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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.
 
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).


<table border="1" align="right" width="400"><tr><td>
<table border="1" align="right" width="400"><tr><td>
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To view a PDB file from a PDB code-titled page in Proteopedia, click on the OCA link beneath the molecule. At OCA, scroll down to the Data Retrieval section, and click on ''complete with coordinates'' in the first line there.
To view a PDB file from a PDB code-titled page in Proteopedia, click on the OCA link beneath the molecule. At OCA, scroll down to the Data Retrieval section, and click on ''complete with coordinates'' in the first line there.


To view a PDB file at the [http://www.pdb.org RCSB PDB], go to the page for the [[PDB identification code]] of interest, then on the left, click ''Display Files'', and under that heading, ''PDB File''.
To view the text of a PDB file at the [http://www.rcsb.org RCSB PDB], go to the page for the [[PDB identification code]] of interest, then at the upper right, click ''Display Files'', and under that heading, ''PDB File''.


*[http://proteinexplorer.org/gpsi/pdbtext.htm Simple Diagram of ATOM Records in the PDB Format] (see also [[HETATM]])
*[http://proteopedia.org/wiki/images/0/0c/Pdb_file_diagram.png Simple Diagram of ATOM Records in the PDB Format] (see also [[HETATM]])
*[http://proteinexplorer.org/gpsi/pdbdata.htm What are protein 3D structure data?] with explanations in Jmol.
*[http://www.wwpdb.org/documentation/file-format Protein Data Bank PDB Format Description]
*[http://www.wwpdb.org/docs.html Protein Data Bank Format Description]


====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 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 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===
The [http://www.ncbi.nlm.nih.gov/ US National Center for Biotechnology Information] (NCBI) maintains a macromolecular structure database (derived from the [[Protein Data Bank]]) that is integrated with their ''Entrez'' cross-database search system, and their other databases of sequences, medical literature, inheritance, taxonomy, etc. They have chosen to maintain their [[Atomic coordinate files|atomic coordinate files]] in the Abstract Syntax Notation One (ASN.1) data format.
The [http://www.ncbi.nlm.nih.gov/ US National Center for Biotechnology Information] (NCBI) maintains a [https://www.ncbi.nlm.nih.gov/structure macromolecular structure database] (derived from the [[Protein Data Bank]]) that is integrated with their [https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Entrez/ ''Entrez'' cross-database search system], and their other databases of sequences, medical literature, inheritance, taxonomy, etc. They have chosen to maintain their [[Atomic coordinate files|atomic coordinate files]] in the Abstract Syntax Notation One (ASN.1) data format.


*[http://www.ncbi.nlm.nih.gov/Sitemap/Summary/asn1.html Introduction to ASN.1 at NCBI]
*[https://www.ncbi.nlm.nih.gov/Structure/asn1.html Introduction to ASN.1 at NCBI]


==Bonds: Connectivity==
==Bonds: Connectivity==


Typically, atomic coordinate files do not specify covalent bonds between atoms. Molecular modeling or visualization software determines the positions of covalent bonds using simple rules. Typically, any two non-hydrogen atoms within 1.9 &Aring;ngstroms of each other are deemed to be covalently bonded. (The distance for a bond involving a hydrogen atom is less.) The [http://www.wwpdb.org/docs.html PDB data format] requires that covalent bonds be specified between atoms that are not members of [[Standard Residues]] in protein or nucleic acid chains. These are specified in CONECT records.
Typically, atomic coordinate files do not specify covalent bonds between atoms. Molecular modeling or visualization software determines the positions of covalent bonds using simple rules. Typically, any two non-hydrogen atoms within 1.9 &Aring;ngstroms of each other are deemed to be covalently bonded. (The distance for a bond involving a hydrogen atom is less.) The [http://www.wwpdb.org/documentation/file-format PDB data format] requires that covalent bonds be specified between atoms that are not members of [[Standard Residues]] in protein or nucleic acid chains. These are specified in CONECT records.


==See Also==
==See Also==

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