The output produced by Surface Diver consists of a number of files:

DX scalar data

srfc.dx – DX-formatted file describing the volume of a molecule (optional, –grids option)

hb.dx – DX-formatted file with hydrophobicity assigned to grid points (optional, –grids option)

chrg.dx – DX-formatted file with charges assigned to grid points (optional, –grids option)

phi.dx – DX-formatted file describing the electrostatic potential in the whole space (input DX-file translated to the geometric centre of the molecule) (optional, –grids option)

 

Data files

(i enumerates spherical surfaces)

i.radius.dat – this file contains the values of physicochemical parameters of the studied protein mapped onto spherical surface of a given radius:

radius=2.000000 order=32
x=0.049082 y=0.000000 z=1.999398 theta=0.024544 phi=0.000000 density=6.725776 hydrophobicity=4.489162 charge=-0.243362 potential=-11.960450
x=0.048846 y=0.004811 z=1.999398 theta=0.024544 phi=0.098175 density=6.722406 hydrophobicity=4.486836 charge=-0.244764 potential=-11.960450
x=0.048139 y=0.009576 z=1.999398 theta=0.024544 phi=0.196350 density=6.718655 hydrophobicity=4.484260 charge=-0.245980 potential=-11.960450
x=0.046969 y=0.014248 z=1.999398 theta=0.024544 phi=0.294524 density=6.714560 hydrophobicity=4.481459 charge=-0.246996 potential=-11.960450
……………..

i.radius.HB.dat – hydrophobicity at points of the spherical surface of a given radius

i.radius.Qp.dat – positive charge at points of the spherical surface of a given radius

i.radius.Qm.dat – negative charge at points of the spherical surface of a given radius

i.radius.Vp.dat – positive values of the electrostatic potential at points of the spherical surface of a given radius

i.radius.Vm.dat – negative values of the electrostatic potential at points of the spherical surface of a given radius

i.radius.shape.dat – shape of the molecule mapped onto the spherical surface of a given radius

The last six from files described above contain complex data. These files are formatted as follows:

Real(0)
Imaginary(0)
Real(1)
Imaginary(1)
Real(k)
Imaginary(k)
……………..

where k enumerates points of the spherical surface.

Next six files contain coefficients of the spherical harmonic decomposition for each property:

i.SHD_HB.dat

i.SHD_Qm.dat

i.SHD_Qp.dat

i.SHD_Vm.dat

i.SHD_Vp.dat

i.SHD_shape.dat

These files are formatted as follows:

L -L Real Imaginary
L -L+1 Real Imaginary
……………..
L 0 Real Imaginary
……………..
L +L-1 Real Imaginary
L +L Real Imaginary

with L enumerating frequencies.

Descriptor files

Descriptors of shapes and physicochemical properties are written to the following files:

matrix_HB.dat

matrix_Qm.dat

matrix_Qp.dat

matrix_Vm.dat

matrix_Vp.dat

matrix_shape.dat

using the following format:

dsc(1,1) dsc(1,2) dsc(1,3) …
dsc(2,1) dsc(2,2) dsc(2,3) …
dsc(3,1) dsc(3,2) dsc(3,3) …
dsc(4,1) dsc(4,2) dsc(4,3) …
……………..

where columns are enumerated by the frequency and rows by the radius.