SURFNET Operating Manual

7. 3D density distributions

SURFNET can generate density distributions of data points in 3D, writing out grid-maps which can be contoured in 3D using any of the standard molecular modelling packages.

The example below shows the relative distribution of carboxyl oxygens in contact with arginine sidechains as observed in a dataset of protein structures. The plot shows the Arg sidechain (black bonds) surrounded by the clusters of carboxyl oxygen atoms (red). The purple contours surround the most dense regions where the clustering of the oxygens is the greatest (ie where the most favourable hydrogen-bonding locations are). The grey projections onto the three back walls give an idea of the relative disposition of the various objects in the scene in 3D. The plot was produced using SURFPLOT.

The surfnet.par file used in generating the above plot 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
Carboxyl oxygen contacts with Arg sidechains
 
INPUT FILE
arg_o.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
arg_a        A     -2      -2     0.0      10        10   G    0.3
arg_b        B     -2      -2     0.0      10        10   G    0.15 SOLID
oxygen       A      9       9     0.0      10        10   G    0.10 
contour1     C      9       9    30.0%      9         9        0.15

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)
N         <- (C)CP4, (I)nsightII, (Q)uanta, (S)ybyl contour files, or (N)one
Y         <- Calculate gap volume - (Y/N)?
1.0       <- Scaling factor

SURFACE
(Currently no additional parameters)

SURFPLOT
C             <- (C)olour/(B)&W Postscript file, (P)DB-format, (R)aster3D
0             <- Background colour
12            <- Colour of "walls" in back-projections
A             <- (F)loor, (L)eft wall, (R)ight wall, (A)ll three, (N)one
Y             <- Display foreground object (Y/N)?
Y             <- Margin round object - (Y/N)?
0.20          <- Atom radius (in Angstroms) for plot - NOT USED
N             <- Print sequential numbers by the atoms (Y/N)?
Y             <- Maintain x-,y-,z-axes (ignore matrix below) (Y/N)?
 0.0          <- Rotation about x-axis
 0.0          <- Rotation about y-axis
 0.0          <- Rotation about z-axis
1.0 0.0 0.0
0.0 1.0 0.0
0.0 0.0 1.0
  50.0 100.0 100.0    <- Position of light-source
 40  32        <- Raster3D size, number of tiles in x and y (Max: 80 64)
Y              <- Infinite planes for back wall(s) in Raster3d (Y/N)?

Note that all the data is in a file called arg_o.pdb (under the INPUT FILE keyword) and that the atoms in that file are numbered such that the ATOM records making up the Arg sidechain have atom-number -2, while all the ATOM records corresponding to the carboxyl oxygen locations have atom-number 9. (The choice here is purely arbitrary and dependent only on the program that generated the data).

Any of the three back walls in the above plot can be removed, if required, by amending the (F)loor, (L)eft wall, (R)ight wall, (A)ll three, (N)one parameter under the SURFPLOT keyword.

So, for example, the same plot as above, but with only the floor shown (option F) would become:-

The contours can be generated at several levels. The example below shows three contour levels, the innermost shown as a solid surface in red. (The carboxyl oxygens have been omitted from this example).

The parameters in the OUTPUT FILES section of surfnet.par used to generate the above plot are as follows:-

OUTPUT FILES
arg_a        A     -2      -2     0.0      10        10   G    0.3
arg_b        B     -2      -2     0.0      10        10   G    0.15 SOLID
contour1     C      9       9    60.0%      8         8        0.15 SOLID
contour2     C      9       9    30.0%      6         6        0.15
contour3     C      9       9    10.0%      1         1        0.15

Viewing the same plot using Raster3D, with only the Floor selected and with the Infinite planes for back wall(s) in Raster3d (Y/N)? option set to Y, gives:-

The next picture shows a complicated example for illustrative purposes only. It depicts a Raster3D plot of a Ser-His-Asp catalytic triad in a box, with dashed lines for hydrogen bonds.

The atom coordinates used to generate the plot are given in the file triad.pdb, while the SURFNET parameters are given in this surfnet.par file.