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Miscellaneous Tools

Miscellaneous Tools

NUTS Help

Miscellaneous Tools

FP — FID Play

Creates a .wav file from the currently displayed FID and plays it through the computer’s speakers. You may be surprised at how much you can tell about your data just listening. This works whether the data is an FID or a spectrum, but it only makes sense to use it with FIDs. This is only implemented on the Windows versions greater than version 971106, not on the Mac or OS/2. Obviously, your computer needs to be equipped for sound.

SR — Spectrum Reverse

Reverses spectrum right-to-left.

RI — Exchange Real & Imaginary data

This can be performed on both FIDs and spectra. When performed on a FID, the spectrum after FT will look different, depending on whether the data were acquired by simultaneous acquisition of data points into the 2 quadrature channels or by sequential acquisition of data points alternately into the 2 channels (as is done on many Bruker spectrometers). In the former case, the spectrum will be reversed. In the latter case, artifacts will appear in the spectrum which resemble quadrature images. A flag can be set in the Nuts.ini file which causes RI to be executed automatically whenever data is imported.

See also: Special considerations for Bruker data

II — Invert Imaginaries

Performs a 180 degree phase shift on the imaginary half of complex data. This is useful if the sense of direction with the mouse movements while phasing seems backwards. If performed on an FID, this will reverse the resulting spectrum after FT.

Ernst  — Calculate Ernst angle

A non-2-letter command to calculate the most efficient excitation pulse angle for a given total recycle time and T1

ERNST <Total Recycle Time (sec)> < T1 (sec) >

SN — Signal to Noise

Calculates the ratio of the tallest peak in the currently defined Zoom region to the RMS noise of the baseline.  The user must first define the zoom region, to be sure which peak is being used in the calculation.  Even if the entire spectrum is displayed (with Ctrl-F), the calculation is performed on the tallest peak within the current Zoom frequency limits.  Nuts automatically determines the RMS noise of every spectrum, so the user does not need to define a noise region.  

NF — Calculate system noise figure

Measurements must first be made as described:

First replace the NMR spectrometer’s probe with a 50 Ohm metal film resistor. At the gain and frequency settings of interest for the NMR instrument take one scan of data with the resistor at room temperature and save the file with a file name like “HOT.NMR”. Cool the resistor in liquid nitrogen and take another scan and save this file with a file name like “COLD.NMR”. 

In NUTS, enter the NF command and follow the directions. NUTS will load the two data files and calculate the system noise figure. In the non-2-lettered command mode the user can also enter the name of the hot file as argument 1 and the name of the cold file as argument 2.

More information on system noise figure can be found in the Application Notes section

IV — InValidate the data

NUTS uses a sophisticated data compression algorithm to minimize the time required to display data on the screen. Occasionally, NUTS fails to redraw the screen following some operation. IV can be used to force NUTS to recalculate and redraw the screen.

See also: UD

XL — Extract Line

Extracts the real and imaginary sections of a spectrum defined by the zoom region such that the tallest peak in the zoom region is at the center of the NMR spectrum. Points outside the zoom region will be zeroed. This is useful in creating a reference deconvolution function. Show me how to use XL.

XT — Extract Spectral Region

This command uses the currently defined frequency limits to extract a spectral sub-region from a spectrum. Use Zoom to set the frequency limits and type Ctrl-E to display the chosen region. On executing XT, this region is extracted. (Note that this may result in a data set whose size is not a power of 2). The values of Sweep Width, Offset and Number of Points are therefore modified. Show me how to use XT.

This command was created for a specific problem, as described below, but is available for the user to implement for other uses as needed.

A set of kinetics data had been acquired over time on a spectrometer operating without lock. Some field drift occurred during the course of the experiment, so that successive spectra did not line up properly in a stacked plot. In each spectrum, the region 10ppm to 0 ppm was selected after setting the shift reference, and XT was executed. Each resulting spectrum was saved under a new file name (using SB) with sequential file extensions. The complete data set was converted to a 2D file* and when plotted with SP, the peaks were displayed with the correct chemical shift and lined up nicely.

* Viewing a series of 1D files is often best done with utilities available only for 2D files. (These utilities are available in both 1D and 2D versions of NUTS.) Converting a series of 1D spectra to a 2D file is simple, provided they have sequential file extensions (such as file.004, file.005, file.006, etc). Create and execute Link consisting of the command string

GA SC IN

NUTS will prompt for the file name for the first 1D file and for the file name for the resulting 2D file. To view the file, first read in the 2D file with GA.

X0 – X9 — Extract pre-defined spectral region

These 10 commands each perform an extraction (similar to XT command) of a region previously defined by the corresponding Zoom region (defined using 0 – 9 while inside Zoom, with the EZ command or by the macro command Set Zoom_Region).  To perform an extraction from inside a macro, use the Do Extract_PPM command.

RE — Resonance Elimination

This subroutine can be used to remove a single, dominant, low-frequency resonance from an FID. This is done with a fitting routine, in which amplitude, frequency, phase and Lorentzian/Gaussian linewidth are adjusted to match the actual data. This can be useful to remove a residual water line in the center of a spectrum. Results depend heavily on having a good, symmetrical lineshape, but can reduce the water resonance by more than 1000x in some examples.  Show me how to use RE.

Subcommands, available from the Edit menu, are:

D Delete (subtract) the calculated F
ID from the data
E Edit the fit parameters
F Perform fit
R Reset parameters to default settings
<ENTER> Exit the RE subroutine
 
See also: Eliminate Dispersion component

2S — 2-Point Smooth

Performs a 2-point running average to reduce apparent noise in the currently displayed data set. This is useful, for example, to remove the "wiggles" at the base of narrow peaks following resolution enhancement. This command is available only as a keyboard command. A similar command, 3S, performs a 3-point smoothing operation.

3S — 3-Point Smooth

Performs a 3-point running average to reduce apparent noise in the currently displayed data set. This is useful, for example, to remove the "wiggles" at the base of narrow peaks following resolution enhancement. This command is available only as a keyboard command. A similar command, 2S, performs a 2-point smoothing operation.

SO — Smooth

This two letter command (non-2-letter command SMOOTH) was added to allow more flexibility in a smooth operation. With no arguments (or in the 2-letter command mode), a three point smooth is done. In the non-2-letter command mode, the first argument is used as the number of points to smooth.  An optional second argument is the number of times to repeat the smooth operation.

CH — Chloroform lineshape display

Used for viewing the lineshape at the base of the peak. This command performs two actions: The frequency scale is adjusted to make the largest peak in the currently displayed region equal to zero (see SZ command) and the vertical scale is increased by a factor of 80.

CL — Chloroform lineshape

Displays horizontal lines on the screen and plot at 0.55% and 0.11% of the largest peak in the currently displayed region. The command is a toggle, so entering it a second time turns off the displayed lines.

With the lines displayed, the cursor can be used to read off width at each height.

 

Main Help page

Command Index

 


Last updated: 12/22/04.