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==Data Formats==
==Data Formats==


Atomic coordinate files use many possible data formats. The [http://openbabel.org/wiki/XYZ_(format) XYZ format] (file type .xyz) is specifies only the coordinates and chemical element for each atom, and is useful for small molecules. This format is not adequate for macromolecules because additional information is needed for their atoms.
Atomic coordinate files use many possible data formats. The [http://openbabel.org/wiki/XYZ_(format) XYZ format] (file type .xyz) specifies only the coordinates and chemical element for each atom, and is useful for small molecules. This format is not adequate for macromolecules because additional information is needed for their atoms.


Macromolecular atomic coordinate files need to specify quite a bit of information in addition to the position of each atom in space and its chemical element. Each atom either belongs to a [[Standard Residue]] or not. If not, it is designated a ''[[Hetero atoms|hetero atom]]''. The position of each atom within a [[Standard Residue | standard residue]] is specified, e.g. carbon atoms in amino acids can be the carboxy carbon (C), the alpha carbon (CA), the beta carbon (CB), and so forth. Nitrogen atoms can be in the main chain (N), or on the sidechain, e.g. in the terminal zeta position in lysine (NZ). In addition to the name of the residue to which an atom belongs are provided the name of the chain where the residue is found, and its sequence number position. In addition to the X, Y, and Z coordinates are given an occupancy value, and an ''isotropic B value'' or [http://help.proteinexplorer.org#temperature ''temperature value']'.
Macromolecular atomic coordinate files need to specify quite a bit of information in addition to the position of each atom in space and its chemical element. Each atom either belongs to a [[Standard Residue]] or not. If not, it is designated a ''[[Hetero atoms|hetero atom]]''. The position of each atom within a [[Standard Residue | standard residue]] is specified, e.g. carbon atoms in amino acids can be the carboxy carbon (C), the alpha carbon (CA), the beta carbon (CB), and so forth. Nitrogen atoms can be in the main chain (N), or on the sidechain, e.g. in the terminal zeta position in lysine (NZ). In addition to the name of the residue to which an atom belongs are provided the name of the chain where the residue is found, and its sequence number position. In addition to the X, Y, and Z coordinates are given an occupancy value, and an ''isotropic B value'' or [http://help.proteinexplorer.org#temperature ''temperature value']'.
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===PDB Data Format===
===PDB Data Format===


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'' or ''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).


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====Retirement of PDB Format====
====Retirement of PDB Format====
In February, 2019, the PDB announced that new depositions must be in the mmCIF format beginning July 1, 2019<ref name="endOfPDBFormat">[https://lists.sdsc.edu/pipermail/pdb-l/2019-February/006209.html Mandatory PDBx/mmCIF format files submission for MX depositions]: posted on the PDB email list Feb 20, 2019 by Jasmine Young, Biocuration Team Lead, RCSB PDB. The wwPDb website also posted [http://www.wwpdb.org/news/news?year=2019#5c6ad3c5ea7d0653b99c8766 this document].</ref>. The PDB expects to retire PDB format files by 2021, in part because all 3-character ligand (chemical component identifier) codes will have been used<ref name="endOfPDBFormat" />. The PDB sometimes refers to the mmCIF format as "PDBx", which should not be confused with the original PDB format.
In February, 2019, the [[wwPDB]] announced that new depositions must be in the mmCIF format beginning July 1, 2019<ref name="endOfPDBFormat">[https://lists.sdsc.edu/pipermail/pdb-l/2019-February/006209.html Mandatory PDBx/mmCIF format files submission for MX depositions]: posted on the PDB email list Feb 20, 2019 by Jasmine Young, Biocuration Team Lead, RCSB PDB. The wwPDb website also posted [http://www.wwpdb.org/news/news?year=2019#5c6ad3c5ea7d0653b99c8766 this document].</ref>. The PDB sometimes refers to the mmCIF format as "PDBx", which should not be confused with the original legacy PDB format.
 
In December, 2023, the [[wwPDB]] announced that all 3-character ligand ID codes had been exhausted <ref name="nomore3s">[https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 PDB Entries with Novel Ligands Now Distributed Only in PDBx/mmCIF and PDBML File Formats], wwPDB News, December 12, 2023.</ref>. Thereafter, new entries with novel ligands will be available only in mmCIF format, since the legacy PDB format cannot accommodate the new 5-character ligand IDs. Examples that use 5-character ligand IDs: [[8rox]] has [https://www.rcsb.org/ligand/A1H17 A1H17]; [[8vkz]] has [https://www.rcsb.org/ligand/A1ACE A1ACE].
 
In 2024, the [[wwPDB]] estimates that all 4-character [[PDB ID code]]s will be consumed by 2029<ref name="spring2024">[https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2024q2/deposit.html#two Resources for Supporting the Extended PDB ID Format (pdb_00001abc)], Spring 2024 Issue of the RCSB PDB Newsletter.</ref>. Thereafter, new entries will be available only in mmCIF format using [[PDB_identification_code#Future_Plans_for_Expanded_PDB_Codes|12-character ID codes]].


===mmCIF Data Format===
===mmCIF Data Format===


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. While this 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, in 2021<ref name="endOfPDBFormat" />.
[[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]
====Models 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.
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===
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