The Normalized Packing Value is calculated for each residue. This value is 0.0 for completely exposed residues and is 1.0 for the impossible case where 100% of molecular surface is in contact with other van der Waals surface. The average for a protein is dependent on the molecular weight of the protein.
For each atom that has occluded surface, the value of (os*[1-raylength]) is calculated. These are summed for each residue to give the parameter listed in column four of the output file below. This parameter is divided by the total surface area for that amino acid type to give a normalized packing value listed under "PakVal" in the output file.
Thus, if the complete residue surface is occluded, and all rays have a length of zero, the packing value is the same as the total residue surface area and PakVal = 1.0.
Output is in the file, prot.pak
Resnum Resname OS os*[1-raylen] PakVal
74 THR 36.93 27.61 0.263
75 ? 0.0 0.0 0.0
76 ILE 41.35 20.30 0.178
77 ILE 41.15 24.81 0.219
78 PHE 56.07 38.81 0.269
79 GLY 46.99 35.25 0.659
80 VAL 55.52 38.29 0.397
...
Note: If a residue has zero occluded surface (highly unusual) the residue name will not be listed as for residue 75, above.
The output file, pak.plt, contains columns 1 and 5 from the above file without the column labels for plotting residue number versus Normalized Packing Value.
Revised: