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26.1.3 Atom Manipulations

Prior to the transformation of atoms into a spheres list, the user may select the atoms he wishes to display, what color they will be displayed with, and the radii to be used. By default, all atoms in the PSF are displayed. The radii are initialized to the radii given by the van der Waals parameters. The default colors for the atoms are set using the following table:

Nitrogens
Cyan
Carbons
Gray
Hydrogens
White
Oxygens
Red
Sulfur
Yellow
Others
Magenta

The commands for this section are as follows:

26.1.3.1 ADD — Mark Atoms for the Spheres List

Syntax:
ADd atom-selection
Function:
The atoms in the atom selection (see Atom Selection) are marked for inclusion into the spheres list.
26.1.3.2 COLOR — Color Atoms

Syntax:
COlor color atom-selection
Function:
The color for atoms in the atom-selection (see Atom Selection) is set to the color. Colors may be specified as either a word or an integer. The word gives the color name, and the integer gives the position of the color in the color table. Ten colors have guaranteed numbers, namely, 
          
              1       Red
              2       Green
              3       Yellow
              4       Orange
              5       Blue
              6       Magenta
              7       Cyan
              8       Gray
              9       White
             10       Black

You may defined additional colors using the DC command below.

26.1.3.3 DC — Define Colors

Syntax:
DC color real real real real real real
Function:
Defines a color. The color keyword is the name of the color and must not be an integer. The six real numbers following give the range of intensities using the RGB (Red, Green, and Blue) color scheme. The first two reals give the low and high limits for the red channel, the next two give the limits on green, and the last two specify blue. All limits should be between 0 and 1.
26.1.3.4 SFR — Set Radius for Surface Coloring

Syntax:
SFR real
Function:
Specifies the radius for identifying pixels that are accessible. If this variable is positive, then all pixels which correspond to accessible points will be colored according to the SFCO (surface color) commands. NB: This option is very expensive to compute.
26.1.3.5 SFCO — Set Color for Accessible Surface

Syntax:
SFCO color atom-selection
Function:
Same as the COLOR command above except the surface colors are set.
26.1.3.6 RA — Set Atom Radii

Syntax:
RA real atom-selection
Function:
The radii of the atoms in the atom selection, see Atom Selection, are set to the real number specified.
26.1.3.7 RC — Reset Colors

Syntax:
RC
Function:
Reset Colors. The colors of the atoms are reset to the default scheme given above.
26.1.3.8 RM — Unmark (Remove) Atoms

Syntax:
RM atom-selection
Function:
The atoms in the atom selection (see Atom Selection) are removed from the list of atoms to be included into the spheres list. This is the inverse of the AD operation.
26.1.3.9 RR — Reset Atomic Radii

Syntax:
RR
Function:
Reset Radii. The radii of the atoms are reset to the values given in the parameter set. Be careful using this after reading in a spheres list, see Data Flows for Drawing Spheres, because the PSF entries pointing to the parameter list (if it exists at all) are likely to be inconsistent.
26.1.3.10 ZMARK — Mark Atoms by the Z Coordinate

Syntax:
ZMARk real
Function:
Mark atoms by their Z coordinate. Any atom whose Z coordinate plus its radius is greater than the parameter specified by this command will be removed from the list of atoms to be transformed into the spheres list. See the command, ZCUT, Transformations for Sphere Drawing, a variant of this command.