The Nanoscope


The VNL Toolbar	Using the Molecular Builder

1. Open the Nanoscope

Before we start looking at the electronic structure of various systems, we will have a quick look at the Nanoscope , the tool used in Virtual NanoLab (VNL) for visualizing atomic geometries (and other things, as we shall see later).

For this purpose, we will use the water molecule , defined by the icon H20 which already is present on the examples folder.

navigate to the examples directory located in the directory where you installed VNL
import the file molecules/h2o.vnl

Now, drag-and-drop the H2O file onto a Nanoscope and a representation of the molecule appears

A water molecule visualized by the Nanoscope. By default, the covalent radius covalent radius is used to determine the size of the atoms. The context menu Nanoscopecontext menu is opened by right-clicking anywhere in the Nanoscope window.

Figure 2: A water molecule visualized by the Nanoscope. By default, the covalent radius is used to determine the size of the atoms. The context menu is opened by right-clicking anywhere in the Nanoscope window.

2. Rotate, zoom, and pan the camera

You may think of the Nanoscope as a camera through which you observe the atomic system. The camera can be zoomed, rotated, and moved (panned) in order to obtain a different view of the system:

To rotate the camera angle , hold down the left mouse button (without pressing any other keys) and move the mouse around.
To zoom in and out, use the scroll-wheel of the mouse , or hold down the Ctrl key while pressing the left mouse button and move the mouse backwards and forwards.
To pan the camera across the molecule, press the middle mouse button (or hold down the Shift key and press the left mouse button) and move the mouse.

Initially, you may find it a bit difficult to master the mouse to obtain the desired view, but with some practice the movements should appear natural.

The mouse commands described above are used also in other tools to zoom, rotate. and pan the camera in the 3D preview windows.

3. Change the properties of the plots

You can change the size of the atoms and the thickness of the bonds, by choosing Properties from the context menu which appears when you right-click anywhere on the Nanoscope window. In the appearing dialog, you will find a left panel containing a list of all plots currently defined for this particular Nanoscope. To change the appearance or options for a plot, select the respective entry in the tree to see the available options. Right-clicking a plot (either in the 3D preview window or in the Properties dialog) offers the possibility to delete or rename the plot.

The Properties dialog Properties dialogfor the water molecule in the Nanoscope.

Figure 3: The Properties dialog for the water molecule in the Nanoscope.

If you want to export or print the image which is displayed in the Nanoscope, right-click the plot windows and choose the corresponding entry from the Camera context menu.

Exit the Nanoscope by closing the window.