Atomic coordinate file: Difference between revisions
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The most popular macromolecular data format among crystallographers is the one developed and used by the early (1970's) [[Protein Data Bank]], called the ''Protein Data Bank Format'', ''PDB Format'', or ''legacy PDB format''. Data files in this format are called ''PDB Files'' (file type .pdb). Although this format has serious limitations, it remains popular partly because the data files are in plain text, and are relatively easy to read by humans. | The most popular macromolecular data format among crystallographers is the one developed and used by the early (1970's) [[Protein Data Bank]], called the ''Protein Data Bank Format'', ''PDB Format'', or ''legacy PDB format''. Data files in this format are called ''PDB Files'' (file type .pdb). Although this format has serious limitations, it remains popular partly because the data files are in plain text, and are relatively easy to read by humans. | ||
The [[wwPDB]] provides the [https://www.wwpdb.org/documentation/file-format complete description of the final PDB format] (version 3.30, November, 2012). | |||
PDB format cannot accommodate >99,999 atoms/model, or >62 chains (see [[Jmol/Visualizing large molecules]]). In August, 2021, the PDB format accommodates >99% of [[X-ray crystallography]] entries, but only about 86% of [[cryo-EM]] entries<ref>The ''advanced search'' at RCSB.org has a field ''Deposition'', ''Compatible with PDB format''.</ref>. The remainder are available in mmCIF format (see below). 88% of entries were determined by X-ray, and 4.5% by cryo-EM. For the entire database as a whole, 98.8% of entries are available in PDB format (August, 2021). | PDB format cannot accommodate >99,999 atoms/model, or >62 chains (see [[Jmol/Visualizing large molecules]]). In August, 2021, the PDB format accommodates >99% of [[X-ray crystallography]] entries, but only about 86% of [[cryo-EM]] entries<ref>The ''advanced search'' at RCSB.org has a field ''Deposition'', ''Compatible with PDB format''.</ref>. The remainder are available in mmCIF format (see below). 88% of entries were determined by X-ray, and 4.5% by cryo-EM. For the entire database as a whole, 98.8% of entries are available in PDB format (August, 2021). | ||
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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 2029<ref name="spring2024" /><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] | ||
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====Models Available Only in mmCIF Format==== | ====Models Available Only in mmCIF Format==== | ||
In | In January, 2026, 5.0% of the entries in the [[wwPDB]], 12,341 of 247,417 entries, are available only in mmCIF format. 42% of these were determined by electron microscopy, whereas only 13% of '''all''' entries were determined by electron microscopy. 83% of all electron microscopy entries are available in PDB format. | ||
available in | *In July, 2025, 4.1% of entries (9,743 of ~238,000) were available only in mmCIF format. | ||
*In April, 2024, 2.3% of entries (5,038 of 218,,293) were available only in mmCIF format. | |||
*At the end of 2019, 0.7% of entries (1,086 of 158,815) were 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 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. | ||
