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:
The commands for this section are as follows:
18.104.22.168 ADD — Mark Atoms for the Spheres List
- ADd atom-selection
- The atoms in the atom selection (see Atom Selection) are marked for
inclusion into the spheres list.
22.214.171.124 COLOR — Color Atoms
- COlor color atom-selection
- 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
You may defined additional colors using the DC command below.
126.96.36.199 DC — Define Colors
- DC color real real real real real real
- 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.
188.8.131.52 SFR — Set Radius for Surface Coloring
- SFR real
- 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.
184.108.40.206 SFCO — Set Color for Accessible Surface
- SFCO color atom-selection
- Same as the COLOR command above except the surface colors are
220.127.116.11 RA — Set Atom Radii
- RA real atom-selection
- The radii of the atoms in the atom selection, see Atom Selection,
are set to the real number specified.
18.104.22.168 RC — Reset Colors
- Reset Colors. The colors of the atoms are reset to the default scheme
22.214.171.124 RM — Unmark (Remove) Atoms
- RM atom-selection
- 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.
126.96.36.199 RR — Reset Atomic Radii
- 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
188.8.131.52 ZMARK — Mark Atoms by the Z Coordinate
- ZMARk real
- 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.