Polyhedra
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Dialog Box - called from: Input1 Menu

This lists the current polyhedra. Click on individual items in the list, then on the buttons to add, modify or delete polyhedra. The Revise and Add Polyhedra buttons call up the Polyhedron Data dialog.

To calculate bond distances and angles, for use in bond and polyhedra input, use the Coordination button in the Input Atoms dialog.

If the Show back edges dashed box is checked, the invisible back edges of polyhedra will be drawn as dashed lines - the dash parameters are set in the Crystal Edges dialog. Polyhedra are still opaque. This applies to unshaded polyhedra only.

The possibilities for showing polyhedra are diverse, depending on the Drawing mode. It may be necessary to select settings in the 3D Polyhedra dialog and also the Ellipsoid Parameters dialog as well as this dialog. These two other dialogs are accessible directly from this one with buttons.

The 3D parameters button calls up a dialog (3D Polyhedra) for specification of polyhedron properties unique to the 3D Drawing modes. This includes options to draw the polyhedron faces as transparent and to show the central atom and interior bonds. In the 3D Polyhedra dialog, and also the Ellipsoid Parameters dialog, there is an option to show corners and/or central atoms of polyhedra as thermal ellipsoids in the 3D Drawing mode.

The Ellipsoid Parameters button calls up the Ellipsoid Parameters dialog. In the Ellipsoid Model mode (which mimics ORTEP) polyhedra are never shown with actual flat faces, but there is an option in the Ellipsoid Parameters dialog to draw the ligand-ligand "bonds" or polyhedron edges, and also the central-ligand "bonds" as standard ORTEP bonds.

The Show ligands as spheres group has three options. If the None button is checked, only the polyhedron faces are shown and ligands are represented as points at the corners. If one of the other boxes is checked, ligands are drawn as spheres. In the 2D Drawing mode, this option is an approximation in that junctions between the atoms and the polyhedra are straight lines. In the 3D Drawing mode, junctions are always correct. For spherical atoms (not thermal ellipsoids) you can use the Atom radii entered for each input atom, or you can use a Single radius for all ligands, entered in the edit box to the right of this option. The Single radius option is not applicable to ellipsoids in the 3D Drawing mode; if either the Atom radii or Single radius option is selected, ellipsoids will be shown at polyhedron corners. If atoms are not shown at polyhedra corners (None option), the bonds to such corners are always cylindrical, not tapered as they could be if they were to ellipsoids. This option does not function as well when Hachure patterns (Polyhedron Data dialog) are used - the junctions of the polyhedron corners with the spheres are not correctly drawn.

The Test for incomplete polyhedra group determines how atoms in incomplete polyhedra are handled. As detailed in Generated Atom Data, when ATOMS locates polyhedra, it assigns a certain plot code (5) to atoms which are parts of polyhedra which have fewer than the specified number of ligands. This will always be done, even if the option selected is No test, and the atoms thus flagged can either be omitted or plotted as spheres, depending on the setting discussed in the previous paragraph. However, some further screening of possible polyhedral atoms can be made, to eliminate display of potential ligands which are not found to bond to any of the specified central atoms within the given boundaries. While locating polyhedra, ATOMS can make a list of either the Input atom numbers or the Atom types involved (as ligands) in polyhedra. Then after all polyhedra are located, the generated atom list is searched to find those atoms with the specified numbers, and these atoms are then marked with plot code 5, i.e. as belonging to incomplete polyhedra. The normal option for crystals is Input atom numbers. However, this option is of no use when the structure is of type Input=Generated, or for a molecule with no symmetry, since every input atom corresponds to a single generated atom. Thus the default for Input = Generated is No test. The Atom types option works well when each input atom type (normally the atomic number) plays only one structural role, i.e. is either always a polyhedron ligand or not. However when an atom type can be a polyhedral ligand in some cases, and a non-ligand in others (for example when oxygen atoms are ligands in phosphate radicals or other groups and also are present in water molecules or hydroxyls), the atoms which are non-ligands will be incorrectly omitted. When using the Atom types option, it may thus be necessary to assign special types to atoms with different structural roles, for example 8 for oxygens which are in phophate (or other) groups; 108 for hydroxyls; and 208 for waters.