Questions for Morris et al. paper

Definition. You can conveniently define the inside and the outside of a molecule in the following way. A point X is outside if there exists a sphere of radius Rw with center at X that does not intersect any atoms of the molecule. Typically, Rw is taken to be the size of a water molecule, Rw = 1.4 Angstrom, although larger or smaller values of Rw may also be useful. It is assumed that each atom in the molecule is represented by a sphere of the appropriate radius (typically in a range of 1.0 to 1.7 Angstroms, corresponding to the radii of Hydrogen and Carbon atoms, respectively. ) For simplicity, you may assume that these spheres do not interpenetrate. You can visualize the boundary between the inside and the outside as follows. Imagine rolling a sphere of radius Rw around the molecule (wherever it fits). The center of the sphere will trace the molecular boundary, which is often called the solvent accessible surface in this case.

Note. No rigorous proofs are required, just good logic. A good description (with pictures!) of spherical harmonics is available from Wolfram's Math World . You may also work out your answers in 2D. The principle remains the same, but recall that in 2D the spherical harmonics simplify to just cosine and sine functions. If you want to see what real molecular surfaces look like, download and install VMD, then open any protein structure file from the protein data bank . You will need to choose an appropriate surface representation in VMD.