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Overview

Overview

NUTS Help

NUTS Overview

This section is an introduction to the basics of navigating around the program, scaling the display, using the cursor, setting the chemical shift reference, plotting and copying.

In addition to the operation of the program from the menus, a command line user interface is also active. When the menus are pulled down with the mouse and the menu choices are displayed, the keyboard letters corresponding to each command are also shown. This "learn as you go" approach allows the user interested in operation of NUTS from the command line to become familiar with the necessary commands in the course of normal operation and minimizes the frustrations of searching through manuals. Some of the more advanced features are not available from the menus. On-line Help is also available.

Show me how to get started.

Base Level Operation

The base level of operation is the starting point when the NUTS program is run. Many functions of NUTS, such as Zoom and Integration, operate as subroutines of the base level. Sample files are available for download, and can be opened in NUTS by using the menu and selecting File/Open. A dialog box appears and allows the user to select an NMR file. If the file is an FID it will need to be transformed (FT) and phased. If the file was a spectrum (previously processed and stored) it will be displayed and is ready for further perusal. The spectrum can be printed using the File/Print menu option, which displays a Print Setup dialog box. The Zoom subroutine is used for horizontal expansions, to display a selected region of the spectrum. The horizontal scroll bar at the bottom of the screen will shift the display left and right if an expanded region is currently displayed.

The NUTS base level of operation is characterized by the following general features.

Vertical scaling The spectrum will be automatically scaled to display the tallest peak full height. Vertical scaling can be done using the scroll bar on the right. Vertical scaling can also be done with the "<", ">", up and down cursor control keys, PAGE UP, or PAGE DOWN keys. At any time, the vertical scale can be reset to zero with S0 or the largest displayed peak can be made full height with Control-Y. See also scaling the display.

Cursor A mouse cursor (ARROW) will be shown on the display and its position is a function of the mouse movements. If the left mouse button is depressed and held, a full window crosshair will replace the mouse cursor and its x and y position displayed in real time in the lower right corner of the window as the mouse is moved. The x position is shown as data point number, Hertz, and PPM. The vertical position is shown as a percent of the tallest peak in the spectrum. This information is displayed as long as the mouse button is depressed. 

The cursor information can optionally be displayed in difference mode. While holding down the left mouse button, click the right mouse button. The current x position of the vertical crosshair will be marked and an additional line of readout will be displayed at the bottom right of the window. This additional line of display shows, in real time, the current cursor x position relative to the marked position. As the mouse is moved, while still holding down the left mouse button, this difference display is updated. This is useful for quickly measuring coupling constants, line widths, etc.  This line also shows the average of the frequencies of the marker and crosshair cursors, for easy determination of the chemical shift of mutiplets such as doublets.

All functions return to the default base state of operation when the left mouse button is released. Users with a single-button mouse can press the period key on the keyboard in place of the right mouse button.

Show me about using the cursor.

Setting Chemical Shift Reference

The easiest way to set a peak to a specific chemical shift is to hold down the left mouse button, place the cursor on the peak and type O (for offset). A dialog box appears which allows you to set the frequency in either Hz or PPM. Note that this function operates at the base level of NUTS and not in the Zoom subroutine.

If the current file is a 2D file, the same procedure is used to set the shift in both dimensions.

If the chemical shift of the reference peak is to be set to zero, the SZ command provides a quicker way to set the reference. Use Zoom to expand around the peak and SZ sets the value of the largest peak in that region to zero.

The way Nuts keeps track of the chemical shift is via the O1 (offset) parameter. (Note that this does not have the same meaning as in Bruker software.) O1 is the offset, in Hz, from the center of the spectrum to 0 ppm.

It is also possible to reference an X-nucleus spectrum indirectly, via the proton frequency of TMS on a specific spectrometer.  See sample macro.

SZ — Set Frequency to Zero

Sets the frequency of the largest peak in the currently displayed region to Zero. This can be used to set the chemical shift reference by first Zooming in on the TMS peak, then typing SZ. This now works for 2D data as well. If the data is displayed as a contour plot or intensity plot, then the largest displayed peak will be set to a shift of zero in both dimensions. Note that in cases of limited digital resolution, the zero value may not appear in the center of the chosen contour, and will need to be adjusted using the cursor and the Offset (O) command, as described in the preceeding paragraph.

PR — Position Reference

Sets the frequency of the largest peak in the currently displayed region to a value previously set in a macro with the Ask Shift command.

Plotting The displayed spectral region is plotted using the File/Print menu selection. The NMR data will be plotted as it is currently being displayed. Spectral parameters will be plotted at the bottom of the NMR plot. These parameters are spaced expecting a Landscape 8.5" x 11" plot. If the printer is not currently in the landscape mode, it should be placed into the landscape mode with the printer dialog box when printing. The printed spectrum will have the characteristics of the displayed spectrum. The spectrum height will fill the plot the same as the display window. The axis type will be the same as the displayed axis type. If an integral is being displayed with values on the screen, it will be plotted with values on the paper. There is a Page Setup option under the File menu which allows several plot features to be set.

PL — Plot

Prints the displayed spectrum to the currently selected printer. The first time PL is executed (unless a Print Setup has already been performed) a Print Setup dialog box is displayed, allowing selection of printer device and print parameters. Once printer parameters are selected, clicking OK causes the plot to be printed. Thereafter, when the PL command is entered, printing is performed directly. The printer parameters can be changed at any time by selecting Print Setu
p from the File menu. Printing can also be performed from the File menu.

The user can set several options, including whether or not to print parameters on the bottom of plots, whether or not to draw a box around plots, margins, color printing and line thickness by selecting Page Setup under the file menu. NUTS plots are configured for 8.5×11 paper in Landscape orientation and are sized to be as large as possible. By default, plots include the parameter list and box, and all colors on the screen are mapped to black for printing.

Page Setup allows larger margins to be set. Even when margins are set to zero, the plot will always have small margins on all sides. The size of these margins is dependent on the particular printer and printer driver being used. Setting margins to non-zero values adds the entered values to the default small margins. Note that margins are set in mm.

There is also an option in the Page Setup box for making 2D plots square, making it easier to view data from homonuclear experiments. The plot will be the maximum size possible, which is about 7 inches, plus axes, for 8.5×11 paper. This option affects only 2D plots.

Fonts for the different types of text can be changed by choosing Set Fonts from the Edit menu.

Some of these options can be set in the NUTS.INI file, so that they are invoked every time NUTS is run.

Copy and Paste to the Windows Clipboard The currently displayed spectrum can be placed in the Windows clipboard using the Edit / Copy menu option. From the clipboard, it can be placed into other Windows programs, such as word processing programs for inclusion in reports, using Paste. The picture is a bit map and the result will have the best quality if the NUTS window is set at maximum size, completely filling the screen, before the Edit / Copy operation is performed. NUTS also provides the option of copying the spectrum as a Metafile, rather than a bitmap, which results in a better quality picture.  See details.

See also: Zoom, Phasing, Integration, Peakpicking

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Last updated: 1/5/05.