Atomic coordinate file: Difference between revisions

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Atomic coordinate files use many possible data formats. The [http://openbabel.org/wiki/XYZ_(format) 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 an ''isotropic B value'' or [http://help.proteinexplorer.org#temperature ''temperature value']'.

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 atoms|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 Data Format===

Atomic coordinate file: Difference between revisions

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@@ Line 7: / Line 7: @@
 Atomic coordinate files use many possible data formats. The [http://openbabel.org/wiki/XYZ_(format) 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 an ''isotropic B value'' or [http://help.proteinexplorer.org#temperature ''temperature value']'.
+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 atoms|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 Data Format===