Box dimensions in Direct Read Out
The direct readout energies are based on statistical potentials of base-amino acid interactions. (Reference) The amino acid and DNA atoms for these calculations are assumed to be enclosed in a box and the box is divided into cubic grids to let the atomic positions only vary by multiples of these grid dimensions. X, Y and Z ranges refer to the box dimensions along these directions. Molecule will be centered first and then the maximum and minimum values of each coordinate are postive and negative values of half the length selected as the range for that coordinate. e.g. If a x range of 30.0 is chosen all atoms within -15.0 to +15.0 will be included in direct energy calculations. These -15.0 and +15.0 are not the coordinates in the PDB file but in the transformed space obtained by centering the molcule.