Diamond Version 5 User Manual: Modes of operation

Selecting objects

Additive and subtractive selection, molecule selection, a selection filter, and "Expand Selection" make it easier to edit objects in a multitude of other atoms, bonds, etc.

This article is about:
- How to select objects of the structure picture (atoms, labels, etc.).
- Normal vs. additive and subtractive selection. Usage of Ctrl and Shift key.
- Select the molecule when you click an atom, or expand selection to whole molecule.
- Expand or reduce selection stepwise to or from the next (bonded) neighbouring atoms and bonds.
- Use the mouse wheel to expand current selection to neighbouring atoms and/or bonds. (Cf. Tools/Mouse Wheel Action/Expand Selection command.)
- Selecting disorder parts.
- The "Selection Filter" enables you to choose object types (atoms, bonds, labels, etc.) that are to be considered when you click on objects in the structure picture. This reduces inadvertent matching of wrong objects.
- Selecting fragments, i.e. any moiety of atoms with connecting bonds.
- Selecting other objects than atoms and bond, e.g. labels of selected atoms.
- Selecting atoms and other objects at symmetry-related positions.

Previous article: Overview
Next article: Tables of objects like atoms, bonds, molecules etc.

Selecting objects in the structure picture

This article describes, how objects of the Diamond structure picture (that means, atoms, labels, etc.) can be selected.

The following object types of the structure picture can be selected. The table lists how an object is selected by clicking into an object-dependent 2D range within the structure picture.

Standard selection

The most common way to select an object is to move the mouse cursor to a suitable position of the object (see table above) and then click the left mouse button. The selection is reflected by a rectangle which surrounds the selected object. All other selections will be restored in that moment.

Using Shift or Ctrl key

You can use the auxiliary Shift key to mark multiple objects. While you hold down the Shift key when you click on an object, the other already selected objects do not loose their selection state. Usually the Shift key is used to select multiple objects that cannot be "catched" with a rectangle (see below). That means, object at different positions may be clicked and selected one after the other.

The auxiliary Ctrl key behaves in a similar way (and unless no other objects are selected in the same way): If you hold down the Ctrl key when you click on an object, the selection of that object will be inverted independent from the selection state of all other objects in the structure picture. This is useful to quickly change the selection state of an inadvertently clicked object, for instance.

Rectangle selection

If you press down the left mouse button outside of an object, then pull up a rectangle by moving the mouse cursor with left mouse button down, and then release the button, you will select all objects that lie completely inside that rectangle. You can additionately press the Shift key to prevent other objects from being deselected or the Ctrl key to invert the selection of all objects in the rectangle.

Lasso selection

In addition to the definition of a rectangle to select all objects inside, there is a special command Lasso Selection in the Edit menu, which selects all objects inside a user-defined free-hand figure.

To start the definition of the free-hand figure, click with the left mouse button outside any object. (If you click an atom, bond, etc., this object will be selected but no lasso selection started.) With the left mouse button down, "draw" the figure (like in an image drawing program) and close the figure by releasing the left mouse button when the mouse cursor is back in the small square that symbolizes the starting point.

You can also define a polygon by single-clicking a corner each. To close the polygon, return to the smal square or double-click (which automatically connects the last point with the starting point).

If you neither press Ctrl nor Shift key, all previous selection will be reset during the lasso selection. To add a selection independent from previous selection, hold down the Shift key. To invert selection, hold down the Ctrl key.

Temporarily hiding of objects

You can hide objects of selected types temporarily for a better access to other objects. For example, it is easy to select atoms that are covered by labels or to access polyhedra by their associated central atoms when the polyhedron faces are closed. To hide objects temporarily, choose the Hide command from the Display menu. Please note that the objects will not be discarded, and the hiding is not stored in the structure document.

Indirect selection with auxiliary object lists

You can select objects of the structure picture by selecting the corresponding items in the lists that can be displayed in the secondary pane (text pane or data pane). To open a list (table) in the text pane, choose the corresponding command from the submenu which opens when you choose the Table command from the View menu.

If the table of created atoms is displayed in the text pane, the selection of each atom in the structure picture is reflected in the atom table. On the other hand, you can change the selection of the atoms in the picture by changing the selection of the corresponding items of the atom table. That means, by sorting the atom table in a suitable way, you have varied possibilities to select a very special portion of the atoms in the picture.

Like atoms, bonds can be selected from the bond table. For example, if you sort the bonds in the table for bond lengths, you can select all bonds with lengths within that given range.

Polyhedra (that means, the corresponding central atoms) can be selected with the help of the polyhedra table.

The tables of atomic parameters, atom groups, and bond groups offer enhanced features to select atoms and bonds, rsp. For example, if you want to select all atoms that have been created from a special atom of the atomic parameter list (e.g. all symmetry-equivalent atoms of "Fe 3"), first select the atom in the atomic parameter table, and then choose the Select atom(s) command from the context menu of the atomic parameter table. The atom group table and the bond group table can be used to select all atoms and bonds, rsp., that belong to the selected atom group(s) and bond group(s), rsp.

The usage of the tables of created atoms etc. are described in more detail in the article "Tables of objects like atoms, bonds, molecules etc.".

Commands for selection

To select all objects of the structure picture, choose the Select all command from the Edit menu or simply use the "hotkey" Ctrl+A.

To invert the current selection, choose the Invert selection command from the Edit menu or simply use the "hotkey" Ctrl+I. This command can be used to select all but one molecule, for example.

Additive and subtractive selection mode

When selecting objects in the regular selection mode (with the default arrow pointer as mouse cursor symbol), every click on an object resets the other objects' selection states (unless you hold down an appropriate status key Shift or Ctrl). Diamond offers two additional selection modes, additive and subtractive selection, to support selection of multiple objects without the need to hold down the Shift or Ctrl key. In additive selection mode, the mouse cursor symbol shows an arrow with a plus sign, in subtractive selection mode with a minus sign instead. You can activate these modes through the Select command in the Edit menu or - as shown in the screenshot below - from the main toolbar.

In additive selection mode, simply click on the objects (or include them into a track rectangle), to add the objects to the list of selected objects. To remove a selection state of an inadvertently matched object, hold down the Ctrl key while clicking on it again. (That is the same behaviour as in normal selection mode -- Ctrl key is to toggle the selection state independent from the other objects's selection states.
Subtractive selection removes every clicked object from the list of selected objects. (It is like clicking on a selected object while holding down the Ctrl key in normal selection mode.) It is useful to remove a lot of selections without the need to have the Ctrl key pressed.
In both modes, the Ctrl key still works as before. It can be used to change a clicked objects' selection state independently from the other objects' selections.

Select molecule command

The Select Molecule command in the Edit menu (or available from the context menu) automatically expands the current selection to the whole molecule. (More exactly: The moiety of atoms and bonds currently in the structure picture, which may be a part of an inorganic or organic polymer or simply a sulfate or phosphate ion or so.)

There is an alternative command available from the context menu of the atomic parameter table: Select Molecules From Sites selects all molecules in the structure picture where at least one of the currently marked atom sites in the atomic parameter table belong to, meaning it first selects the symmetry-related atoms of the marked atom sites and then complete the selection to the end of the molecules, each.

Expand or reduce current selection

To expand the current selection stepwise to the neighbouring (bonded) atoms and bonds, run the command Expand Selection from the Edit menu (or simply press the Ctrl+E key combination). The first click selects the bonds, the second click each selects the bonded neighbouring atoms, etc.

The opposite function of Expand Selection is Reduce Selection. It removes selections beginning at the most outstanding selected atoms and/or bonds of the moiety of atoms and bonds (which can be a complete molecule or part of a molecule or part of an inorganic or organic polymer). It is also available from the Edit menu and with the Ctrl+R key combination.

Use the mouse wheel to expand or reduce a selection

A comfortable way to expand (and reduce) the selection to the neighbouring bonded atoms and bonds, is the usage of the "Expand selection" mouse wheel mode. (To get more informations about the several mouse wheel modes, read the article "Using the Mouse Wheel".) In the following example, we select the "C1" atom in the center of the molecule, then start the mouse wheel mode "Expand selection" with the command Tools -> Mouse Wheel Action -> Expand Selection. The mouse wheel control window shows the atom counts in the neighbouring coordination spheres. Turn the mouse wheel up to first select the bonds at "C1", then the neighbouring atoms bonded to "C1", etc. Turning the mouse wheel back reduces the selection. In the screenshot below, we have the first and second sphere neighbour atoms (and bonds) selected as well as the bonds to the third sphere.

Use "Select molecule/fragment" (bottom of mouse wheel control window) to expand the selection to the whole molecule, i.e. to maximum state in this "Expand selection" mode, or press the icon in the bottom right to remove all selections.

When you are done with the selection, terminate the "Expand selection" mode by pressing the 'x' symbol in the top left of the mouse wheel control window (not the small red/white 'x', which only hides the window).

Selecting disorder parts

Starting from a selected atom (or selected bond) you can select the disorder parts which the selected atom (or selected bond) belongs to. The command Select Disorder Parts in the Edit menu selects all atoms in the structure picture that have been derived from one of the atoms of the parameter list with the same "disorder assembly" and "disorder group", cf. the command Structure -> Atomic Parameters and the article "Support for disorder parts" for more informations about disorder parts.

When selecting the whole disorder part, the bonds between the atoms of this disorder part will also be selected but not the bonds to the non-disordered neighbouring atoms. You can expand the selection to these bonds by executing the command Edit -> Expand Selection once immediately after the Select Disorder Parts command.

Selection filter

If you have a lot of objects of different kinds, e.g. atoms, bonds, labels, atom vectors, etc., it may become tricky to match the wanted object when clicking with the mouse. The Selection Filter command in the Edit menu defines a filter that prevents objects (atoms, bonds, labels, etc.) of certain types from being selected with a mouse click in the structure picture. The object types can be selected in the Selection Filter dialog.

The selection filter applies to "Select & Edit" mode (where the mouse cursor has the arrow symbol) as well as to "Lasso selection" - but not to "Grab mode". If the filter is active, i.e. at least one object type cannot be selected by mouse click, the mouse cursor symbol has a chessboard-like interior. The selection filter can optionally be reset (in order to allow all object types to be selected again) with the Escape key. (The default setting is that the Escape key does not reset the Selection filter.)

Fragment selection

A fragment is a moiety of atoms that are connected with (strong) bonds (but not with H-bonds or non-bonding contacts). Typically it is part of a molecule that has not (yet) been completed to a molecule, or it is part of an inorganic or organic polymer. Here, for the selection commands, we also define a molecule as fragment, if it is actually a completed molecule. You define the fragment by pre-selecting the moiety of atoms, either by clicking them in the structure picture or by defining the constituent atoms from the table of atomic parameters, for instance.

Diamond offers commands to select the bonds between theses atoms or to deselect these bonds or the fragment (i.e. both atoms and bonds) at all. The commands are collected in the Extended Selection sub-menu of the Edit main menu or in the Extended Selection sub-menu of the context menu of the structure picture view.

Selecting a fragment from selected atoms

Presupossed the atoms that determine the fragment have already been selected, the Select Fragment(s) From Atoms command from the Edit/Extended Selection sub-menu selects all bonds connecting the currently selected atoms.

You can select multiple fragments at one time. This requires that you have multiple moieties of atoms each at different places in the structure picture that are either isolated from each other or there is a buffer of unselected atoms between, so they are not treated as one single big fragment.

The Select This Fragment command from the Extended Selection sub-menu of the structure picture's context menu is a comfortable alternative to quickly define a fragment or to exclusively define the moiety of atoms at the clicked position as fragment. If there are multiple moieties of selected atoms in the structure picture, it only considers the moiety of atoms (i.e. the fragment) at the clicked position. This is different from the above mentioned Select Fragment(s) From Atoms command of the main menu, which selects these multiple fragments from multiple moieties at one time.

Deselecting bonds from fragments

The command Unselect Bonds From Fragment(s) in the Edit/Extended Selection sub-menu is the reverse of the Select Fragment(s) From Atoms command. It removes the selection of the bonds connecting the atoms of the currently selected fragment (or the currently selected fragments, if there are multiple fragments).

The command does not remove the selections of the atoms of the fragment(s) nor does it remove (i.e. delete) the bonds itself from the picture.

There is also an alternative in the Extended Selection sub-menu of the structure picture's context menu: Unselect Bonds From This Fragment. This command removes the selection of bonds of the fragment at the clicked position only but leaves other fragments in the structure picture unchanged.

Deselecting both atoms and bonds of fragments

The command Unselect Fragment(s) in the Edit/Extended Selection sub-menu removes the selection of atoms, bonds, and associated objects (e.g. labels) belonging to the currently selected fragment(s). Unlike the above mentioned Unselect Bonds From Fragments command, this command is not limited to deselecting bonds only.

The command Unselect This Fragment in the Extended Selection sub-menu of the structure picture's context menu removes the selection of the fragment (atoms, bonds, labels, etc.) at the clicked position while other fragments remain unchanged.

There is also another command in the context menu to completely deselect fragments: Unselect All But This Fragment. Unlike the Unselect This Fragment command, this command removes the selection of all fragments but leaves the fragment at the clicked position unchanged.

Selecting multiple fragments directly from atom site table

The following command is available from the context menu of the atomic parameter list: Select Fragments From Sites. It selects all fragments in the structure picture that derive from the currently marked atom sites in the atomic parameter table, including symmetry-related atoms/fragments.

Selecting other objects than atoms and bonds

The Objects Selection command in the Edit/Extended Selection sub-menu offers versatile options to select atoms, bonds, contacts as well as objects like atom or bond labels or to remove selections ("unselect"). This is done with the Objects Selection dialog where you choose the types of objects to become selected or deselected as well as options how to apply the selection process to these objects.

The types of objects are listed in the upper part of the dialog, as there are "atoms", "bonds", as well as "atom labels", etc., each of them as checkbox, so it can be activated independently from other object types.

Selecting or deselecting labels etc. directly

To select or deselect all occurrences of objects whose types are checkmarked in the above list, use the option (radio button) All objects of the above checked types in the Apply to part of the dialog. (This is the default setting.) When pressing the Select Now push button, all objects of the types checked in the checkboxes from Atoms down to Coordinate system will become selected. On the other hand, they will be deselected rather than selected, if the Unselect Now button is used instead.

Selecting objects associated to atoms or bonds

The second option at Apply to is Objects of the above checked types that are associated with objects already selected in the picture. This is the method of choice to select associated objects. Associated objects are e.g. an atom label or an atom vector that belongs to a certain atom. If this option is activated, only objects of the above checked object types that belong to objects that are currently marked as selected in the structure picture. This option is useful to e.g. select just the atom labels that belong to atoms that are currently selected whereas other labels will not be considered. This also works in the opposite way, e.g. you can specifically select only these atoms whose labels are currently marked as selected.

If you want to deselect rather than select such associated objects press the Unselect Now button rather than Select Now.

By default, the atom (for instance) will keep its selection when you select its associated atom label in this way. If you want to deselect the atom after its label has become selected, set the checkmark at Remove selection of associated object [...]

Note: You will be prompted, if this option is active but currently no objects are selected. Press the "Yes" button in the message box in order to change the application to all objects of the check-marked object types. "No" will neither select nor deselect objects.

Selecting H-bond components or non-bonding contacts

The checkmark at Bonds refers to real bonds but no pseudo-bonds like cell edges as well as no non-bonding contacts and no "H-bonds" (i.e. H...acceptor contacts).

The checkmarks below Bonds - such as H-bonds: H - - A - can be used to specifically select (or deselect) H-bond components and/or non-bonding contacts. These are the H...acceptor contacts of H-bonds (checkbox H-bonds: H - - A), the donor...acceptor contacts (D - - A) as well as the donor---H-atom bond (D - - H).

Non-bonding contacts can be (de)selected indepently from strong bonds and H-bonds with the Contacts check box.

Please note that the Bonds checkbox also includes the strong (covalent) bonds between donor atom and H-atom. To select donor---H bonds only but no other strong bonds, set the checkmark at D - - H but clear the checkmark at Bonds.

Selecting atoms and other objects at symmetry-related positions

The Edit/Extended Selection sub-menu also contains commands to select atoms, bonds, or other objects (atom labels, bond labels, and atom vectors) that are symmetry-related to the currently selected atoms etc. or remove the selection of symmetry-related atoms etc. "Symmetry-related" means the atoms etc. belong to the same atom site or the bonds or bond labels belong to the atom sites of the connected atoms each but have a different symmetry operation and/or additional x-, y-, or z cell translations. Thus these commands are available only for crystal structures.

The Select Symmetry-Related command extends the current selection of atoms, bonds, labels, and/or atom vectors to its symmetry-related atoms, etc.

The Unselect Symmetry-Related command removes the selection of symmetry-related atoms, bonds, and other objects. It restores the selection from a previous call to the Select Symmetry-Related command, since the Select Symmetry-Related command backups the selection before it extends the current selection to the symmetry-related atoms etc. When called from the main menu without a previous Select Symmetry-Related command, it removes the selection states of all atoms etc. that are not at the "x,y,z" position, i.e. that have either a symmetry operation other than "x,y,z" and/or have an additional integer cell translation.

The Unselect Symmetry-Related command is also available from the Extended Selection sub-menu of the context menu of the structure picture. In this case it refers to the symmetry of the atom or bond where the context menu has been requested for, i.e. usually where the context menu has been opened with a right mouse button click. All symmetry-related objects having a different symmetry operation and/or different cell translations, will then loose its selection states. If the context menu has been called in a different way, e.g. by using the context menu button on the keyboard or by using Ctrl+right click anywhere in the picture, it will access the backupped selection from a previous call to Select Symmetry-Related or - if not available - will keep the "x,y,z" positions only as selected.

Selecting all atoms at x,y,z positions or those at symmetry-equivalent positions

The Select All Atoms At x,y,z command from the Edit/Extended Selection sub-menu of the main menu first clears all selections (atoms as well as other objects' selections), then selects all atoms of the current structure picture that either have been derived from the atomic parameter list without any application of symmetry operations or integer cell translations.

In contrast to the previous command the Select All Atoms Not At x,y,z command selects all atoms with at least a symmetry operation (excluding the trivial "x,y,z" identity operation) or an integer cell translation in x, y, or z direction, e.g. at "x,y-1/2,-z", or "1-x,-y,z+1/2" etc.

Previous article: Overview
Next article: Tables of objects like atoms, bonds, molecules etc.

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).