OS is a package of programs to calculate the occluded surface and atomic packing of protein model structures.
Occluded surface is defined as the Molecular Surface that is less than 2.8 Angstroms from the van der Waals surface of neighboring, but non-bonded, atoms. The idea is that if a water molecule cannot fit between two atoms, they occlude each other. Occluded surface is similar to buried surface but is more sensitive to packing geometry.
To calculate occluded surface normals at the molecular surface are extended outward until they intersect neighboring van der Waals surface. The collection of extended normals, and their respective lengths, defines the packing of each atom in a structural model. A graphic of the unit normals at the surface of a valine residue and the extended normals that result from extension to neighboring atoms is here.
Analysis of the occluded surface enables one to identify amino acid residues in unusual occluded surface environments compared to a database of high resolution structures. Residues in an unusual environment are frequently incorrectly modeled, involved in crystal contacts, or involved in ligand binding.
A weighted parameter, Psr, related to the occluded surface is within a narrow range for native protein structures; if your model has a Psr value outside this range the model is probably wrong in at least some areas.
Analysis of the collection of extended normals (raylengths) enables an estimation of the packing of the protein both at the residue level and for the protein as a whole. The output list identifies all atoms which interact with each atom in the structure, the surface area involved in the interaction and the average raylength for that interacting patch of surface area.
Analysis of inter-chain occluded surface allows a detailed calculation of protein-protein interactions.
Set the environmental variables each time you start an OS session:
setup os (or source /sgi/local/setup/os.set)
To use the programs you require three files:
1. A PDB file of coordinates. This must be a 'clean' file with no alternate conformations; no hydrogens; and only one chain. You should renumber your multi-chain files to be sequentially numbered, otherwise the output will be unintelligible because chain identifiers are not kept.
A script to clean up a PDB file is described here.
A simple FORTRAN program to renumber your clean PDB file is described here; the executable is:
/sgi/local/os/bin/renum
How to handle RNA, DNA, prosthetic groups and other ligands is described here.
2. A command file, os.run, which is automatically deposited in your current working directory when you set up the environment by typing the following command:
setup os (or source /sgi/local/setup/os.set)
You should uncomment the appropriate lines in os.run to run the different programs in the package.
An example of os.run is here.
3. A data file, os.fil, which tells OS the PDB filename, the residue numbers to calculate, and whether or not you want a file to display the extended normals using MidasPlus.
An example of os.fil with further explanation is here.
If the above have been done, to start simply type:
./os.run
Note: OS takes 5 to 15 secs per residue (depending on the total number of residues). So you should put OS jobs into a short or medium queue. A batch file for submitting an OS job must contain the following:
#!/bin/csh # setenv OSDIR /sgi/local/os setenv PWD $cwd os.run
2. Evaluation of occluded surface environment.
3. Evaluation of the packing of the model.
4. Evaluation of interchain occluded surface.
5. Display of the extended normals using MidasPlus.
If results derived from the calculation of occluded surface are published please cite the following:
Pattabiraman, N., Ward, K.B. and Fleming, P.J. (1995) Occluded Molecular Surface: Analysis of Protein Packing, Journal of Molecular Recognition, 8:334-344.
A description of the normalized packing value calculation has been published in the following:
Brian S. DeDecker, Ronan O'Brien, Patrick J. Fleming, James H. Geiger, Stephen P. Jackson, Paul B. Sigler (1996) The Crystal Structure of a Hyperthermophilic Archaeal TATA-box Binding Protein, J. Mol. Biol., 264, 1072 - 1084
The OS package requires a dot surfacing program. We use MS or DMS which are distributed with MidasPlus. Both of these are in the directory paths of users in the CSB Core Laboratory. Currently the default is MS; if you would like to use DMS please see P. Fleming.
Bug reports to Pat Fleming are appreciated.
Last Modified:
