Atom Modify

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.


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).


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.


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).


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.