There are several sets of general parametric data required for various operations on atomic coordinates and sequences. These files are all located in the bsoft/parameters directory.
This file contains atomic properties such as the atomic number, the atomic weights (Pure Appl. Chem., Vol. 73, No. 4, pp. 667-683, 2001.) and the electron scattering coefficients required to calculate atomic cross-sections for electron microscopy (Peng et al., Acta Cryst. (1996). A52, 257-276). Any program reading atomic coordinates requires this file to retrieve at least the atomic weights. The program "bsf" uses the scattering curves to calculate the Fourier space representation of atomic structures.
This file contains protein residue properties such as mass, volume, charge, and hydrophobicity. In addition, it has a residue similarity matrix based on the BLOSUM62 matrix. Most of the sequence analyses requires information from this file.
This file encodes all the symmetry information for the crystallographic space groups. This was derived from the symop.lib file from the CCP4 software suite.
These files specify kernels for convolution filters used by the program bfilter. The first line of the file gives the dimensions of the kernel. The subsequent lines give all the values of the kernel in order, with the arrangements per line being arbitrary. Here is a typical kernel for a Sobel filter in the y direction, called SobelY.krn:
3 3 3
1 3 1
0 0 0
-1 -3 -1
3 6 3
0 0 0
-3 -6 -3
1 3 1
0 0 0
-1 -3 -1