Bond Modify

Change here the visual representation for a single bond or a list of bonds.

To modify a bond, click over its graphic image, or write its id on the Bond entry. To modify a list of bonds, press the button List (after creating the list of bonds with Bond->Select). Parameters for empty entries or Local choices remain unchanged.

To change a bond name write the new name in the Bond entry, followed by the bond number (GAMGI needs the number to identify the bond). To change the name for a list of bonds, press List first and then write the new common name in the Name entry.


The Style option menu controls the bond visual representation: cylinders in Solid mode, simple lines in Wired mode.

The cylinder gives a high visual quality, when coupled with lights and perhaps a perspective projection. A cylinder uses considerable screen space though and is time consuming.

Wired objects do not have a 3D representation, so diffuse and specular lights are not reflected, becoming poorly invisible when using lights, unless the ambient component is important.


In Solid mode, this parameter controls the size of the bond cylinders. Combining bond Size with atom Variancy and Size, it is possible to obtain a wide range of styles to represent atomic structures.

An elegant style is to represent bonds with the same Size as atoms (0.5). To guarantee that bond cylinders are closed by atom spheres, bond Size should not be larger than atom Size.


The Color button controls whether the bond is represented with its own, independent color, or inherits the colors of the parent atoms. By default colors are inherited.

R, G, B

Change the bond color, from black (0.0, 0.0, 0.0) to white (1.0, 1.0, 1.0), when the bond is rendered with its own, independent, color.


Change the bond size, including its child objects. Bond objects are scaled around the bond line. 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.

Line widths in GAMGI are not affected by Scale attributes, so bonds represented in Wired mode remain unchanged by Scale (but not its child).