Diamond 2.1: Individual addressing of objects
Diamond 2.1 Features Overview...
Previous: Useful for all kinds of crystal
structures...
Next: Adjusting bond spheres...
Diamond offers a lot of functions to build up pictures displaying the
contents of a cell range, or a single molecule or a packing diagram. Many of
competitive programs offer similar tools. But if you want to select e.g. one
single or a group of atoms, or bonds, or labels, etc., you have a variety of
comfortable choices. This selection may be necessary to change the style of a
single atom, or to build up its enclosure sphere.
Although the smart handling of data and pictures has been a strength of Diamond
in the past, it has been improved significantly in version 2.0. The method of
editing a structure is analogous to edit a text within a word processor, e.g.
first select particular objects to be edited and then choose a function to be
applied on the selected objects. Thus the problem of editing a complex
structure is reduced to the problem of smart selection.
Reflection between selection in picture and table
The easiest way, of course, is to click with the mouse into the atom, bond,
label, etc. You may also catch the objects inside a rectangular area. The
selection is automatically reflected in a table in the so-called data pane,
which can be opened right beneath the structure picture. Such a table contains
all created atoms, bonds, or polyhedra. You may change the columns to be
displayed and - what is most important - the sort order. For example sort the
list of bonds for bond lengths. Vice versa, clicks in the data tables are
reflected automatically in the structure picture. Context-sensitive popup-menus
and 'flying' toolbars guarantee short ways to frequently used functions.
This example shows the main pane containing the structure picture and (on the
right) the list of created atoms sorted for atom symbols and with "Ag(3)"
highlighted:
With the list of atomic parameters or the list of atom types, you may select all
(symmetry-related) atoms belonging to a selected atom (type).
Polyhedra are selected via the corresponding central atom, as in the following
example, showing the unit cell of Laueite (from ICSD; Collection Code: 23819)
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, sorted
for atom symbols
Inverting the selection
A very helpful command can invert the current selection, e.g. if you want to
delete all but the selected molecules.
What is this atom, bond, etc.?
In the info mode, you can click on objects like atoms, bonds, etc., and get
informations like symbol, symmetry, coordinates, etc. in a special info window.
Additionally you can watch the informations in the table, since the selection
of the atom, e.g., is reflected in that table.
Where in the picture is atom "C121a" ?
Imagine, you want to emphasize a special atom of the parameter list (let us
call it "C121a"), assigning it the color yellow, or label it, or check its
enclosure sphere. With the table of atomic parameters, it is very easy to
locate the atom in the picture.
Diamond 2.1 Features Overview...
Previous: Useful for all kinds of crystal
structures...
Next: Adjusting bond spheres...
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