Evaluation of Interchain OS

Only intermolecular occlusion is considered here. To run intchos concatenate the two chains (A and B, or segid A and segid B) or two interacting molecues into one PDB file and renumber the residues using renum. Then enter the numbers of the first and last residues of one chain or one molecule in the indicated place in os.run and run os.run.

The program int[er]ch[ain]os is in the OS installation 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 one chain or one molecule. 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: Wednesday, 16-Dec-1998 11:49:16 EST