SURFNET parameters

5. SURFPLOT

There are 18 parameters specific to the SURFPLOT program, as follows:-

SURFPLOT
C             <- (C)olour/(B)&W PS file, (P)DB-format, (R)aster3D, (V)RML
11            <- 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
 1.0000   0.0000    0.0000             <-
 0.0000   1.0000    0.0000             <- Transformation matrix
 0.0000   0.0000    1.0000             <-
 100.0 100.0 100.0    <- Position of light-source
 40 32         <- Raster3D size, number of tiles in x and y (Max: 80 64)
N              <- Infinite planes for back wall(s) in Raster3d (Y/N)?

Description of options:-

(C)olour/(B)&W PS file, (P)DB-format, (R)aster3D, (V)RML - The first option defines whether a colour or a black-and-white PostScript file is generated, or whether one of the other three output types is required: namely, PDB-format for input by Rasmol (or any other molecular graphics package), Raster3D format or VRML format. See section 9. Viewing the SURFNET surfaces, or its subsections describing: Raster3D, Rasmol, PostScript or VRML.
Background colour - This option defines the overall background colour of the plot.
The colours are:
Colour of "walls" in back-projections - This is the colour of the back walls, if any, onto which the 3D objects are projected in the PostScript or Raster3D output. As above, the range is from 0 to 12. Which of the walls are plotted is determined by Line 4 below.
(F)loor, (L)eft wall, (R)ight wall, (A)ll three, (N)one - This option determines onto which, if any, of the 3 back walls the 3D objects in the scene are to be projected. The options are:-
- (F)loor - Plots just the base, or floor, projection.
- (L)eft - Plots just the back-wall on the left-hand side.
- (R)ight - Plots just the back-wall on the right-hand side.
- (A)ll - Plots all three back-walls.
- (N)one - Plots none of the three back-walls.
You can select two or three of the walls by specifying a string, such as FL to have the floor and left wall, or LR for just the left- and right-walls.
Lower-case versions of the appropriate letters above (a, f, l and/or r) plot the wall but no projection onto it in the PostScript output.
Display foreground object (Y/N)? - This option determines whether the 3D objects in the scene are to be displayed in the foreground. The point of removing might be to make the back-projections selected by the option in Line 4 above clearer.
Margin round object - (Y/N)? - The overall size of the plot is determined by the extent of the 3D objects being plotted. If an additional margin of white space is required around the picture, set this option to Y.
Atom radius (in Angstroms) for plot - NOT USED - This option is no longer used.
Print sequential numbers by the atoms (Y/N)? - This option allows sequential numbers to be plotted above each atom when plotting a type A or a file. This may be useful in identifying which atom is which in a given picture.
Maintain x-, y-, z-axes (ignore matrix below) (Y/N)? - This option ignores the transformation matrix given in Lines 13-15 below. Thus the `corner' made by the three back walls on the plot gives axes parallel to x, y, and z. This is the standard view, obtained when this parameter is set to Y. With this view the object can still be rotated by the transformations given in Lines 10-12 below. If the parameter is set to N, then the initial view of the objects in the scene will be down the z-axis (ie as it would be in a graphics program such as QUANTA or FRODO). Transformations can then be applied using the rotations in Lines 10-12 below and/or the transformation matrix in Lines 13-15 below.
Rotations about x-, y-, and z-axes - These three lines define rotations, in degrees, to be applied to the objects in the scene prior to display. The rotations are applied about the x-, y- and z- axes in the order given: x, y, and z.
Transformation matrix - The transformation matrix entered here allows a general transformation to be applied to the objects in the scene. It is useful if, say, the contours have been viewed on a graphics terminal using QUANTA or FRODO and a plot of a given orientation is now required. To get the appropriate matrix from QUANTA, create a .vew file using the View option and, once out of QUANTA, look at the contents of the file. Ignore the first three numbers and note the following three groups of four numbers. In each group of four, the first three numbers make up a column of the transformation matrix. For example, if the .vew file contains:
```
 -17.656  14.280 -11.538  -0.566  -0.667  -0.484   0.000   0.256   0.415
  -0.873   0.000   0.783  -0.618  -0.064   0.000   0.000   0.000   0.000
   1.000   0.000   0.000   0.000   0.653   0.653   0.653  13.100 -13.100
```
the matrix would be entered as:
```
-0.566     0.256     0.783
-0.667     0.415    -0.618
-0.484    -0.873    -0.064
```
For the transformation to take effect, the option in Line 9 above (>Maintain x-, y-, z-axes (ignore matrix below) (Y/N)?) must be set to N.
Position of light-source - This gives the location of the light-source used both in the PostScript output and by Raster3D to calculate the shading of the surfaces plotted.
Raster3D size, number of tiles in x and y (Max: 80 64) - This option applies only to Raster3D outputs and defines how large on the screen the generated Raster3D picture is to be.
Infinite planes for back wall(s) in Raster3d (Y/N)? - This option determines whether the back walls generated by SURFNET are to be infinite in extent when rendered by Raster3D.