3.3. Lines and Bonds
Bonds are not really supported in this version of Gnome Crystal. Lines must be used instead. The difference is that bonds should be defined by the atoms they join when lines are defined by the coordinates or their extremities.
Some special lines can be easily added, checking the corresponding box:
Cell edges: if the box is checked, a cylinder is added for each cell edge.
Diagonals: cylinders are added that join opposite vertices in the cell.
Medians: cylinders are added that join opposite face centers in the cell.
For Other lines defined in the list, a cylinder is added to join the points whose coordinates are given in the appropriate entries. A Cylinder is added for every visible cell if the Single checkbox is not checked.
These lines need coordinates x1, y1, z1 and x2, y2, z2 are the coordinates of the two ends of the line or bond. They must be given in cell coordinates for the two ends in the respective entries.
For very line present in the model, the two following parameters must be defined (for special lines, use the appropriate widgets and for the lines added to the list, use the wigets displayed in the Other lines frame):
- Radius
The radius of the cylinder used to figure the bond or line must be given in pm as is the cell size. If the radius is null, nothing will be added to the model.
- Color
The color of the cylinder used to figure the bond or line is selected by clicking on the button and picking a color in the dialog box that pops.
In the screenshot above (got from the diamond sample provided with the sources), cell edges defined with grey color, a 10 pm radius, and some bonds with the same radius, are added and will be repeated in every visible cell.
Bonds and lines effectively visible depend on model size (see Section 3.4) and cleavages (see Section 3.5). If one end of the cylinder lies outside of the visible part of the model, the cylinder will be hidden.
Buttons at bottom right are used to manage the bonds and lines list:
Button adds an item to the list with the current parameters if the radius is not null. If there is an inappropriate value, a message appears and the action aborts.
Button deletes the selected item from the list.
Button removes every item from the list.