Follow the steps below to visualize the LUMO eigenstate of a water molecule, computed with DFT. We will build the molecule from scratch to show some very basic functionality in the Builder tool. We will also calculate the molecular energy spectrum.

1. Start VNL.
2. Open the Builder tool by clicking its icon on the main toolbar.
3. Switch to Molecule mode by clicking the icon  on the toolbar on the left-hand side.
4. Right-click the empty white space in the Basis section and select "Insert element" three times to insert three atoms. All of these will be hydrogen atoms placed at the origin.
5. Change the second atom to oxygen. Now we have the constituents for the water molecule.
6. To get the correct geometry, select all atoms (press Ctrl-A) and click the Z-Matrix button. To use the tool conveniently, double-click it or drag it out of the Builder window, and enlarge the window.
7. Set the distances and angles as shown in the picture below (H-O distance 0.972 Å and H-O-H angle 102.75 degrees).
   
8. Click the "Send to" icon in the lower right-hand corner of the window, and select Script Generator.
9. Double-click "New Calculator" in the left-hand column.
10. Double-click "Analysis" and select "MolecularEnergySpectrum" from the menu that appears.
11. Double-click "Analysis" and select "Eigenstate" from the menu that appears.
12. Click the "..." button next to "Default output file" and define a suitable location and name (for instance "h2o.nc") of the NetCDF file in which the results will be saved.
    
13. Now double-click the "Eigenstate" block that was inserted in the script, in the right-hand panel. Since water has 8 valence electrons (one for each hydrogen and six for oxygen; the two 1s electrons are part of the pseudocore in ATK), there will be 4 occupied states, each one doubly degenerate since this is a spin-independent calculation. Therefore, the LUMO state will have quantum number 4 (remember, counting starts from zero in ATK!).
    
14. Save the script (menu File>Save) for later reference.
    If you are interested in inspecting the actual Python script, you can now send the scipt, again using the "Send to" icon, to the Editor. Note that this will minimize the Script Generator window.
15. To run the script, click the "Send to" icon in the Script Generator, and send the script to the Job Manager. When the Job Manager opens up, click the button "Process Queue" to run the script.
16. When the script has finished (it takes a minute or so), go back to the main VNL window, and navigate to the directory where you chose to save the NetCDF file. Select the created NetCDF file, and the upper right panel will display a list of the objects contained in the file.
17. Select the Eigenstate, and from the list of actions in the lower right panel click "Show" next to Isosurface. Note how the quantum number is also displayed in the lower panel, which is quite useful in case the file contains several eigenstates.
18. Then, drag and drop the "Molecular configuration" also stored in the NetCDF file onto the Viewer window that opened.
19. Pressing Ctrl-P or selecting "Plots>Properties" from the menu now allows us to modify the elements of the plot. The image below was obtained by setting the radius of the atoms to a constant value of 0.2 Å, the isovalue=0.2 for the molecular state, and a grid sampling of 1 (highest quality).
     
20. To export the image to a PNG file, press Ctrl-E (or use the "Plot" menu).