Atomic coordinate file: Difference between revisions
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==mmCIF Data Format== | ==mmCIF Data Format== | ||
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 merit, it is unpopular with crystallographers, who prefer to work in the PDB data format. | |||
*[http://mmcif.rcsb.org/ Protein Data Bank's website on mmCIF] | |||
==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 [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. | 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. | ||
