Official PDB format
| COLUMNS | DATA TYPE | FIELD | DEFINITION |
|---|---|---|---|
| 1 - 6 | Record name | "ATOM" or "HETATM" | |
| 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. |
| 73 - 76 | LString(4) | segID | Segment identifier, left-justified. |
| 77 - 78 | LString(2) | element | Element symbol, right-justified. |
| 79 - 80 | LString(2) | charge | Charge on the atom. |
Typical examples from PDB-files:
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 76 O GLY A9 6.671 55.354 35.873 1.00 14.75 A
ATOM 77 N ASN A10 6.876 53.257 36.629 1.00 16.09 A
ATOM 62 O GLY A 9 6.791 55.214 35.719 1.00 15.61 4AZU 153
ATOM 63 N ASN A 10 6.892 53.135 36.555 1.00 12.64 4AZU 154
The pdb2adf utility is flexible, and should be able to read most PDB files, even those with incomplete or erroneous line formats. From every ATOM/HETATM line, it tries to read:
- atom number
- atom name
- residuename
- chain identifier
- residue number
- X,Y,Z coordinates
Hints for proper formatting:
- always group together atoms that belong to one residue
- always give the atom name on columns 13-16
- when specifying a chain-id use only letters (or a blank)
