Atomic coordinate file: Difference between revisions

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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 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']'.

~~'''~~PDB 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.

==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.

[[Image:Pdb_file_diagram.gif|frame|right|[http://proteinexplorer.org/gpsi/pdbtext.htm Simple Diagram of ATOM Records in the PDB Format] ]]

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*[http://proteinexplorer.org/gpsi/pdbdata.htm What are protein 3D structure data?] with explanations in Jmol.

*[http://www.wwpdb.org/documentation/format30/index.html Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description]

==mmCIF Data Format==

==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 Ångstroms 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/format30/index.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.

Atomic coordinate file: Difference between revisions

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@@ Line 9: / Line 9: @@
 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 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']'.
-'''PDB 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.
+==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.
 [[Image:Pdb_file_diagram.gif|frame|right|[http://proteinexplorer.org/gpsi/pdbtext.htm Simple Diagram of ATOM Records in the PDB Format] ]]
@@ Line 20: / Line 22: @@
 *[http://proteinexplorer.org/gpsi/pdbdata.htm What are protein 3D structure data?] with explanations in Jmol.
 *[http://www.wwpdb.org/documentation/format30/index.html Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description]
+==mmCIF Data Format==
 ==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/documentation/format30/index.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.