PyMOL can render very large (huge) surfaces of proteins, using a few tricks. First off, you should know that because of the size, you do not get the level of accuracy that you would for a smaller molecule. However, if you need to represent a molecule (or object) with a few million atoms, this may be your option of choice.
The output from the example below is shown below. The PDB 1AON has nearly 60,000 atoms. This isn't the largest PDB, but it's a good example.
Strategy 1: Low resolution Gaussian Map
# load a whopping big PDB fetch 1aon, struct, async=0 # create a color spectrum over the object spectrum count, selection=struct # === now create a pseudo-fcalc map (a 3D volumetric scalar field) === # set the B-factors nice and high for smoothness set gaussian_b_floor, 40 # ~10 A map resolution set gaussian_resolution, 10 # ~10 A map spacing with a 10 A surrounding buffer # (you may need to vary this) map_new map, gaussian, 10, struct, 10 # create a surface from the map isosurface surf, map, 1.0 # now color the map based on the underlying protein ramp_new ramp, struct, [0,10], [atomic, atomic] color ramp, surf # hide the ramp disable ramp
Strategy 2: CA-only model with oversized radii
# load a whopping big PDB fetch 1aon, struct, async=0 # reduce to CA atoms only remove struct & not guide # create a color spectrum over the object spectrum count, selection=struct # increase VDW radii to compensate volume of missing non-CA atoms alter struct, vdw=4 # increase VDW radius of solvent set solvent_radius, 4, struct # show molecular surface as surface