Polyhedron Data
Previous  Top  Next

Dialog Box - called from: Polyhedra Dialog

Polyhedra are defined by specifying the Coordination number, and the Types of the central atom and the coordinating atoms or ligands. Note that atom types are used, not individual atom numbers, so that chemically similar atoms may be grouped. It is usually convenient to use atomic numbers for the types. You must further specify the Maximum distance for the bonds from the central atom to the ligands.

If the coordination number is given as 3 or larger, only complete polyhedra are identified and displayed; that is, both the central atom and all the ligands must be within the structure boundaries defined in the Boundary option. Atoms belonging to incomplete polyhedra can be displayed as spheres with the radii assigned in the Revise Atom dialog, unless their atomic radii are zero - then they will be marked as permanently non-plotting. The display of these atoms is controlled by a checkbox in the Polyhedra dialog. If more coordinating atoms are found than specified within the given distance, an error message is shown and the polyhedron is skipped.

If you do not know the coordination number or the bond distances, you may wish to make one or more runs with the coordination number set to zero. In this case, all polyhedra with three or more ligands within the bond-distance limit will be accepted, and you can examine the Calculation Output to see what the proper coordination number or distance limits should be.

If you want to show polyhedra which do not have central atoms, it will be necessary to enter dummy central atoms. The best way to do this is to take the average of each coordinate for all the atoms in one polyhedron.

In 2D Drawing modes, polyhedra are always opaque; if you wish to show only the skeletons, you can define bonds among the ligands (next section). Once the ligands are located, central atoms are never shown in 2D Drawing modes.

If a nominally planar coordination is not strictly planar, within tolerances, it will be shown as a polyhedron. In 2D Drawing modes, strictly planar polyhedra will vanish when seen edge-on if display of rims or edges is not turned on with the Rims dialog in the Input2 menu.

In 3D Drawing modes, planar polyhedra have finite thickness. There are also several options for showing polyhedra as opaque, translucent or skeletal (see 3D Polyhedra).

Colors and patterns/shades. Each polyhedron may have a rim and a fill, the colors for which are specified independently. Rims are turned on and off, and their widths are set, in the Line Widths dialog in the File2 menu. Shading applies only to fills. See Input Colors/Patterns/Pens for general aspects of input.

Line Width. If the Use individual box for polyhedra 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.

Hachure patterns are patterns of lines based on a square grid which may be applied to polyhedra. The patterns are drawn on the surface of each polyhedron face in 3 dimensions (not simply applied in 2 dimensions to the projection of the face), so that they give some illusion of depth or shading. Thus they enhance the 3-dimensional appearance of the drawing while at the same time allowing differentiation of the different types of polyhedra. Differentiation of polyhedra types is almost impossible using gray shades (above ) alone.

Hachure patterns are not used in 3D Drawing modes, and this entire section is not applicable to 3D display/output.

The Spacing is the distance between lines, in Angstroms. The colors/shades of the patterns are same as those selected for the outlines or edges (above), and the widths are also as selected (above) for each individual polyhedra type, or as selected overall in the Line Widths dialog (Input2 menu).

If the Use shade box is checked, the gray shade selected in this dialog will also be applied as fill, in addition to the pattern, in black-and-white non-shaded output. This choice is overridden if the Use initial patterns box is checked in the Shading dialog (Input2 menu) - in that case, gray shades or dot patterns will always be applied.

In color display and output, the fill color (above) is always used. Shading, as selected in the Shading dialog (Input2 menu) is applied independently of hachure patterns, and it is possible to have both either in color or black and white. If hachure patterns are used in conjunction with shading for atoms and bonds, the illumination vector (Shading dialog) should probably be 1,0,0, as this is the effective illumination direction for hachures.

Differentiating polyhedra. The size and shape of different polyhedra are not generally sufficient to allow identification of the polyhedron type in a drawing. There are several different display attributes of polyhedra which may be varied alone or in combinations to allow differentiation.

1) Color. This is certainly the best option when it is available, especially when using shading, except that a significant fraction of people are at least partially color-blind.

2) Hachure patterns. Both the pattern itself and the scale can be varied.

3) Gray shade of fill (black-and-white). This does not usually work well in combination with shading.

4) Width of edges.

5) Gray shade of edges. Lines of one dot width (width 0.0 in this dialog) are always black.