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 Move02_icon on the left toolbar, but take care to first consider which atoms you wish to operate on (see below). The Move Tool will also automatically be activated if you drop a system from the stash onto the 3D window.

When the Move Tool is active, a widget appears, where you can set some parameters that control the operations. The parameters will be discussed in detail below.

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Fig. 14 The benzene molecule has been dropped from the stash onto the 3D window with the pyridine, and three anchor atoms have been selected (red markers).

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 icon SelectRectangle02_icon on the toolbar at the top of the window.

Selection control

The Move tool operations are applied to the atoms which are selected when the tool is opened. This selection, i.e. the atoms marked with yellow selection markers, is called the selection group. In Fig. 14 the selection group is the benzene molecule.

Note

If no atoms are selected when the tool is opened, the first atom you click will be selected, along with all atoms in the same fragment (a fragment is a set atoms connected by bonds).

The selection group cannot be modified once the Move Tool is activated (except in the special case mentioned in the previous paragraph). To define a new selection group to operate on, you must first close the Move Tool, select new atoms, and then activate it again.

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.

Anchor atoms

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. 15 you can see that anchor atoms have been selected.

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Fig. 15 The three anchor atoms on the nanotube cap (in the process of being added to the open end of the nanotube) are indicated by an index and red markers.

You can also see in Fig. 15 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).

Translation

To move (translate) the selection group, select one anchor atom in the selection group. Then use the mouse to drag this atom to a new position, holding down the left mouse button. The entire group will follow rigidly, i.e. the same translation vector will be applied to all atoms in the selection group.

The translation is carried out in the view/screen plane (except for snapping, as explained below). For example, to control the translation such that the atoms are moved only in the XZ-plane, but keep their Y coordinates, click one of the buttons xz or zx to set the view plane.

You can also type in the exact new position of anchor atom 0 in the widget by entering its new cartesian or fractional coordinates in the table, in the row for \(r_0\).

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.

Rotation - bond angle adjustments

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 \(r_1−r_0 =(0,0,1)\).

Dihedral adjustments

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.