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

[[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>.

[[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]

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====Models Available Only in mmCIF Format====

In ~~April~~, ~~2024~~, 2.3% of the entries in the [[wwPDB]] are available only in mmCIF format.

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.

*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.

Atomic coordinate file: Difference between revisions

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@@ Line 41: / Line 41: @@
 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 2026<ref name="endOfPDBFormat" /><ref>PMID: 30988261</ref>.
+[[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]
@@ Line 47: / Line 47: @@
 ====Models Available Only in mmCIF Format====
-In April, 2024, 2.3% of the entries in the [[wwPDB]] are available only in mmCIF format.
+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.
+*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.