The Spectrum Window

The Show Parameters command displays all information about the data acquisition stored together with the file, namely the parameters of the sample, instrument, optic, acquisition, Fourier transformation etc. This is done in the form of a report window (see Chapter 3.4). An example of these parameters is illustrated in Fig. 3.8 for the Raman file DIAMOND. Load other files and look at the relevant data. 

The last two commands. Copy Entry and Clone Original, are used to duplicate spectrum files. Use Copy Entry to make a copy of a data file that has been manipulated. Clone Original creates a copy of the original data of such a file. 

If you right-click on a data block you have access to another pop-up menu, shown in Fig. 3.9. Herewith you can change the display color of the spectrum or remove it from the spectrum window. The other commands will be discussed later. 

When the default settings are loaded, the spectrum window is located in the right pane of the OPUS user interface. After a file has been loaded, all spectral features of this file such as spectra and interferograms can be displayed. As an example, the transmittance spectrum, the single channel sample spectrum, the sample inter-ferogram, and the single channel reference spectrum of the MIR file INDIGO are displayed in Fig. 3.10. 

For illustration, in the frame of the default settings for Fig. 3.10 it is a little difficult to figure out the interferogram. But, if you use J or o in the overview window, you can change the display areas to best meet your needs. 

---

With ID WIN-NMR the panel title indicates the current operational mode of the button panel, either ID for the spectrum window or Text, Relaxation or Preview for the corresponding windows. The function of the buttons in the panel change to reflect the functionality of the selected mode. 

The next three buttons change the current mode of the mouse pointer, which affects how the pointer behaves in the window which shows the spectrum. The current mouse pointer mode can be changed by clicking with the left mouse button on one of these buttons (which become highlighted). The current mouse pointer mode is also indicated by the shape of the pointer in the spectrum window. 

Button for placing a spectrum cursor on the top of peaks in the spectrum Maximum Cursor mode). Selecting this mode automatically inserts an info line at the top of the spectrum window which lists information about the pointer position, i.e. the x- and y- co-ordinates of the spectrum cursor in Hz/ppm, the number of the associated data point and its intensity. 

The next buttons in the button panel are highlighted when active and are toggles which may be used to alter how data is displayed in the spectrum window ... 

When an FID or spectrum is read into the spectrum window, the following short-cut buttons for rapid access to the most frequently applied processing, display, edit and plot tasks are available. For most of these buttons a dedicated dialog box to set up and adjust the corresponding parameters is available by clicking with the right mouse button. 

If an FID is read into the spectrum window, special FID short-cut button.s are available. Their functionality will be discussed in chapter 5. 

Click this button to exit from the current button panel mode, and return to the display ground state of the spectrum window from which another function with its own button panel mode may be chosen. Selecting an entry from the pull-down menu bar in the main menu automatically causes a change in the display ground state of the spectrum window. The Return key on the keyboard has the same function. 

This command performs the same operation as the ALL button in the Spectrum window button panel. It resets the x- and y-axis scales so that the complete speclrum/FID i.s visible. 

Clicking this button opens a new dialog box showing all the various options available for the current display mode of the Spectrum window. The contents of this dialog box depend on which display mode is currently active different content.s are visible for the normal, dual and multiple display modes. Use the Help tool for more detailed information. 

This option lets you define colors for the elements in the Spectrum window. Again the self-explanatory dialog box opened by this option depends on the currently selected display mode (normal, dual, multiple). 

The scroll bars in the Spectrum window let you scroll the spectrum in the x- and y-... 

After defining a plot area by means of the x-Area... and y-Area... buttons, the user can still change the display of the spectrum in the Spectrum window. The Show Area button resets the display in the Spectrum window to the same as in the plot. 

Items that are currently active in the Spectrum window can be selected for the hardcopy or Preview output by checking the respective filters in the Display Options group. 

This button opens a dialog box in which you may select the font to be used in plotter or preview output for the spectrum window (scale, peak picking, integral). It does not affect the fonts for the parameter and the title window. 

Click the Output Font... button and define the output fonts for and the style according to your preferences. Note that this influcences only the fonts in the Spectrum window (peak picking values, scale (ppm/Hz) values), but not the fonts for the title and parameter windows of the plot layout. The latter fonts may be set with the Preview option (4.7.3). 

Sends the plot as a vector-oriented metafile to the MS-WINDOWS clipboard from where it can be transferred into any other MS-WINDOWS program. The plot area of the output is taken from the currently displayed area in the Spectrum window. Parameter lists and the title cannot be transferred using this method. They can be copied by transferring the output, including the title and lists, first into the Preview window, from where it may be copied to the MS-WINDOWS clipboard using the Copy option in the Edit pull-down menu in the Preview window menu bar. 

Lets you view the history file, which contains all the commands for the current processing session that have changed the data in the Spectrum window. 

Expand Causes a dialog box to appear on screen, which allows you to define the regions in both dimensions of a 2D spectrum, either in ppm or Hz. For quick expansions the mouse may be used within the spectrum window. 

The primary function of the buttons in the top part of the button panel is to change the appearance of the data displayed in the spectrum window irrespective of whether the data is a FID or spectrum. The functionality of these buttons is independent of the current processing command whilst the lower part of this panel may contain addition buttons specific to the current task. The special buttons for allowing the comparison of two or more spectra discussed in section 3.2.3.4 in combination with the output options. 

Step 1 Select three representative rows containing both cross and diagonal peaks. The first row is selected by clicking the Rows and then the Chi button. Move the mouse cursor in the spectrum window until the horizontal cross hair is positioned on a suitable row. As... 

Step 2 With the cursor in the spectrum window click the right mouse button. The button panel changes to the layout shown on the left and at the same time a cursor appears at the top of the spectrum window designating the reference peak to be used for the zero-order phase adjustment. By default the cursor is set on the maximum signal (Big Point), clicking the Cursor button allows the reference peak to be set manually. Click on the Correct the Phase button to continue with the zero-order phase correction. 

The final processing steps before plotting or the export to the clipboard are the definition of the ID spectra to be used as projections, the choice of the number and relative intensity of the contour levels and the selection of the plot parameters. The main functions of the spectrum window are combined in the upper part of the button panel as shown in Fig. 3.17 and are executed or enabled by a click of the left mouse button. Some functions have their own special cursor mode and it is only possible to leave these functions by clicking the function button again. 

Most functions such as 2 and /2 have the same functionality as in ID WIN-NMR and have been explained already whilst some are specifically for the manipulation of 2D data. The utmost right column of four buttons can be used to toggle between the different 2D representation modes contour plot, density mode, stacked mode and 3D mode (from top to bottom). The button measures distances in the spectrum window the first point is fixed using a left mouse button click and as the crosshair is moved the distance is displayed in the information bar at the bottom of the window. A right mouse button click releases the fixed point for a new distance measurement. The buttons marked with a frequency scale and f 1 or f2 can be used to toggle the chemical shift scales between ppm, Hz or data points. 

The next step is to choose between the extraction of Rows or Columns by clicking the corresponding button in the button panel. A dialog box similar to Fig. 3.20 appears on the screen and the currently selected row or column is shown in the spectrum window with the associated number appearing in the Row Nr or Column Nr field. A different number can be entered from the keyboard or selected interactively using the slider button in the dialog box panel. Clicking the Transfer button extracts and saves the selected row or column and the data is automatically transferred and loaded in ID WIN-NMR. 

Load the file ch5214.cfg (File I Experiment setup I Load from file...). Check the pulse lengths of pi 2.5u (90° pulse) and p3 0.5u (4.5° pulse) (Go Check Experiment Parameters). In the Options I NMR-Sim settings... dialog box select the Modify RF field option. To simulate the decoupler pulse calibration, open the parameter optimizer dialog box (Go I Optimize parameter). Select the Show results as 1D series, N 8 and p3 for optimization. Click on the OK button. In the next dialog box enter the start value p3 0.5u and increment size inpO 2.0u. Click on the OK button and enter then the path and name for the calculated and saved files. Run the series of simulations. In 1D WIN-NMR the last simulated FID will be automatically loaded into the spectrum window. Process the FID (zero filling Sl(r+i) 16k, apodization EM, LB 1.0 [Hz]) amd... 

Chapter 3 introduces the basic functions of OPUS. Here you will find general information about the OPUS windows and the handling of the data files. Once you have worked through this chapter you will be able to use the Browser, load and unload a spectrum into the Spectrum Window, select a spectral range, and deal with a Report Window. 

After clicking once again on the OK button the standard OPUS user interface will be displayed as depicted in Fig 2.8. It consists of three windows, the browser window, the spectrum window, and the overview. If you place the cursor on the border between these windows, you will notice the cursor changes to Hl or. This allows you to re-size the windows. 

If you load the same spectrum several times, the numbers following the file name will label the copies. The file name of the active spectrum will appear in a red box. The display icon can be used to toggle the spectrum windows. You can select all spectra in a spectrum frame by holding the Shift key while clicking on a file name. If the cursor is positioned on a file name, the user name, sample name, and the sample form will be displayed in a small extra window. 

---