Gap regions are defined by first filling the region between the two molecules with gap-spheres and then using these to compute a 3D density map which, when contoured, defines the surface of the gap region.
a. Two atoms, A and B, have a trial gap sphere placed midway between their van der Waals surfaces and just touching each one.
b. Neighbouring atoms are then considered in turn. If any penetrate the gap sphere its radius is reduced until it just touches the intruding atom. The process is repeated until all the neighbouring atoms have been considered. If the radius of the sphere falls below some predetermined minimum limit (usually 1.0A) it is rejected. Otherwise, the final gap sphere is saved.
c. The procedure is continued until all pairs of atoms have been considered and the gap region is filled with spheres.
d. The spheres are then used to update points on a 3D array of grid-points using a Gaussian function.
e. The update is such that, when the grid is contoured at a contour level of 100.0, the resultant 3D surface corresponds to each gap sphere.
f. When all the spheres have updated the grid, the final 3D contour represents the surface of the interpenetrating gap spheres, and hence defines the extent of the gap region between the two molecules.