[−][src]Module nom_pdb::coordinate::atom
Overview
The ATOM records present the atomic coordinates for standard amino acids and nucleotides. They also present the occupancy and temperature factor for each atom. Non-polymer chemical coordinates use the HETATM record type. The element symbol is always present on each ATOM record; charge is optional. Changes in ATOM/HETATM records result from the standardization atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary.
Record Format
| COLUMNS | DATA TYPE | FIELD | DEFINITION |
|---|---|---|---|
| 1 - 6 | Record name | "ATOM " | |
| 7 - 11 | Integer | serial | Atom serial number. |
| 13 - 16 | Atom | name | Atom name. |
| 17 | Character | altLoc | Alternate location indicator. |
| 18 - 20 | Residue name | resName | Residue name. |
| 22 | Character | chainID | Chain identifier. |
| 23 - 26 | Integer | resSeq | Residue sequence number. |
| 27 | AChar | iCode | Code for insertion of residues. |
| 31 - 38 | Real(8.3) | x | Orthogonal coordinates for X in Angstroms. |
| 39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y in Angstroms. |
| 47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z in Angstroms. |
| 55 - 60 | Real(6.2) | occupancy | Occupancy. |
| 61 - 66 | Real(6.2) | tempFactor | Temperature factor. |
| 77 - 78 | LString(2) | element | Element symbol, right-justified. |
| 79 - 80 | LString(2) | charge | Charge on the atom. |
Details
ATOM records for proteins are listed from amino to carboxyl terminus. Nucleic acid residues are listed from the 5' to the 3' terminus. Alignment of one-letter atom name such as C starts at column 14, while two-letter atom name such as FE starts at column 13. Atom nomenclature begins with atom type. No ordering is specified for polysaccharides. Non-blank alphanumerical character is used for chain identifier. The list of ATOM records in a chain is terminated by a TER record. If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records. AltLoc is the place holder to indicate alternate conformation. The alternate conformation can be in the entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. Within a residue, all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator. There are two ways of representing alternate conformation- either at atom level or at residue level (see examples). For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:
- In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry.
- In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together.
Alphabet letters are commonly used for insertion code. The insertion code is used when two residues have the same numbering. The combination of residue numbering and insertion code defines the unique residue. If the depositor provides the data, then the isotropic B value is given for the temperature factor. If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor. Columns 79 - 80 indicate any charge on the atom, e.g., 2+, 1-. In most cases, these are blank. For refinements with program REFMAC prior 5.5.0042 which use TLS refinement, the values of B may include only the TLS contribution to the isotropic temperature factor rather than the full isotropic value.
Structs
| AtomParser |