The data file, os.fil, tells OS
1. the name of the clean PDB file
2. the range of residues to calculate the occluded surface for (all atoms are considering as potential occluding atoms, but the occluded surface is only calculated for those given in the range)
3. whether or not to create a file for display of the extended rays using PyMOL as described here
The format of os.fil is as follows;
filename.pdb 2 167 n
An example to display the rays as in the figure on the first page is:
1stn.pdb 23 23 y
The "y" in the last line causes a file called rays to be generated. How to display the rays using PyMOL is described here.
