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.

You may also display the occluded surface dots on one chain or the other as in the following figures of glycophorin A transmembrane helix dimer. Any dimeric protein structure may be used, but the PDB file must be renumbered as described above.

These images were created in PyMOL where the occluded surface dots are color coded to raylength, green=long, red = short.
For example, if running on a PDB file with renumbered two chains where chain one was 70-98 and chain two was 99-127, you must run os twice.
The first os.fil would be, 
pdbfile 
70 
98 
y
Copy the os_v76/bin/Disp_interchain_dots.py to your working directory (where the raydisp.lst file is located).
Then load your PDB file in PyMOL and enter the following: 
PyMOL> run Disp_interchain_dots.py
PyMOL> dots firstres=70, lastres=98
These commands should give you something similar to the figures above.

To obtain corresponding occluded surface dots on the other chain, the second os.fil would be, 

pdbfile
99
127
y
Run os again and visualize occluded dots on chain two, using firstres=99, lastres=127 in PyMOL.