Keywords: viewmol

## 6.3 The Spectrum Window

Choosing `Spectrum` from the main window menu will result in a new window showing the calculated spectrum for the molecule. In this window the mouse acts as follows:

- Clicking with the left mouse button on a line in the spectrum
  The molecule shows the corresponding normal vibration.
- Clicking with the middle mouse button in the window, holding it down and moving the mouse
  This displays a rubber band box with which one can zoom into the spectrum.
- Pressing the right mouse button
  A menu will appear.

  Figure 9: The dialog box for setting options for the spectrum

  The menu contains the following topics:
  - Settings for spectrum ... (Alt+S)
    Selecting this topic displays the dialog box shown in the Figure.
    - Type of spectrum
      The buttons labeled `All modes`, `IR active modes`, `Raman` `active modes`, and `Inelastic neutron scattering` can be used to select the type of spectrum desired. IR active modes are the default.
    - Animation
      The buttons labeled `Animate`, `Draw arrows`, and `Distort` can be used to select whether the normal modes are to be shown animated or with arrows or whether you want to distort the molecule along a normal mode. A distorted molecule can be saved using the `Save molecule` option from the main menu. Animation is the default.
    - Line shapes
      The buttons `Line spectrum` and `Gaussian spectrum` can be used to select whether the spectrum is drawn as simple line spectrum or whether a Gaussian band shape [1] should be applied. Line spectrum is the default.
    - Set weights for inelastic neutron scattering
      When you activate this option you can enter a value in the field to the right. After choosing the `OK` button all weights are drawn at the atoms in the main window and you can set an atom's weight just by clicking on it with the left mouse button. All weights are set initially to zero, so that selecting `Inelastic neutron scattering` as spectrum type produces nothing.
    - Wave numbers shown on top
      This option controls the orientation of the spectrum. The default is to have zero intensity on top with the bands pointing downwards. If this option is deactivated zero intensity is at the bottom and the bands are pointing upwards.
    - Show grid
      This option controls whether a grid is shown in the spectrum window. The default is on.
    - Line width
      The value entered in this text box controls the line width of the drawing in the spectrum window.
    - Temperature
      This slider can be used to set the temperature. The temperature is used for the calculation of the inelastic neutron scattering intensities and for the Gaussian shaped spectrum.
    - Amplitude
      This slider can be used to change the amplitude of the vibration. Its value is multiplied with the standard amplitude of a vibration. This slider can also be used to change the distortion of the molecule while `Distort` is selected.
    - Scale wave numbers
      This slider can be used to scale the wave numbers.
  - Select molecule
    Provides a submenu with the names of all molecules currently loaded and can be used to change the molecule for the currently displayed spectrum. Another possibility to select a molecule consists of pressing the `Tab` key, which cycles through all entries in the `Select molecule` submenu.
  - Imaginary wave numbers
    If the conformation of the molecule is a saddle point you have imaginary wave numbers. The corresponding ``normal modes" can be shown by selecting a imaginary wave number from this submenu.
  - Read observed spectrum ... (Alt+R)
    This topic can be used to read a spectrum from a file and display it along the calculated spectrum. Selecting this topic opens a file selection box to chose the file. This file has to contain a spectrum with one wave number and intensity per line. All points read are connected by a line to form a continuous spectrum (there is currently no possibility to read a line spectrum). Lines with a '#' or a letter in the first column are ignored.
  - Delete observed spectrum ... (Alt+E)
    This topic deletes a spectrum read with ``Read observed spectrum".
  - Zoom out (Alt+Z)
    This topic can be used to zoom out of the spectrum after previous zoom-ins. The zoom mechanism stores all previous enlargement steps. By selecting this topic you move back one step.
  - Save drawing (Alt+D)
    The same dialog box as for `Save drawing` in the main menu is shown and allows you to save the spectrum as a TIFF, PNG, HPGL, or PostScript file (cf. p. ).
  - Foreground color (Alt+F)
    The foreground color of the spectrum can be changed using the color editor (vide infra, p. ).
  - Background color (Alt+B)
    The background color of the spectrum can be changed using the color editor (vide infra, p. ).
  - Quit spectrum (Alt+Q)
    This closes the spectrum window.
- Pressing the arrow keys and , respectively
  The next lower and higher wave number, respectively is selected and the molecule shows the corresponding normal vibration. Normal vibrations of imaginary wave numbers can be displayed in this manner, too.