Diamond Version 5 User Manual: Modes of operation

Neighbouring Preview

Get a preview of the atoms and molecules around the atom (molecule) under the mouse cursor

In this article:
- Move mouse cursor over an atom and see its neighbouring atoms (and molecules, if molecular structure) as semi-transparent preview.
- Turn mouse wheel forward/backward to increase/decrease the preview sphere size.
- Neighbourhood preview can also be applied to whole molecule.

Previous article: Grab Mode
Next article: Exploring bonding and contact spheres: Overview

To demonstrate the neighbourhood preview, we use the sample file "COD-1500005-one-Co(NH3)6-molecule.diamdoc". We also change from the default "select and edit" mode to "grab mode" by clicking on the hand symbol in the main toolbar or using accelerator key Ctrl+G or using the command "Grab Mode" from the "Edit" menu. This changes the mouse cursor to the hand symbol. If you are not yet familiar with "grab mode", please read the article "Grab Mode".

Neighbourhood preview in hovering mode

To start the neighbourhood preview, run the command "Neighbourhood Preview" in the "Tools" menu or simply press the F8 function key. The mouse cursor changes to a combination of hand and crosshairs.

(1) Move the mouse cursor to the "Co1" atom in the center of the Co(NH3)6 molecule. Diamond emphasizes the center of the preview with a blinking blue rectangle and the current sphere's boundary with a blue circle. The status bar informs you that the current size is 1.97 Angstroem, which is the size of the coordination sphere of "Co1" with its six direct N neighbour atoms.
(2) Turning the mouse wheel forward increases the size of the neighbourhood preview with 0.1 Angstroem per standard mouse wheel tick. (This increment may be smaller, if your mouse wheel has a finer granularity.) At 2.5 Angstroem all H atoms have been captured, so the formula sum of the neighbourhood atoms reads "[H18N6]". The formerly dimmed H atoms have turned into white indicating that they are now inside the preview sphere.
(3) At 3.9 Angstroem, the first neighbouring molecules semi-transparently enter the stage -- one O atom of two AsO3(OH) molecule ions each have been captured (top right). (Note: Diamond automatically completes the found neighbouring atoms to molecules.)
(4) The next wheel tick adds another four AsO3(OH) molecule ions (bottom left).
(5) Some wheel ticks later at 4.765 Angstroem we have a total of 14 neighbouring atoms partially inside the preview sphere, actually the formula sum of the neighbouring atoms inside the sphere is "[H32N6O12]". (Note: The bottom right picture uses a somewhat smaller enlargement factor. You can increase or decrease the enlargement factor by holding down the Shift key while turning the mouse wheel.)

This kind of neighbourhood preview is called "hovering" because the semi-transparent neighbouring atoms/molecules vanish when you move the mouse cursor out of the preview sphere (i.e. leave the blue circle). When you return to the same central atom, the preview mode continues with the same sphere size, so that the same neighbours as before appear. To see the neighbourhood of another central atom, move the cursor outside the blue boundary sphere and then to the other central atom.

Permanent (non-hovering) neighbourhood preview mode

To prevent loosing the previewed neighbourhood when leaving the sphere boundary, click with the mouse wheel into the preview sphere's center. The mouse wheeling control window appears indicating that you have turned the hovering neighbourhood preview into non-hovering mode. This is useful to get infos about atoms lying outside the preview sphere (info tip). You can also click on other atoms than the center of the preview sphere to select it. Press the pin button in the top right to prevent the control window from closing after a few seconds. (The control window is also used for the other mouse wheeling modes -- this is described in more details in the next article: "Mouse wheeling".)

To terminate the neighbourhood preview mode, click on the 'x' symbol in the top left of the wheeling mode control window, or simply press the Escape key. The semi-transparently previewed neighbouring atoms and bonds will then disappear.

Preview the neighbourhood of a whole molecule

While the examples above use a single atom as the neighbourhood's center only, we now want to check the neighbourhood of an entire molecule. For that make a long click on the "Co1" atom, that means press down the mouse wheel button and hold it down for longer than one second. The animated blue rectangle enclosing the "Co1" atom explodes onto the corners of the rectangle enclosing the molecule. Instead of a single blue circle you see the outlines of the spheres of all constituent atoms of the molecule. (Note: The mouse wheel click leads us directly into permanent - non-hovering - mode.)

The screenshot below shows the start of the neighbourhood preview of the Co(NH3)6 molecule...

... and after some mouse wheel ticks we come to the following scenario:

Previous article: Grab Mode
Next article: Exploring bonding and contact spheres: Overview

Reference: COD:1500005: Hexaammine cobalt(III) hydrogenarseniate tetrahydrate - Pccn (56) - Ritu Bala, Raj Pal Sharma, Rajni Sharma, Juan M. Salas, Miguel Quiroos, William T.A. Harrison: Cationic cobaltammines as anion receptors: Synthesis, characterization an X-ray structure of bis-(hexaamminecobalt(III)) tris-(hydrogenarsenate) tetrahydrate - Journal of Molecular Structure, 828, 174-180 (2007).