Change here the visual representation for a single atom or a list of atoms.
To modify a atom, click over its graphic image, or write its id on
the
Atom entry. To modify a list of atoms, press the button
List (after creating the list of atoms with
Atom->Select).
Parameters for empty entries or
Local choices remain unchanged.
To change an atom name write the new name in the
Atom entry,
followed by the atom number (GAMGI needs the number to identify the atom).
To change the name for a list of atoms, press
List first
and then write the new common name in the
Name entry.
Style
The
Style option menu is to select the atom visual representation.
Currently supported styles are: 1) a sphere, for
Solid; 2) a cross, for
Wired. The sphere gives a hight visual quality, when coupled with lights
and perhaps a perspective projection. A sphere uses considerable screen space
though and is time consuming.
The cross uses much less screen space and computing time. Moreover, when atoms
are bonded, crosses are not represented at all, and atoms are identified just
by the ends of the bond lines, decreasing even further computation needs.
However, wired objects do not have a 3D representation, so diffuse and
specular lights are not reflected, becoming poorly visible when using
lights, unless the ambient component is important, about (0.5, 0.5, 0.5).
Size
In
Solid mode, this parameter controls the size of the atom spheres.
Combining atom
Size and
Variancy with bond
Size, it is
possible to obtain a wide range of styles to represent atomic structures.
In
Solid mode, the default is to represent atoms as constant
spheres (
Variancy =
0.0 and
Size =
0.8),
slightly larger than the bonds (
Size =
0.5). An elegant
style is to represent atoms as constant spheres with the same
Size
as bonds (
0.5).
To represent compact cristalline structures, atom
Size
and
Variancy must be
1.0, to be consistent with
cell dimensions. This style can also be used to represent molecules,
in order to emphasize the atomic radius and electronic distribution.
To change the default
Size select
Atom->Config.
Variancy
The intrinsic size of an atom is given by:
Size x (Variancy x Radius + (1 - Variancy) x Min)
where
Radius is the atom radius and
Min is the minimum
radius, by default the H covalent radius (currently 0.37). To change
this default select
Atom->Config.
In
Wired mode,
Variancy is always
0.0 so
all atom crosses have a constant size, given by
Size x
Min.
In
Solid mode, when
Variancy is
0.0 the atom spheres
have all the same size, when
Variancy is
1.0 the atom spheres
are scaled directly by the atom radius.
R, G, B
The
R,
G,
B entries define the atom color,
from black (0.0, 0.0, 0.0) to white (1.0, 1.0, 1.0).
Scale
Set the atom size, including its child objects. Atom objects are
scaled around the atom center. The visual representation of an object
is always scaled by its own scale factor multiplied by the scale factor
of all its parent objects until layer, inclusive.