Diamond Version 5 User Manual: Building up structural parts

Using the Mouse Wheel

Several options to use the mouse wheel to change properties (enlargement factor, zoom in/out, change atom radii) or to change surroundings (blow up polyhedra, expand molecule cluster, etc.)

This article describes how to use the mouse wheel to:
- Blow up coordination spheres/polyhedra.
- Find non-bonding contacts.
- Expand molecules to clusters.

Previous article: Pump Up or Shrink Polymeric Frameworks
Next article: Destroying all or parts of the structure picture

The so-called "Mouse wheeling" modes are available through the Mouse Wheel Action sub-menu in the Tools menu. These modes have in common that a tick of the mouse wheel changes a property each. The modes and the properties changed are the following:
(1) Expand selection: A forward tick extends the current selection to the bonds of the selected atom(s), the next tick each extends the selection to the bonded atoms, etc.
(2) Atom radii: This wheeling mode applies to the selected atoms or to all atoms, if no atom is selected. Every tick increases the radius of the selected atom(s) by some percent. (Starting point is 100 percent).
(3) Bond radii: Analogously to "Atom radii" this refers to the selected bonds -- or all bonds, if no bond is selected.
(4) Coordination sphere: This mode varies the coordination sphere around the selected atom. A forward tick adds another atom from the list of neighbouring atoms sorted for distances, whereas a backward tick removes one each.
(5) Pump up or shrink: A forward tick adds broken-off bonds to the neighbouring atoms each, the subsequent tick converts these broken-off bonds to normal bonds each, etc.
(6) Expand via contacts: A forward tick increases the search radius to find non-bonding contacts by 0.1 Angstroem each. To check out the sphere, you can use the mouse wheel to create neighbouring atoms/molecules with a mouse wheel tick each.
(7) Molecule cluster: This mode searches for molecules neighbouring to the selected atom or molecule. Every tick adds another molecule from the list of molecules sorted for increasing distances from the selected atom/molecule.

The wheeling modes "Pump up or shrink", "Expand via contacts", and "Molecule cluster" are demonstrated below.

The wheeling mode "Expand selection" is described in the article "Selecting objects".

The wheeling modes "Atom radii" and "Bond radii" are described in the articles "Designing atoms" and "Designing bonds and contacts".

The usage of the mouse wheel to change the enlargement factor or to zoom in or out is described in the article "Grab mode".

Pump up or shrink

The "Pump up or shrink" wheeling mode adds/removes atoms of the n-th sphere around selected atom, while stepping via broken-off bonds.

As an example we use the document COD-10004001.diamdoc: We start with a single atom of the parameter list, that is the first one: "W1", and complete the molecule step-by-step then expand via contacts and H-bonds to neighbouring molecules' atoms and continue with step-by-step building up...

(1) Destroy all ("Build/Destroy/All" or Shift+Ctrl+D). This deletes the whole molecule, the picture is now blank.
(2) Run "Build"/"Add Atoms...". In the dialog select the atom "W1", which is the first atom in the parameter list, and press OK. This creates a single "W1" atom (at x,y,z) in the center of the picture.
(3) Click on this single "W1" atom to select it.
(4) To start the "Pump up or shrink" wheeling mode, run "Tools/Mouse Wheel Action/Pump Up or Shrink". The blue blinking square indicates the center of the sphere that will be pumped up and the mouse wheeling control window opens, too.
(5) With a mouse tick each, you first create broken-off bonds to the neighbouring atoms of the current sphere, then, with the second tick each, the neighbouring atoms are shown and the broken-off bonds turn into normal bonds.
(6) This is subsequentally repeated with every next two wheel ticks each.

This is the mentioned sequence for "W1" as center. (We omitted some steps between the fifth and the sixth picture):

Note: Screenshots have been made with version 4 of Diamond.

Expand via contacts

In the following example, we first examine a contact sphere, then try out to find subsequently neighbouring molecules via these contacts. We open the example with one molecule of COD:1501635 from COD-1501635-molecule.diamdoc, click on the "Br1" atom at (x,y,z) (in the top left when viewed along -a-axis), and run the command "Tools"/"Mouse Wheel Action"/"Expand via Contacts". The blue blinking marker appears and the mouse wheeling control window opens for "Expand via contacts" mode.

There are three atoms in the neighbourhood of "Br1", not more than the sum of van der Waals radii plus an offset of 0.1 Angstroem away. You get these three neighbours ("Br2", "C11", "H3") by turning a mouse wheel tick each, as the sequence of four pictures show below:

Now we make two sequences of neighbouring molecules using (a) the Br1--Br2 contact only, or (b) Br1--Br2 plus Br1--C11 contacts. To change from contact sphere evaluation (mouse wheel changes search radius) to expansion (a mouse wheel tick adds another contacted neighbouring molecule each), press the "Expand Cluster" button in the control window (see picture below).

(a) The iteration via the Br1--Br2 contact only leads to the following sequence:

Molecule cluster

Again we start with the example COD:1501635. Best is to close and re-open the file COD-1501635-molecule.diamdoc and start again with the single molecule.
(1) Select "Br1" (at x,y,z) -- that is the top-left Br atom.
(2) Run command "Tools/Mouse wheel action/Molecule cluster". This marks the selected Br atom with a blinking blue square and opens the mouse wheeling control window:

(3) The first mouse wheel tick generates the molecule that is closest to "Br1" with a Br1--H3 distance of 3.211 A.
(4) Continue rotating the mouse wheel, and every tick generates the next less closer molecule each.
The following picture shows the situation with four (left part) and with 18 molecules, rsp., found:
 

Checking the whole molecule's neighbourhood
We now check the whole molecule rather than the single "Br1" atom only for closest neighbouring molecules:
(1) Click on "Rebuild all" and terminate this mouse wheeling mode.
(2) Long-click on "C1" (in the center of the molecule): Blue markers explode to embrace whole molecule indicating that molecule clustering now refers to the whole molecule rather than to one atom ("Br1") only.
(Note: Same works with "Select molecule" and then "Tools/Mouse wheel action/Molecule cluster".)
(3) Generate neighbouring molecules with a mouse wheel tick each.
The following picture shows the start situation (left) and with 24 neighbouring molecules (right):
 

Previous article: Pump Up or Shrink Polymeric Frameworks
Next article: Destroying all or parts of the structure picture

Reference: COD:1501635 - Ulrich Darbost, Janie Cabana, Eric Demers, Thierry Maris, James D. Wuest: Molecular Tectonics. Use of Br...aryl Supramolecular Interactions for the construction of Organized Networks from 9,9'-spirobifluorene in the Crystalline State. CheM, 1, 52-12369 (2011).