Diamond Version 5 User Manual: Polyhedra

Modification and duplication of polyhedra

In this article:
- Changing a polyhedron's design after polyhedra have been created.
- Removing unwanted edges or adding edges to a polyhedron.
- Copying a polyhedron building to other atoms of the same atom site.

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Changing Designs After Creation

You can change the design of existing polyhedra. That means you may alter colors, edge, hatching, material properties and the style (which faces to open). But you cannot change the coordination sphere of a polyhedron, that means you cannot change the composition of the polyhedron (ligand atoms, geometry, etc.). If you want to change the composition, you must first destroy the polyhedron, and then create a new one with new settings concerning sphere size or what so ever.

To change the design select the polyhedron (or multiple polyhedra at one time), and then choose the Polyhedra command from the Edit sub-menu of the context menu. This opens the Polyhedron Design dialog, which works in principal like the Polyhedron Design dialog for a new (coordination or Voronoi) polyhedron. For that refer to the article "Polyhedron design and hatching".

Adding and Removing Edges

This command Build -> Polyhedra -> Add or Remove Edges enables you to remove (unwanted) edges from polyhedron faces, i.e. to expand triangular polyhedron faces to higher polygons, for instance two triangles to one square each in a cubic environment. This is useful, if the epsilon angle value in the "Add Polyhedra" or "Construct Polyhedron" dialog does not automatically combine triangles to higher polygons as you may intend.

The reverse functionality is also available, that means splitting polygons to smaller polygons (down to triangles, if wanted).

When you run the command, the mouse cursor symbol changes and you begin a mode where you click on two atoms each to remove the edge between. (If already two atoms are selected before you run the command, this edge will be removed automatically and you continue the "Add or Remove Edges" mode.)

You can add an edge, if you hold down the Shift key while you click two atoms.

To terminate the edges removing and adding mode, simply press the Escape key, and the mouse cursor will restore to its normal shape.

Copying and Pasting Polyhedra

There are two commands in the Build/Polyhedra sub-menu that help you to transfer polyhedron buildings to other (central) atoms: Copy Polyhedra and Paste Polyhedra.

These commands enable you to make a copy of a coordination polyhedron and add this polyhedron building to other symmetry-equivalent atoms of the same site. This is useful, if the normal function to add polyhedra around selected atoms or atoms of selected atom groups semi-automatically by defining a sphere or an environment fails. It is especially useful, if you have constructed a polyhedron and/or added or removed edges (i.e. changed some polyhedron faces to higher or lower polygons).

To copy a polyhedron, select the central atom and run the Copy Polyhedra command. (You may select multiple atoms of different sites, and Diamond creates a copy for every site each.)

To paste the copied polyhedron to one or more atoms of the same site, select these atoms and run the Paste Polyhedra command. Since Diamond handles copies for every site each, you may paste polyhedra even to multiple atoms of different atom sites with one single Paste Polyhedra command.

The Copy Polyhedra command is also available in the table of polyhedra. Select a polyhedron in the table and run the Copy Polyhedra command to create a copy of that polyhedron building, which can be pasted later with the Paste Polyhedra command from the main menu's Build/Polyhedra sub-menu.

Previous article: Polyhedron selection and properties
Next article: Creating Voronoi polyhedra