How I Render Molecular Orbitals

I want to start by saying that I don't like GaussView. It makes rendering of molecular orbitals well enough to convey information but I want very fine grained control over how I stylistically represent data and it bogs down our old Macs. Also, it is not free, which is odd because it is useless without Gaussian. I know that they are making money off of it, but I feel like the freemium model would work better case.

Anyways, Gaussian is a pretty impressive piece of software with really terrible I/O options. To render my molecular orbitals (MOs), I have to use the formchk utility to make .fchk files for the cubegen utility to make .cube files. I usually make a fine mesh for a nicer rendering.

MOs are usually rendered by their isosurface value of the wavefuction or electron density. I use electron density for my isosurfaces. Once I have my isosurface density chosen, I pick a density above and below that and remove all the cells that are outside that range. This filtering drastically speeds up the next step. I scan through all the cells and compute a linear polynomial fit for each cell and its 8 nearest neighbours. Basically, it uses a cell and neighbours to make linear local density function of the form:

rho = a*x + b*y + c*z + d

Since the desired isosurface forms a plane in this function, we can find the point in the plane that is closest to the center of the cell. If this closet point is inside the cell of interest the point is added to the surface point list. 

For each point in the list, I add a sphere with a size close to that of the cell size. This collection of spheres for representing a surface is blended together in POV-Ray using the blob object. The blob object blends the spheres together using the metaballs method for a smooth look. I color the spheres by the sign of the wavefunction at each cell. Here is an example using the highest occupied MO of subphthalocyanine chloride.

Bonus C60 molecule.