SURFNET Operating Manual

2. How to run SURFNET

1. Edit the parameter file, surfnet.par (see Editing the surfnet.par file). The information in the file includes:-
   • The input PDB file
     
   • The surfaces (and other objects) to be generated from it
     
   • The output format (ie QUANTA, SYBYL, O, etc.)
   • Various parameters, including extents and grid-spacing of the surface-maps to be generated.

   (If this is the first time you are running SURFNET and do not have a surfnet.par file, then first type surfnet and a copy of the file will be created in your current working directory).

2. Run SURFNET by typing: surfnet

   For each surface, a .srf file is written out (which is in the internal format used by the SURFNET programs). If you have defined one of the molecular graphics output formats (eg QUANTA, InsightII, etc.), a file in the required format is additionally produced - with the appropriate extension to identify it (.mbk for QUANTA, .grd for InsightII, etc.).

   Surfaces in all these formats are stored as 3D grids of "density" values. The densities are computed by SURFNET such that, when contoured at a contour level of 100.0, the desired surface is obtained in 3D.

3. View the surface(s) on the appropriate molecular graphics package. Alternatively, run SURFACE and SURFPLOT to generate a PostScript plot or to produce one of the other possible outputs (see Viewing the SURFNET surfaces).

   The SURFACE and SURFPLOT programs are also controlled by the parameters in the surfnet.par file (see Editing the surfnet.par file).

Running SURFNET the first time

The first time you run SURFNET in a given directory, you will get the message:-

*** Parameter file surfnet.par not found
 
A new file has been created for you. Please edit it and re-run surfnet
 
-rw-r--r--    1 user     bsm         5662 Jan  1 09:30 surfnet.par

You must then edit the surfnet.par file as required and re-run the SURFNET program.

SURFNET Operating Manual