The format for an atom record is an integer which describes what to expect in each column of a PDB ATOM record. Each bit in the atom format has a meaning described below.
Bit 0 describes what to expect in the chain letter column (column 22). If there is a chain letter bit 0 should be 1 otherwise it should be 0.
Bit 1 describes what to expect in the occupancy and bfactor columns of the standard PDB ATOM record. If bit 1 is 0, the occupancy and bfactor columns are treated as the occupancy and bfactor. If bit 1 is 1 the bfactor and occupancy columns are treated as if they contain the electrostatic and Van der Waals interaction energies of the atom with respect to the protein. This format is especially useful for output from Blob when the molecule is being positioned in a binding site of the protein.
Bit 2 describes what to expect in the column after bfactor column. This spot is usually blank and if bit 2 is 0 the column is assumed to be blank. If bit 2 is 1 a charge for the atom is expected in this column. This bit is particularly important when a molecule is being positioned in a binding site of the protein. In this case charges are necessary for both the protein and the molecule being positioned.
Bit 3 also describes what to expect in the column after the bfactor column. If Bit 3 is 1 the final column is interpreted as the density score of the atom. This is particularly useful as part of the output format from Blob and the input format for Hits (I would always set this bit for these two situations).
Bits 2 and 3 should never simultaneously be set to 1. Both bits describe the same column. I believe that if both are set the final column is assumed to contain charges.
The above information is summarized in the following table:
| Information | Bit | Flag Number |
| Chain Letter | 0 | 1 |
| Force Field Score | 1 | 2 |
| Charge | 2 | 4 |
| Density | 3 | 8 |
Finally, you calculate the atom format via the deciding which of the feature are present in input or you want present in output and summing their flag numbers. I stress that the density and charge flags should never both be set. If all this seems a bit confusing some examples might help:
Example 1: If your small molecule has no chain letter but does have charges then
Example 2: If you want to save your small molecule with the electrostatic, Van der Waals, and electron density scores of each atom then
Example 3: If your protein PDB file has a chain letter and has charges then