Atomic coordinate file: Difference between revisions
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Atomic coordinate files use many possible data formats. The 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 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. | ||
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 | 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 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. | ||
