Diamond Version 5 User Manual: Building up structural parts

Destroying all or parts of the structure picture

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Functions for the controlled dismantling of structural parts are almost as important as functions for building up structures. Most of the dismantling functions can be found in the Destroy submenu of the Build menu:

More commands to delete (individually selected) atoms and/or bonds or other objects like polyhedra, labels, etc. are available from the context menu for the selected objects:

In this article we describe in details

- how to delete selected atoms or bonds,

- how to delete selected molecules or fragments (that means how to cut off parts of molecules),

- how to keep selected atoms and bonds or molecules but to delete the unselected atoms, bonds, or molecules instead,

- how to destroy the entire structure picture.

The article "Destroying polyhedra" describes how to delete selected or all (coordination or Voronoi) polyhedra. Besides this, there are hints how to destroy special objects like atom labels, bond labels, user-defined text, atom vectors, and more in the corresponding articles where these objects are described: Display of structure picture.

Deleting Atoms or Bonds

Diamond offers a lot of ways to delete atoms or bonds:

1. Using the Delete key

This is the most common method to delete one single or multiple atoms and/or bonds. First select the atom(s) and/or bonds, rsp., then hit the Delete key. See the article "Selecting objects" (and following) how to select atoms and bonds.

2. Using commands from the structure picture's context menu

If multiple kinds of objects have been selected (e.g. both atoms and bonds that have been selected inside a mouse-defined rectangle), but you want to delete selectively atoms or bonds only, choose the appropriate command from the Destroy submenu of the context menu. To open the context menu for the selected objects, click into one of the objects with the right mouse button. This selective deleting does not touch any selected objects of other kinds.

3. Deleting atoms or bonds from the tables of created atoms or table of created bonds etc.

If you want to delete atoms and the "table of created atoms" (that means table of all atoms in the current structure picture) is active in the data pane, or if you want to delete bonds and the "table of created bonds etc." is active in that pane, you can choose the Destroy Atom(s) or Destroy Bond(s) command, rsp., of the table's context menu to delete all selected atoms or bonds, rsp.

For more details how to use tables for selecting objects, see the article: "Tables of objects like atoms, bonds, molecules etc.".

4. Deleting using enhanced selections

The lists in the data pane offer comprehensive methods to select atoms and bonds for very special criterions. This selection works in principle like that:

(1) Open the table of created atoms, if you want to delete atoms (View/Tables/Table of Created Atoms)

(2) Sort the atoms for a suitable criterion.

(3) Select the atoms in the table. This is easy if these atoms are arranged in a block due to a suitable sort criterion.

(4) Continue like in method #3.

5. Deleting all created atoms belonging to selected atoms or atom types

You can use the table of atom groups or the table of atomic parameters instead of the table of created atoms to select and delete all atoms that belong to selected atoms from the parameter list or selected atom groups (atom types):

(1) Open the table of atom groups or the table of atomic parameters. (Choose the appropriate command from the Tables submenu of the View menu.)

(2) If necessary, sort the list. This may be suitable in large atomic parameter lists, where you mostly sort for element symbols.

(3) Select the atoms or atom groups in the table.

(4) In the table of atomic parameters, choose the Select Atom(s) command from the context menu of the table. In the table of atom groups, the corresponding command reads Select Atoms by Group. This selects all atoms belonging to the selected atoms or atom groups, rsp., in the structure picture.

(5) Click with the right mouse button into one of the selected atoms in the structure picture, and then choose the Atoms command from the Destroy sub-menu context menu.

6. Deleting all created bonds belonging to selected bond groups

This works like method #5, but with the table of bond groups in the data pane, and with commands like Select Bonds by Group (table's context menu) and Destroy -> Bonds (structure picture's context menu) instead.

7. Deleting all bonds with a selected bond length

One special application of method #6 is to select and delete all bonds with lengths within a well-defined distance range. For that, choose the Table of bonds etc. command from the Tables submenu of the View menu to show the table of bonds in the data pane. Sort the bonds for bond lengths, and select a block of bonds having the desired bond lengths. Then choose the Destroy Bonds command from the context menu of the bond table.

Note: This works also for H-bonds or non-bonding contacts or other pseudo-bonds used in the structure picture, e.g. cell edges.

8. Deleting all non-bonded atoms

Diamond offers a special command that deletes all non-bonded atoms. This command is mostly used to remove solvation molecules from structure pictures showing molecules. To delete all non-bonded atoms, choose the Non-bonded atoms command from the Destroy submenu of the Build menu, or push the drop-down button right beneath the Destroy All button in the Build toolbar and choose the Destroy Non-bonded Atoms command from the drop-down menu:

Deleting Molecules or Fragments

You can delete a complete molecule with one mouse-click or a fragment of a molecule with two mouse-clicks.

To delete a molecule, select an atom of the molecule, and then choose the Destroy Molecule(s) command from the Destroy submenu of the Build menu (or from the structure picture's context menu: Destroy ->Molecules). Or use the drop-down arrow beneath the Destroy All button in the Build toolbar:

Deleting a fragment means that you destroy a bond within a molecule and then delete the cut part. To delete a fragment, first select the atom at the residual side of the bond, and then select the atom at the fragment that will be discarded. Then choose the Destroy Fragment command from the Destroy submenu of the Build menu.

Destroying unselected atoms, bonds, or molecules

In contrast to the above described commands that delete selected atoms, bonds, or other objects from the structure picture but keep the unselected ones, there are two commands available that keep the selected atoms, bonds, or molecules but delete the other ones that are not selected from the picture.

Both commands are available from the Destroy submenu of the Build menu:

Unselected Atoms and Bonds deletes all unselected atoms and bonds as well as contacts and H-bonds but leaves the selected atoms, bonds, contacts, and H-bonds unchanged.

Unselected Molecules can be used to protect all atoms and bonds belonging to a molecule from being deleted, if at least one atom or bond of this molecule is selected. With other words: You need not first select all atoms and bonds of the molecule and then run the Unselected Atoms and Bonds command. "Molecule" means the moiety of atoms, connected with bonds (not contacts or H-bonds), "as is" in the structure picture. This means it may be a complete molecule or a fragment of a molecule (that may be completed later or not) or a part of an inorganic or organic polymer structure. Molecules where no atom and no bond is selected will be deleted from the picture.

Both commands delete atoms from the structure picture - together with associated bonds, contacts and H-bonds as well as other associated objects like polyhedra, atom vectors, or atom labels, but do not touch cell edges. If there are selected atom labels, bond labels, or atom vectors whose associated atoms and bonds (or contacts or H-bonds) itself are currently not selected, you will receive a warning message and you have the chance to cancel the command. Otherwise the labels and vectors associated with unselected atoms and bonds will be deleted, too.

Destroying all cell edges or all picture contents

You can simply discard the entire contents of the structure picture (except user-defined text) with the All command from the Destroy submenu of the Build menu, or with the "hotkey" Shift+Ctrl+D. Or use the (left marked) button in the Build toolbar (the arrow opens a drop-down menu with more commands):

This command deletes the entire structural part, that means all created atoms and thus all bonds between them, cell edges and coordination polyhedra. Text(s) in the structure window (but not atom or bond labels) will remain.

Up to Diamond version 4.5, the "Destroy All Cell Edges" command ("Build/Destroy" sub-menu) removed all cell edges from a structure picture but left the unit cell axes a, b, c (if activated in the "Display/Cell Edges Design" dialog) visible. Since version 4.6 and in version 5 you are prompted if you want to also hide these axes. (Unlike the cell edges, which are bond-like objects and can be added when building a structure picture or destroyed, the unit cell axes a, b, c or "base vectors" are always defined in the picture but can be switched on or off.)

Analogously, the "Destroy All" command left user-defined text, plane and line objects as well as unit cell axes a, b, c left unchanged - so you are now prompted to keep them or to delete (or hide, rsp.) them.

To adjust this behaviour, open the page "Build & Destroy" in the "Tools/Options" dialog. It offers settings, if to hide the unit cell axes a, b, c when destroying all cell edges and - additionally in the case of running "Destroy All" - if to delete all user-defined text as well as all plane and line objects, too.

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References:
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 (2011), 52-12369.
COD:1500005: Hexaammine cobalt(III) hydrogenarseniate tetrahydrate. 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).
COD:7103386: Rang, Alexander; Nieger, Martin; Engeser, Marianne; Lützen, Arne; Schalley, Christoph A; "Self-assembling squares with amino acid-decorated bipyridines: heterochiral self-sorting of dynamically interconverting diastereomers."; Chemical communications (Cambridge, England), *, 4789-4791 (2008).