Figure 3.

Grid transformation algorithms in SCT. (a) A two-dimensional schematic of the grid conversion shows how coarse-grained sphere models are derived from atomistic structures. A grid of equal divisions is created that contains all atoms within the input structure. If more than a specified cutoff number of atoms is found within a division, a ‘sphere’ is added to the final model with a radius of half the grid box width. This algorithm is applied in three dimensions to create sphere models from atomistic structures. (b) This schematic shows how up to 26 hydration spheres as required are added to each existing sphere in the ‘dry’ model to produce a hydrated sphere model. Hydration spheres are located on the corners and mid-points of the sides of a cube, with a dimension of four times the sphere radius (r). The original sphere is shown in green, with the hydration locations in black. (c) A hydration layer is required when modelling X-ray scattering data. The hydration layer of water molecules at the surface is added by surrounding each green sphere in the coarse-grained sphere model of the dry protein (top view) with blue hydration spheres of the same radius as shown (middle view). Overlapping and excess blue hydration spheres are subsequently filtered out to match the hydrated volume calculated from the macromolecular sequence, as shown at the bottom.