The maximum number of atoms allowed in the PDB files is 200,000. To analyze larger files, download the program and increase the limits. The diffusion accessibility analysis is applied only to the protein atoms (i.e. 'ATOM' records and not heteroatoms or solvent), and only those atoms are contained in the returned PDB file.
The analysis relies on solving Poisson's equation on a 3D grid. The program is set up to use a 0.75 Ang grid. If the protein or nucleic acid molecule is unusually large, the program will automatically increase the grid space to bring the entire grid within set memory limits. After solving Poisson's equation, the program calculates the maximum gradient of the concentration function in the immediate viccinity of each atom and takes that value to be the diffusion accessibility of the atom.
After calculating the diffusion accessibility on a per-atom basis, the program rescales the values to be between 25 and 99 for the purposes of visualization/coloring.
Typical times for a medium size protein and a large protein assembly are as follows:
Fortran program can be downloaded here.