Only interchain occlusion is considered here. To run intchos concatenate the two chains (A and B, or segid A and segid B) into one PDB file and renumber the residues using renum. Then enter the numbers of the first and last residues in chain A in the indicated place in os.run and run os.run.
The program int[er]ch[ain]os is in /sgi/local/os/bin/intchos and can be run standalone if you have a prot.srf file in your directory. The program intchos will ask you for the residue numbers of the first and last residues in chain A. The output will be in intch.os.
For each atom that has occluded surface, the value of os and (os*[1-raylength]) is calculated. These are summed for each residue to give the parameters listed in columns three and four of the output file, intch.os, as shown below.
Output is in the file, intch.os
Resnum Resname OS os*[1-raylen]
...
74 THR 0.45 0.00
75 ? 0.0 0.0
76 ILE 17.29 4.34
77 ? 0.0 0.0
78 PHE 4.05 1.95
79 GLY 23.35 17.54
80 VAL 23.16 14.20
81 ? 0.0 0.0
82 ALA 8.05 4.02
83 GLY 25.96 18.73
84 VAL 21.07 12.72
...
Note: If a residue has zero interchain occluded surface the residue name will not be listed as for residues 75, 77, and 81above.
Note for ligand docking OS: To calculate the ligand/protein OS and os*[1-raylen] change the name of the ligand to UNK in the prot.srf file. The program intchos will not calculate parameters for unrecognized residue names.
Revised: