In this format, there is one line per atom. The line starts with the word ATOM for fractional crystallographic coordinates, ATOMC for Cartesian coordinates in Ångstroms, or ATOMG coordinates in crystallographic grid points, followed by the atom type, the atomic coordinates, the individual temperature factor, the occupancy, the atom name (i.e. CA, O, NE1, etc.), the residue name, and chain name (optional) in that order. All alphanumeric fields (atom type, atom name, residue name, and chain name) are left justified. The programs in this package will read a coordinate file with any spacing between elements on a line. To allow the user to write programs to read and write coordinate files using Fortran FORMAT statements the following format is adhered to - (A6,A4,3(1X,F9.4),1X,F6.2,1X,F6.4,1X,A6,2(1X,A4)). The program Convert and can be used to punch a coordinate file in this format if given an arbitrarily spaced ATOM, ATOMC, or ATOMG file.
They also can change coordinate files from one file format to another. Both of these functions are carried out by the PUNCH command.
The coordinate system used for the Cartesian system uses the three axes , , c (This is not the PDB's convention). The program Geometry will display the orthogonalization and deorthogonalization matrixes for any crystal when given a CELL statement followed by the command REPORT STRUCTURE.
REMARK statements may be placed anywhere in the coordinate file. They usually will be echoed to the output device when read and are not passed to any other file.
Here is an example of the format.
ATOMC N 34.6140 40.2998 -0.9950 25.56 1.0000 N 1 ATOMC C 33.6483 41.1420 -0.2133 24.46 1.0000 CA 1 ATOMC C 33.9352 42.6028 0.0604 24.32 1.0000 C 1 ATOMC O 35.0805 43.0812 0.2754 25.61 1.0000 O 1 ATOMC C 33.5180 40.4243 1.2352 22.76 1.0000 CB 1