Atomic coordinate file: Difference between revisions
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'''PDB Format.''' The most popular macromolecular data format among crystallographers is the one 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''. 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.''' The most popular macromolecular data format among crystallographers is the one 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''. 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. | ||
*[http://www.wwpdb.org/documentation/format30/index.html Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description] | |||
==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 Ångstroms of each other are deemed to be covalently bonded. (The distance for a bond involving a hydrogen atom is less.) The PDB 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 Ångstroms of each other are deemed to be covalently bonded. (The distance for a bond involving a hydrogen atom is less.) The PDB 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. | ||
