GAMGI Interfaces: Atom Config

# Atom Config

- Element
- Analysis
- View

Set here default visual data that does not depend of the atomic element.

### Style

The Style menu is to select the default 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

The Size menu is to select the default atom size. 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.

In Wired mode, all atom crosses have a constant size, given by Size x Min, as Variancy is 0.0.

In Solid mode, Size selects the default size of the atom spheres. Combining default atom Size and Variancy with default 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.

### Variancy

Choose here the default value for Variancy. In Wired mode, Variancy is always 0.0.

In Solid mode, by default Variancy is 0.0 so the atom spheres have all the same size. When Variancy is 1.0 the atom spheres are scaled directly by the atom radius.

### Min

Min fixes the minimum size for crosses and spheres, as defined by the equation above for Size. By default this is the H covalent radius.

### Slices

In Solid mode, sets the number of fragments used to represent curved surfaces such as atom spheres and bond cylinders, thus controlling the visual quality of these objects. Increasing the number of fragments improves noticeably the visual quality but also decreases performance substantially.

### Width

In Wired mode, controls the line width used to draw atoms and bonds.
Home