of computer scientists, it is unpopular with crystallographers, who prefer to work in the PDB data format. Therefore, the PDB has maintained the entire database in both formats. However, new depositions must be in the mmCIF format beginning July 1, 2019, and it is anticipated that the PDB format will be phased out, of necessity, around | [[Protein Data Bank | World Wide Protein Data Bank]] have adopted the ''macromolecular crystallographic information format'' (mmCIF) as their primary data format for macromolecules. mmCIF is also sometimes referred to as PDBx (not to be confused with the PDB format). While the mmCIF/PDBx format has considerable merit from the perspective of computer scientists, it is unpopular with crystallographers, who prefer to work in the PDB data format. Therefore, the PDB has maintained the entire database in both formats. However, new depositions must be in the mmCIF format beginning July 1, 2019, and it is anticipated that the PDB format will be phased out, of necessity, around 2026<ref name="endOfPDBFormat" /><ref>PMID: 30988261</ref>. | ||
*[http://mmcif.wwpdb.org/ World Wide Protein Data Bank's website on mmCIF] | *[http://mmcif.wwpdb.org/ World Wide Protein Data Bank's website on mmCIF] | ||
Models with >99,999 atoms, or >62 chains, do not fit in the PDB format (see [[Jmol/Visualizing large molecules]]). Such models are available only in mmCIF format, and not in the PDB format. However, in | ====Models Available Only in mmCIF Format==== | ||
In April, 2024, 2.3% of the entries in the [[wwPDB]] are available only in mmCIF format. | |||
Models with >99,999 atoms, or >62 chains, do not fit in the PDB format (see [[Jmol/Visualizing large molecules]]). Such models are available only in mmCIF format, and not in the PDB format. However, in 2024, such models are available in subsets in PDB format. For example, at [https://www.rcsb.org/structure/5LEG 5LEG], look for "PDB format-like files" in the ''Download Files'' menu. | |||
Models containing ligands with 5-character ID codes (see above) also do not fit in PDB format, and are | |||
available only in mmCIF format. | |||
===ASN.1 Data Format=== | ===ASN.1 Data Format=== | ||