SURFNET parameters

4. SURFNET

There are 9 parameters specific to the SURFNET program, as follows:-

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

Description of options:-

• Origin of grid-box - The three values entered here define the x-, y-, and z-coordinates of the origin around which the 3D grid is to be be defined. The size of the grid, in Ångströms, is defined by the Grid separation parameter two lines below.

  Note that the values entered here are ignored unless the atom range given in the next line is 0 0.

• Atom range defining grid bounds - If a range of atom numbers is entered here, then the grid-box will be defined by the x-, y- and z-extent of the coordinates of these atoms. So, for example, to define a box just round an inhibitor in a protein complex, the range you would enter here would be the range of atom numbers of the inhibitor.

  If the range entered here is 0 0, then the grid-box will be defined by the origin entered in Line 1 above and the boundary size in Line 3 below.

• Additional boundary - This parameter defines the size of the extra boundary in the x-, y- and z-directions around either the origin defined in Line 1 or the coordinates defined in Line 2. The three sizes are given in Ångströms.

• Grid separation - The grid separation is the distance between the grid-box's successive grid-points, in Ångströms. In effect it defines the resolution of the contours obtained. If the protein is very large, the grid-size may go over the program's array bounds. In this case, either reduce the size of the grid by adjusting the parameters in Lines 1-3 above, or increase the grid separation here.

• Minimum and maximum gap spheres - Gap regions are defined by SURFNET by inserting trial gap spheres between relevant pairs of atoms (see Appendix A). The two parameters here define the minimum and maximum size of the trial gap spheres. The minimum size should not be too small (ie not less than about 0.5Å) as not only will this generate very many spheres (possibly too many for the program to handle), but the resultant contours will merge into one another and the net effect will be a single surface on the outside of the protein and no surface contours inside it.

  The maximum sphere size for the gap spheres influences how far the gap regions bulge out of the protein and how large a cleft region can be spanned and detected in this way.

• (C)CP4, (I)nsightII, (Q)uanta, (S)ybyl contour files, or (N)one - This option determines the type of output files to be generated:-

  The C option generates CCP4 density maps that can be converted into brick files that can be viewed by FRODO or O

  The I option generates .grd grid files that can be contoured by Insight II

  The Q option generates .mbk brick maps that can be read by QUANTA

  The S option generates .cnt contour files for SYBYL

  The N option produces no brick files at all. Entering an X will generate no output files at all, not even the .srf file that is usually generated.

• Calculate gap volume - (Y/N)? - This option provides an estimate of the volume of each contoured object, including the gap regions. The volumes are listed in order of decreasing size and are written out to a file called volumes.pdb. The volumes of any gap regions are written out to a file called gaps.pdb. The latter file can be used in conjunction with the MASK program to select out the required gaps region(s) - for example, to extract just the gap region corresponding to a protein's binding site.

• Scaling factor - This should be left at 1.0.

SURFNET parameters