Fourier Transform Options
Spectra acquired on different spectrometers with different pulse sequences require different kinds of processing. iNMR can guess what kind of processing is required by each spectrum. You can simply trust it and ignore the details. If your spectrometer is old or rare, read this page.
Most options have a straightforward meaning, therefore it is easy to set their values if you know the type of experiment you are processing or the kind of defect you need to reduce. You can also explore the effect of each parameter by changing its value.
| Use this option | To get this effect |
|---|---|
| Live ! | The frequency-domain spectrum is displayed before you click OK. Every time you change a parameter, the display is updated to show the effect on the spectrum. This mode is available for 1D spectra and for 1D extracts of multidimensional spectra. |
| Size | The number of complex points in the final spectrum. This number can be reached by truncation, zero-filling or linear prediction. |
| Use Linear Prediction | Fast linear prediction is used instead of zero-filling. The parameters are set automatically by iNMR. To perform LP with parameters of your choice, choose Process > Linear Prediction before transforming the spectrum. |
| Remove the first n points | Removes the first points of the FID. Useful when the true signal starts after an echo. Only used in solid NMR. |
| Swap Sides | Swaps the left and right sides. For example, the word “MOLFETTA” becomes “ETTAMOLF”. Numerically it consists of changing the sign of the even points of the complex FID. |
| Mirror Image | Inverts the frequencies in the spectrum. For example, the word “MOLFETTA” becomes “ATTEFLOM”. Numerically it consists of conjugating the FID (changing the sign of the imaginary component). |
| Real FT | Old Bruker spectra require this type of FT. It is also necessary for some phase-sensitive 2D spectra, acquired with the TPPI protocol. In this case, use the normal FT along the direct dimension (f-2) and the real FT along the indirect dimension (f-1). |
| Magnitude | This is a convenience shortcut. It puts the spectrum in magnitude (= absolute value) representation after applying the rest of the processing. You can toggle between real and magnitude representations with the command Process > Magnitude. |
| Balanced | Old analog spectra can suffer from a spurious central signal, if the two channels used for quadrature detection are not balanced. This option subtracts from each channel the average of the last 6% (tail of the FID), thus alleviating the problem. |
| Hypercomplex | Before processing the indirect dimension of a phase-sensitive 2-D spectrum, the imaginary data are normally discarded. At the end of processing, it is no longer possible to correct the phase along the direct dimension. With the Hypercomplex option you do not discard the imaginary part and you can still correct the phase along both dimensions, at the cost of doubling the memory usage. The value of this option is not stored when you save a document. |
| Shuffling | This operation is the pillar of the multidimensional phase-sensitive acquisition. It is only required when processing along the indirect dimension. Traditional phase-sensitive spectra require the phase-sensitive shuffling. Gradient enhanced spectra (Rance-Kay), such as the phase-sensitive HSQC, require the echo-antiecho shuffling. In the case of 3-D Varian spectra, the Rance-Kay editing is already applied when the data points are read from disk, so you should select the phase-sensitive shuffling. |
| Apply these Weights | The main switch for weighting. You can use it to force a live update (there is no live update when you type the value of a weighting function). It is safe to leave this switch always on. You can apply together the functions here below, in any combination. |
| Exponential | Multiplies the FID by the exponential function: f(t) = exp( - λ t ). The frequency-domain equivalent is a Lorentzian curve: F(ω) = λ / (λ2 + ω2). The width W of the Lorentzian curve is given by the relation: λ = π W. From a practical point of view, W, measured in Hz, is the parameter that best describes the applied weight, and it is also the parameter required by iNMR. Line broadening is accompanied by sensitivity enhancement. You can specify a negative value for W, that corresponds to a positive exponential and causes a resolution enhancement. Example: let's say all your peaks have a linewidth of 3 Hz. If you apply an exponential of 1 Hz, the weighted peaks will have a linewidth of 4 Hz. If you apply an exponential weight with a value of -1 Hz, the weighted peaks will have a linewidth of 2 Hz. |
| Gaussian | Multiplies the FID by the Gaussian function: f(t) = exp( - σ2 t2 / 2 ). Its frequency-domain equivalent is a Gaussian bell: F(ω) = √(2 π) exp[-ω2 / (2 σ2 )] / σ. The width W of the bell is given by the relation: σ = π W / √ loge2 = 1.2 π W. Like in the case of the exponential, the parameter requested by iNMR is the linewidth W, in Hz. In this case, however, it can only have positive values. The Gaussian is an apodization function. By forcing the FID to decay smoothly toward zero, it reduces truncation artifacts (“wiggles”) in the frequency domain. Example: let's say all your peaks have a linewidth of 2 Hz. If you apply a Gaussian weight with a value of 1 Hz, the weighted peaks will have a linewidth of 3 Hz. |
| Sine Bell | Shifted Sine Bell. When the shift is 90°, it becomes a cosine bell. In all cases, it goes to zero at the right extreme (180° shift). |
| Squared Sine | The square of the function above. |
| Cut After... % | Works as an additional parameter of the above sine-bell functions.
It can go from 5% to 200% of the FID and becomes the effective length of the sine bell
(where the sine becomes zero).
When it is less than 100% the FID is truncated.
If you already truncate the FID with the size menu, there is no need to set this parameter.
It makes sense if you want to combine truncation with zero-filling.
When the value is more than 100%, the bell is truncated (it would go to zero too late, beyond the end of the FID).
It can also be used without the sine-bell functions, in which case it has completely different meanings. For values under 100%, it applies a trapezoidal window. For values between 100 and 200, it applies a linear ramp. For higher values, it applies a Traficante function optimized for (value-200) Hz. |
| Multiply 1st Point By | This can be useful to correct the baseline. It applies a user-defined weight only to the first point of the complex FID. Use this correction when, for whatever reason, you do not like to correct the baseline after the FT. The value 0.5 is routinely used in many 3-D experiments. |
| Max IST iterations | This parameter only appears before transforming the indirect dimension of a spectrum which has been acquired with non-uniform sampling (NUS). The allowed values range from 1 to 2000. The non-sampled part of the spectrum must be reconstructed using an iterative algorithm; the implementation in iNMR is called “Iterative Soft Thresholding” (IST). You set the upper limit of iterations to ensure the reconstruction finishes in a reasonable time. Normal and safe values are between 100 and 500. If your computer is slow, you can set a lower value, but the result may be less accurate (peak intensities may change). If you set a higher value, the reconstruction will be slower but the result may be more accurate. At each iteration, the threshold is slightly decreased by multiplying it by a parameter called λ. With a higher λ, the algorithm becomes slower and more accurate. If M is the value for “max IST iterations”, λ = 0.95 when M < 100, λ = 0.947 + M * 0.00003 when 99 < M < 1434, and λ = 0.99 when M > 1433. |
| Fake | This command skips processing altogether. Data points are subsequently treated as a frequency-domain spectrum. All the operations that are not allowed with a FID, like zooming, panning and phasing, become possible. This mode is useful when you want to inspect the details of the FID. |
If you hold down the Option key, the command Process > Fourier Transform becomes FT now, which skips the dialog and performs the processing with the parameters already stored. If no previously stored parameters are found, a new set is created with default values.
The gears icon inside the palette and its menu equivalent Run are more powerful than the command “FT now”. If iNMR finds the parameters for peak suppression, it performs that as the first operation. If the parameters for linear prediction are found, that is performed in sequence. Finally, FT is performed.