SURFNET Operating Manual

4. van der Waals surfaces

The two plots below show the van der Waals surfaces of the aspartic protease endothiapepsin (yellow) complexed with an inhibitor, pepstatin (red), from the PDB file 3er5. The first plot was produced using QUANTA while the second used the solid rendering of InsightII.

The surfnet.par file used in generating the above plots is shown below, with the section keywords in bold.

For a detailed explanation of all the parameters involved, see Editing the surfnet.par file.

Parameters for SURFNET              (surfnet.par)
----------------------
 
TITLE
van der Waals surfaces for endothiapepsin & inhibitor
 
INPUT FILE
/data/pdb/3er5.pdb

Output files listed below. The information entered for each is as follows.
The numbers in square brackets refer to the notes at the end of the file.
The program names indicate which programs need to be rerun when any of the
parameters are changed.

            <----SURFNET----><-SURFACE-><----------SURFPLOT------------>
                                        Foregrnd  Backgrnd        
                   Atom range            colour    colour     Line 
          File     1st   Last  Contour   /shade    /shade     width  SOLID
Filename  type[1] atom   atom  level[2]  (0-10)[3] (0-10)[3]   [4]  /WIRE

OUTPUT FILES
protein      S      1    2390   100.0       1         1        0.1
inhibitor    S   2391    2482   100.0       8         8        0.1


Program parameters
------------------

SURFNET
  0.0   0.0   0.0  <- Origin of grid box (to use: set atom range below to 0 0)
-1000 10000     <- Atom range defining grid bounds (0 0 to use origin above)
6.0 6.0 6.0     <- Additional boundary round atom-range/origin (Angstroms)
0.80      <- Grid separation
1.0       <- Minimum radius for gap spheres (in Angstroms)
4.0       <- Maximum radius for gap spheres (in Angstroms)
Q         <- (C)CP4, (I)nsightII, (Q)uanta, (S)ybyl contour files, or (N)one
Y         <- Calculate gap volume - (Y/N)?
1.0       <- Scaling factor

Here two output files are defined under the OUTPUT FILES keyword. One .srf file will be generated for each: protein.srf and inhibitor.srf. The S in the second column defines the surfaces as being van der Waals surfaces, while the atom-number ranges in columns 3 and 4 define the molecules in question. (The parameters in columns 5 onwards are only used by the SURFACE and SURFPLOT programs).

The output format has been defined as QUANTA (Q in line 7 of the SURFNET parameters) so the program will also write out two files in QUANTA brick-map format: protein.mbk and inhibitor.mbk.

van der Waals radii

The van der Waals radii used by SURFNET are listed in Appendix D. You can, however, define individual radii for all atoms in the PDB file using the B-factor column in the file (see Appendix B for the PDB file format). For SURFNET to make use of these values, add an asterisk between the filename and file type in the OUTPUT FILES parameters, as follows:-

OUTPUT FILES
protein    * S      1    2390   100.0       1         1        0.1
inhibitor  * S   2391    2482   100.0       8         8        0.1