Atomic coordinate file: Difference between revisions
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Eric Martz (talk | contribs) →Data Formats: PDB, mmCIF, etc.: polishing |
Eric Martz (talk | contribs) →Bonds: Connectivity: polishing |
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==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 [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. | ||
