Atomic coordinate file: Difference between revisions
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Eric Martz (talk | contribs) →Data Formats: PDB, mmCIF, etc.: adding content |
Eric Martz (talk | contribs) →Data Formats: PDB, mmCIF, etc.: adding content |
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==Data Formats: PDB, mmCIF, etc.== | ==Data Formats: PDB, mmCIF, etc.== | ||
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 [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 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']'. | ||
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To view a PDB file from a PDB code-titled page in Proteopedia, click on the OCA link beneath the molecule. At OCA, scroll down to the Data Retrieval section, and click on ''complete with coordinates'' in the first line there. | To view a PDB file from a PDB code-titled page in Proteopedia, click on the OCA link beneath the molecule. At OCA, scroll down to the Data Retrieval section, and click on ''complete with coordinates'' in the first line there. | ||
To view a PDB file at the [http://www.pdb.org RCSB PDB], go to the page for the [[PDB identification code]] of interest, then on the left, click ''Display Files'', and under that heading, ''PDB File''. | |||
*[http://proteinexplorer.org/gpsi/pdbtext.htm Simple Diagram of ATOM Records in the PDB Format] | *[http://proteinexplorer.org/gpsi/pdbtext.htm Simple Diagram of ATOM Records in the PDB Format] | ||
