Format of *.asa-Files produced by NACCESS

The naccess program calculates the atomic accessible surface defined by rolling a probe of given size around a van der Waals surface. This program is an implimentation of the method of Lee and Richards (1971) J.Mol.Biol.55, 379-400. which does just that. The program is dimensioned for up to 20000 atoms, and allows the variation of the probe size and atomic radii by the user.

The atomic accessibility file (.asa file) containing the calculated accessible surface for each atom in a PDB file, as well as the assigned van der Waal radii.

The first 2 residues from an example .asa file are shown below. The output format is PDB, with B-factors and occupancies removed, then atomic accessiblity in square Angstroms, followed by the assigned van der Waal radius. If you want to keep the occupancies and B-factors in, then use the -f option (full) which gives a slightly different (and larger) output format, but is compatible with the hydrogen bond calculation program HBPLUS from Ian McDonald.

ATOM      1  N   ASP A   1     -89.504 -19.110 -26.890  38.573  1.65
ATOM      2  CA  ASP A   1     -89.166 -17.843 -26.186   5.190  1.87
ATOM      3  C   ASP A   1     -89.714 -16.689 -27.001   0.163  1.76
ATOM      4  O   ASP A   1     -90.039 -16.848 -28.177  15.106  1.40
ATOM      5  CB  ASP A   1     -87.651 -17.684 -26.071   9.786  1.87
ATOM      6  CG  ASP A   1     -86.998 -18.791 -25.262   7.899  1.76
ATOM      7  OD1 ASP A   1     -87.430 -19.961 -25.359  18.799  1.40
ATOM      8  OD2 ASP A   1     -86.026 -18.486 -24.535  22.048  1.40
ATOM      9  N   ILE A   2     -89.872 -15.546 -26.355   0.864  1.65
ATOM     10  CA  ILE A   2     -90.356 -14.342 -27.020   0.000  1.87
ATOM     11  C   ILE A   2     -89.124 -13.471 -27.017   0.000  1.76
ATOM     12  O   ILE A   2     -88.662 -13.058 -25.944   0.000  1.40
ATOM     13  CB  ILE A   2     -91.440 -13.617 -26.179   0.000  1.87
ATOM     14  CG1 ILE A   2     -92.624 -14.547 -25.910   7.249  1.87
ATOM     15  CG2 ILE A   2     -91.897 -12.345 -26.878   0.000  1.87
ATOM     16  CD1 ILE A   2     -93.662 -13.945 -25.025   5.352  1.87