Diamond Version 5 User Manual: Polyhedra

Polyhedron selection and properties

This article in brief:
- Selecting a polyhedron from the structure picture
- Choosing a polyhedron from the Table of Polyhedra
- Polyhedron in Properties view

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Next article: Modification and duplication of polyhedra

Selecting a polyhedron from the structure picture

A polyhedron is selected indirectly, which means that its central atom is selected, so you have access to polyhedron commands, e.g. Edit -> Polyhedra or Destroy -> Polyhedra in the context menu of the structure picture.

Note: You cannot select a polyhedron by clicking into one of its ligand atoms (this only selects the other atoms) nor by clicking on an edge or into a face of a polyhedron.

Details about selection of atoms in the structure picture, see here: Selecting objects.

Since the selection of a polyhedron works via its central atom, you can also use the table of created atoms to select the corresponding central atom from there. (The selection of an atom in the table of created atoms automatically selects the corresponding atom in the structure picture.)

Details about selection of objects from tables, see here: Tables of objects like atoms, bonds, molecules etc..

Choosing a polyhedron from the Table of Polyhedra

With the help of the data pane, you can select coordination (or Voronoi) polyhedra from a list (table).

To open the table of polyhedra, choose the Polyhedra command from the Table submenu of the View menu. The table of polyhedra may contain informations about:

- the sequential number of the polyhedron (beginning with 1),

- the sequential number of the central atom in the list of created atoms (beginning with 1),

- the symbol of the central atom, as defined in the atomic parameter list,

- the number of ligand atoms,

- the number of polyhedron faces (polygons),

- the distance (in Angstroems) between central and the closest ligand atom,

- the distance (in Angstroems) between central and the ligand atom which has the largest distance.

This is the default setting for the table of polyhedra. Choose the Table Settings command from the table's context menu to change the columns to be shown in the table and the column to sort for.

When you select an atom that is center of a polyhedron, the corresponding polyhedron is automatically selected in the table of polyhedra. On the other hand, selecting a polyhedron in the table automatically selects its associated central atom in the structure picture.

Example: Unit cell of Laueite (from Crystallography Open Database; Code: 9000136) with purple tetrahedra around P and grey and brown octahedra around Mn and Fe in the structure picture and the list of all polyhedra in the data pane.

Polyhedron in Properties view

The Properties view - by default positioned below the table or data sheet - shows a summary of the properties of the polyhedron that is selected in the table of polyhedra. (Note: When you are in the table of created atoms rather than table of polyhedra, the object info will show only infos about the selected (central) atom but not of the polyhedron.)

Properties of the octahedron at Mn (x+1, y, z+1).

The Object info is the default setting in the Properties view. There are additional options available for a polyhedron (also if you are in the table of created atoms):
- Ligand atoms of selected polyhedron: Lists atom symbol, sequential number of created atom and symmetry code of all ligand atoms along with the distance from the central atom and the atom coordinates (crystal/fractional coordinates).
- Faces of selected polyhedron: Lists all faces with the atoms on the corners each.
- Edges of selected polyhedron: Lists all edges with the two atoms at the ends each.

Properties view listing the faces of the octahedron at Mn (x+1, y, z+1).

Previous article: Design and hatching
Next article: Modification and duplication of polyhedra

Reference:
COD:9000136: Moore, P. B.; "The crystal structure of laueite, MnFe2(OH)2(PO4)2(H2O)6.2H2O"; American Mineralogist, 50, 1884-1892 (1965).