Dialog Box - called from: Bonds Dialog
Bonds are specified by giving the Types of the two atoms involved - in some cases, such as carbon-carbon bonds, these may be the same. The Minimum, as well as Maximum distance must be specified; this allows differentiating bonds to the same atom. A stick bond has the shape of a cylinder, but if the Radius of this cylinder is entered as zero, then the bond is drawn as a single line. The width of this single line, or the width of the lines defining the outline of a stick bond, is normally one dot in screen display or dot-matrix plots, but this can be changed - for all bonds in the Line Widths dialog in the Input2 Menu, or if desired for each input bond (see below).
If the Radius of the bond is greater than the radius of either of the two atoms involved, the result will depend on the Model Mode. In Standard mode, the bond will be shown with both ends terminated by a straight line. In Ellipsoid mode, the bond may normally be absent entirely. In 3D Drawing Modes, the bond will be shown as a half-cylinder.
Bonds to atoms in polyhedra can only be drawn to ligands defined in the Polyhedra input, not to central atoms.
If you wish to show only bonds, not atoms (wire-frame model), you should enter negative radii for the atoms.
If the Inter-molecule box is checked, this bond specification will not be used in locating molecules or groups in either the Molecules in Crystal boundary options, or the Find button in the Generated Atom Data dialog or Locate Groups dialog. Intermolecule bonds are drawn normally by default, but they can be dimmed, highlighted or hidden (Atom/Bond Plot States dialog in the Input2 Menu, or Dialog Bar - Right)
In 2D Drawing modes, the interpenetration relationships of cylindrical bonds with each other, and with the polyhedra to which they are attached, are not drawn accurately. This affects wire-frame atoms (atomic radius negative), and bonds from polyhedral ligands to other atoms. The affect of this limitation is mimimized if the bond radii are kept relatively small. In 2D Drawing modes, if atoms are interpenetrating (interatomic distance less than the sum of the radii), no sticks or lines will be shown, but it is still necessary to specify a bond between the atom types so that the junctions will be handled properly (if no bond is specified, the atom in front will simply be drawn over the other one). The radius and colors of the bond are immaterial for interpenetrating atoms. In 3D Drawing modes, interpenetration relations are always drawn correctly and if atoms are known to interpenetrate it is not necessary to specify bonds between them.
Colors and patterns/shades. Each bond may have a rim and a fill, the colors for which are specified independently. The color for a single-line bond is the same as the rim color for a cylindrical bond. Rims are turned on and off, and their widths are set, in the Line Widths dialog in the Input2 menu. Shading applies only to fills. See Input Colors/Patterns/Pens for general aspects of input.
Line Width. If the Use individual box for bonds in the Line Widths dialog (Input2 menu) is checked, the width specified here will be used, rather than the overall value in the Line Widths dialog.
Individual input bonds may be dashed if they are single-line (radius 0.0). The length of the dashes is specified in the Crystal Edges dialog.