Using the Move Tool

The Move Tool in the Builder is used to move, rotate, and align atoms, using either the mouse or exact coordinate and vector control. This section will explain the basic features and how to use them.

To activate the Move Tool, click the button icon_mode_move on the toolbar. The Move Tool will also automatically be activated if you drop a system from the stash onto the 3D window (see below).

When the Move Tool is active, a widget appears in the panelbar in the right side of the window, where you can set some parameters that control the operations.

There are four modes of move interaction - Translate, Rotate, Align and Advanced Move. Each mode can be activated either by selecting buttons available in the 3D window, or by selecting one of the tabs in the widget.

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Fig. 29 Benzene molecule as an active Stash Item. Move Tool was activated by clicking icon_mode_move.

Also note that when the Move Tool is active, all other plugins are unavailable, to avoid interference (in the same way other plugins are disabled in Preview mode ). To use any other plugin, you must first exit the Move Tool, either by closing the widget, or by clicking the shape select button icon_select_rectangle on the toolbar at the top of the window.

Selection control

The Move tool operations are applied to the atoms which are selected. In Fig. 29 all atoms in benzene molecule are selected.

Tip

If you hold your mouse on an atom or a bond in the window, you can get detailed information on that atom or bond.

Translation

To move (translate) the selection drag one of the atoms in the selection group to a new position, holding down the left mouse button. If multiple atoms are selected the entire selection group will follow rigidly, i.e. the same translation vector will be applied to each selected atom.

The translation is carried out in the view/screen plane (except for snapping, as explained below).

Position or move the center of the selected group by entering its new cartesian coordinates in the table given to the right of the window. Change the row for \(u_1\) to set a new position, or row \(Δu\) to move the center of selected group for a specific amount. The center of the group is given in the row \(u_0\).

Anchor atoms

Another way to activate the Move Tools is to drop a structure from the Stash onto the 3D window. In the Fig. 30, benzene molecule has been dropped with the pyridine. In a addition, three anchor atoms have been selected (red markers).

When the Move Tool is active, you can select up to three atoms within the selection group, which are used to guide the actual move operations. These atoms will be indicated by red selection markers, and will also be marked by the numbers 0, 1, and 2 to show the selection sequence. These are called anchor atoms. In Fig. 30 you can see that anchor atoms have been selected.

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Fig. 30 The three anchor atoms on the pyridine molecule are indicated by an index and red markers.

You can also see in Fig. 30 that when the anchor atoms are selected, the three table rows in the widget are populated. The three rows show:

  • \(r_0\), the position of the first anchor atom (index 0).
  • \(r_1 − r_0\), i.e. the vector from the first to the second anchor atom.
  • \(r_2 − r_1\), i.e. the vector from the second to the third anchor atom.

The significance of these vectors, or rather how to use them in a powerful way, will become more obvious in the following sections. As a general rule, select:

  • One anchor atom to translate (move) the fragment,
  • Two anchor atoms to adjust the angle between two bonds,
  • Three anchor atoms to adjust a dihedral angle.

To deselect all anchor atoms, click the background with the left mouse button. To deselect one anchor atom, just left-click it again (if you deselect the first anchor atom, all anchor atoms are deselected, and if you deselect the second anchor atom, the third one is also deselected).

Snap and fuse

If Snap is checked when you translate by mouse, the anchor atom will snap to the positions of other atoms, if you come close enough to them. This can be used to place the anchor atom exactly at the position of another atom, which does not belong to the selection group.

Important

The configuration obtained just after snapping is not valid, which will be indicated by the label showing that there are overlapping atoms. There may be more than one atom pair overlapping as a result of the translation. Click Fuse to delete the overlapping atoms not belonging to the selection group.

The snap option defines the translation vector that is applied to the entire selection group in all 3 directions; X, Y, and Z. Thus, using the Snap option may bring the selection out of the screen plane if the snap atom does not have the same Y coordinate as the anchor atom (in the example case of translation in the XZ plane).

Tip

A very powerful way to use snapping is to add alignment atoms at the positions where you want to place an atom or molecule. This alignment atom could be in a high-symmetry position, e.g. an fcc site a certain distance above a crystal surface. The alignment atom itself is sacrificial, and will be removed by the Fuse operation.

Note

It is common that there are atoms which are close, but not exactly overlapping, after a move operation. In this case Fuse cannot be used, but instead the plugin “Selection Tools ‣ Close Neighbors” is useful to find and delete atoms which are close to each other. Make a habit of checking the structure with this tool after a complex operation, e.g. with the Move Tool, or after mirroring or rotating structures.

Advanced Move

If you select two anchor atoms and start moving either one with the mouse, the selection group will rotate, using the first anchor atom as the rotation center and the vector between the two anchor atoms as the rotation axis. During the rotation, you can snap to any other atom for more exact control.

Alternatively, you can type in the direction vector between the two anchor atoms \(r_1− r_0\) in the widget, to realign the structure with regard to the cartesian directions. Only the direction of this vector matters, not its magnitude. For example, if you want the group to be realigned such that the vector between the two anchor atoms becomes parallel to the Z-direction, enter \(r_1−r_0 =(0,0,1)\).

Finally, if you select three anchor atoms, you can use the mouse to control the dihedral angle between the plane spanned by two of the anchor atoms and the current mouse position. Snap works as above, as well as editing directly in the widget.

To align the group such that the three anchor atoms lie in the XY-plane, enter \(r_1− r_0 = (0,1,0)\) and \(r_2− r_1 = (1,0,0)\). The cross product of these two vectors is \((0,0,1)\), which is the XY-plane normal.