Grid Size 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. Higher resolutions can be achieved by decreasing the grid size at the cost of CPU time. Default value is 3.5 A and should work in most cases.