Mouse and key operations

In this section, you will learn how to operate the 3D view and manipulate atomic structures in a simple way, including how to select a specific atom or a group of atoms.

Controlling the 3D view

Using the right button and scroll wheel of the mouse, you can perform the following operations for the 3D view.

  • Rotate can be done by moving the mouse while holding down the right mouse button.

    If the mouse pointer is near the center of the 3D view, the rotation will be done as a full 3D view rotation.

    Having the mouse pointer at the 3D view edge constrains the rotation to the view plane. If you first align a particular axis with the screen normal, this function will then allow you to rotate the structure around this axis in a controllable manner.

  • Zoom can be easily done by rolling the scroll wheel of the mouse.

    If you do not have the scroll wheel, you can do Zoom by holding down the Ctrl key, simultaneously pressing the right mouse button, and then moving the mouse back and forth to actually zoom the structure.

  • Pan can be easily done by pressing the scroll wheel down, and then moving the atomic structure with the mouse.

    If you do not have the scroll wheel, you can Pan by holding down the Shift key, simultaneously pressing the right mouse button, and then moving the mouse to actually pan the structure.


Fig. 11 The compass in the upper right-hand corner helps you to orient yourself when rotating the 3D view.

Press Ctrl+R to reset the 3D view to the default orientation and zoom.

For a periodic system, the crystal axes labeled as A, B and C are given with the red, yellow and blue sides of the periodic cell, respectively. The coordinate origin is placed at the cell vertex where all the three crystal axes do intersect.


Fig. 12 The red, yellow and blue box edges are used to indicate the A, B, and C crystal axes for a periodic structure, respectively. These are the same colors as used on the compass for the X, Y, and Z axes of the Cartesian coordinate system. In general, the crystal axes are not parallel to these coordinate axes, even for a cubic cell.

Preview mode

Some of the plugins have a Preview button, and may even update the preview when some of the parameters are changed. The preview state is indicated by a text in the upper left corner of the 3D window.


Keep in mind that the stash item has not been modified yet. To confirm the operation, you actually need to press the relevant button, often called Apply.

To dismiss the preview, you can just click on the 3D window. You can then bring it back by clicking on the plugin Preview button again.


All the other plugins become unavailable when a preview is shown. It is meant to avoid confusion about which structure you are operating on.


Selecting an atom or a group of atoms is often an initial step for those plugins that allow us to manipulate the atomic structure in the Builder. A number of plugins apply their operations on selected atoms only. There exist some plugins that act on the whole structure if no atoms are selected.

The Builder therefore has many ways to select atoms and manipulate selections. The selected atoms are indicated by a yellow halo.


Fig. 13 The oxygen atom in this water molecule is selected, as indicated by the yellow halo.

To select an individual atom, click on it with the left mouse button. Note that this operation will cancel any existing selection of atoms that has already been made in the structure.

To add an atom to an existing selection, hold down the Ctrl key and then click on this atom. If you click on an already selected atom, this atom will be removed from the selection.

To select a group of atoms, you may make use of the shape select tool by first clicking on the SelectRectangle02_icon icon in the top toolbar, and then choosing one of the following shapes for the selection area.

  • Rectangle SelectRectangle02_icon.
  • Circle SelectEllipse02_icon. The circle is centered at the initial mouse position.
  • Lasso (free-form) SelectLasso02_icon.

Subsequently, the left mouse button can be exploited to draw a figure of the chosen shape to enclose the atoms of interest.

Note that the shape select tool operates on all the atoms that are visually inside the shape drawn by the mouse as well as on those atoms that may be hidden behind the other atoms, but are virtually projected on the shape. The single-click mouse select operation only applies on the atom you have clicked on.

The selection operations can be modified in various ways using the Ctrl and Shift keys.

  • To add a group of atoms to an existing selection, hold down the Ctrl key and select the atoms of interest with the shape select tool. In this case, the already selected atoms that may appear inside the new selection area will not be deselected.
  • To undo the selection for the already selected atoms, hold down the Shift key and draw a shape with the shape select tool to enclose the atoms to be deselected.
  • Double-click on an atom in a fragment (a fragment is a set atoms connected by bonds) with the left mouse button to select all the atoms of this fragment. If you hold down the Ctrl key and double-click on an atom of the fragment, all the fragment atoms will be added to the existing selection, or removed if the clicked atom was already selected.
  • By holding down the Shift key and double-clicking on an atom, you can select all the atoms of the same chemical element as the doubled-clicked atom in the atomic structure. If you simultaneously hold down the Ctrl and Shift keys, and then double-click on the atom in the fragment, the fragment atoms will then be added to the existing selection, or removed from the selection if the double-clicked atom of that fragment was already selected.

There exist several other useful keyboard tricks.

  • To deselect all atoms, left-click on the background of the 3D window, or press the Esc key.
  • Press the Ctrl+A keys to select all atoms.
  • Press the Ctrl+I keys to invert the selection. In this case, the atoms of the original selection will be deselected, wheres all the other atoms of the atomic structure will be included in a new selection group.

Advanced select

Sometimes the atoms you want to select are not easily accessible with the mouse, or you need a detailed control of the precise atoms to select. In this case, you can use a set of the following plugins available under Selection tools.

  • By Expression plugin allows you to select atoms based on logical expressions.

    For example, you want to select all the oxygen atoms with a Z coordinate larger than 1.5 Å or an X coordinate smaller than -0.5 Å. This can be easily achieved by typing

    \[\begin{split}e\ = 0\quad and\quad (\ z\ >\ 1.5\quad or\quad x\ <\ -0.5\ )\end{split}\]

    in the Expression Select input field, and then pressing the Enter or Tab key.

  • Using By Element plugin, you can select atoms of a particular chemical element.

  • Close Neighbors plugin is designed to locate completely or almost overlapping atoms.

    The overlapping atoms may occur, for example, as a result of a mirror operation, or a translation. This kind of atoms are hard to spot visually, but they must be removed to perform any further calculation for the atomic structure constructed in the Builder.

Select by tags

In the Selection tools, there exists an additional selection feature Tags that allows for assigning one or multiple tags to an atom or a group of atoms. So, each atom can then have many tags, and the same tag can apply to many atoms in the atomic structure. A tag can be any label that identifies an atom or a set of atoms.

One of the purposes of having tags is that you can assign them to a set of atoms when you build the structure, and then use them later on, e.g., in the Script Generator, to assign a special basis set, or initial spin to those atoms. Instead of making a list of the atom indices for all those atoms of special interest, you would just say “use basis set X for atoms with tag Y”. For example, for a work function calculation one might use a basis set with a longer range for the surface atoms than for the bulk atoms in the structure.

To add, remove and modify tags on atoms, use the plugin Selection ‣ Tags plugin. This placement of the plugin indicates that tags are also a handy tool for selecting atoms. The fastest way of selecting atoms with tags is to click on the SelectTag02_icon icon in the top toolbar.

Deleting atoms

To delete atoms, you should first select them in the structure, using any selection method discussed above, and then press the Delete button on the keyboard.


It is possible to delete atoms from the structure, using Coordinate Tools‣Coordinate List. You can also insert atoms with this tool.


Any operation (except selection) in the Builder can be undone by pressing undo_edit_icon in the top toolbar. The undone operation can also be redone using the redo_edit_icon icon, if needed. The keyboard shortcut for undo is the Ctrl+Z keys, while the Ctrl+Y keys stand for redo.


Some of the plugins do not change the atomic structure in the stash item in which you have initiated the change, but they rather create a new stash item for the structure with the change implemented. In this case, there is obviously nothing to undo but delete the new item if it is not what you wanted.