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CHAPTER 14: FFT Workwindow

The FFT workwindow is used to Fast Fourier Transform (FFT) a multidimensional Free Induction Decay (FID) or to import a pre-processed Bruker or Varian spectrum. To display all the input fields available in this workwindow, select from the Edit menu [Preferences...]. Set Mode: [Full NMRanalyst], [Show All Input Fields] switch, and click [OK]. See CHAPTER 12: "Using the Workwindows" for a general description of the function and use of a workwindow.

14.1 Input Files

Specify the experimental multidimensional data in this input field. The format of the specified file is specified by the option menu below. Supported formats include an FID file or spectrum in Bruker or Varian format. To use Varian VNMR to create phase sensitive 3D spectra (rather than using the native transform), specify the location of the VNMR "experiment" directory containing the 3D FID in this input field. Then NMRanalyst's fft program calls VNMR's ft3d program repeatedly as required to create the 8 phase components of a phase sensitive 3D spectrum. (Key: FnFID1)

The upper field is displayed for 2D data. It allows the specification of 4 (F1 absolute value) or 8 (F1 phase sensitive) FFT transform coefficients. If no coefficients are provided, default ones are used and program fft tries to guess whether the 2D FID contains F1 phase sensitive data. For 3D spectra, the second field is displayed when the Transform Order: option menu below is set to [Coefficient File]. The specified file should contain the transform coefficients in VNMR "coef" file format. For 3D data, the first four lines in the file should contain eight coefficients each and specify how the F2 interferograms are formed. The fifth row contains the eight coefficients specifying how the F1 interferogram is formed. See the VNMR documentation for details. (Key: Coefs2D or FnCoef)

NMRanalyst's input data formats are Varian VNMR FIDs and spectra (data file format) and Bruker AMX and DMX FIDs or spectra (for 2D named 2rr, 2ri, 2ir, 2ii and for 3D named 3rrr, 3rri, 3rir, 3rii, 3irr, 3iri, 3iir, 3iii). For Bruker AMX & DMX input files, use the [Load] button in the NMRanalyst window and select a ?/ser or ?/pdata/?/2rr (or equivalent) file located in the acquired data directory. This procedure calls the bruker2txt script to assemble the needed spectral information from the Bruker acquisition (and if present processing) parameter files. After calling bruker2txt, do not alter the input file name as it determines if this file is assumed to contain a Bruker FID or preprocessed spectrum. Bruker FIDs can contain any combination of TPPI, States, States-TPPI, and other acquisition formats for each spectral dimension. Please report if data from a standard pulse sequence is not correctly handled so NMRanalyst can be extended accordingly. In case of problems using a Bruker FID, try to transform the data using Bruker's software (e.g., XWIN-NMR) and analyze the resulting spectrum with NMRanalyst instead.

To analyze spectra taken on NMR spectrometers of other vendors, import the data into the Varian VNMR or Bruker software to Fourier transform the data and then analyze the resulting phase sensitive spectrum with NMRanalyst. (Key: DatFmt)

This option menu only shows for 3D FIDs and applies to NMRanalyst's native FFT (but not to VNMR's ft3d program). The directly acquired dimension (F3 in 3D) is transformed first. The linear combination of phase components for the F2 and F1 interferograms is determined through the selected pulse sequence. The fastest transform results from choosing the used pulse sequence from this menu. If no appropriate pulse sequence is listed, use the [Coefficient File] item and specify VNMR's coef file containing the 40 transform coefficients for 3D phase sensitive transforms in the 3D FFT Coefficient File field above. (Key: OrderFT)

14.2 Output File

Enter the name of the multidimensional spectrum to be created through the FFT. This file is read by the nD Analysis and the Report workwindows and can be displayed by NMRplot. (Key: FnSpec)

14.3 Spectral Description

For the identification of the multidimensional spectrum, an arbitrary text string can be specified in this input field. The first 200 characters of the entered string are stored with the spectrum. The software neither requires an identification string nor assigns a meaning to the specified string. The string is displayed in further analysis steps for spectrum identification. (Key: TxSpec)

NMRanalyst analyzes up to three dimensional NMR spectra. Two-dimensional spectra have F1 and F2 spectral axes and 3D spectra have an additional F3 axis. An Observe Frequency field is provided for each dimension. If the observe frequency is the same for different dimensions, some of these fields might not be needed and are dimmed. (Key: HzPpmF1, HzPpmF1U, ..., HzPpmF3, HzPpmF3U)

Specify in the provided F1 through F2 (F1 through F3 for 3D) input fields the spectral width along the corresponding spectral dimension with unit used. For a 2D INADEQUATE spectrum, the F1 spectral width cannot be smaller than the F2 spectral width. Otherwise, signal assignment ambiguities would result through multiple aliasing of signals. Keeping both spectral widths the same allows the most effective use of spectrometer time. For a heteronuclear 2D spectrum acquired on a Varian spectrometer, the F1 Spectral Width input field should be set according to the sw1, and the F2 input field according to the sw VNMR parameter. (Key: swF1, swF1U, ..., swF3, swF3U)

Specify in the provided F1 through F2 (F1 through F3 for 3D) input fields the low frequency limit of the corresponding spectral axis, and set the unit used. The 1D and the multidimensional spectra should be acquired under the same experimental conditions (e.g., same sweep width and transmitter offset). If that is the case, the Start of Spectrum values of both spectra are identical. For a heteronuclear 2D spectrum acquired on a Varian spectrometer, the corresponding Start of Spectrum values can be calculated as:

F1: rfp1 - rfl1 F2: rfp - rfl

If the sweep width (sw) or the transmitter offset (tof) is different between the 1D and multidimensional spectral axes, then the reference peak position has to be calculated as:

rflnD = rfl1D + (swnD - sw1D)/2 - tofnD - tof1D

Not every spectrometer can reproduce the exact acquisition parameters. Despite this correction, additional frequency mapping might be necessary during the nD Analysis workwindow run. If the 2D spectrum contains a visible signal such as a solvent line, the 2D data can also be referenced using the spectrometer software before the FFT and nD Analysis workwindows are run. (Key: spF1, spF1U, ..., spF3, spF3U)

The F1 through F3 Number of Points input fields allow specification of the points to be used in each spectral dimension. Typically, these input fields are left blank, indicating that all acquired points in the FID should be used for the data analysis. By specifying the number of points in these input fields, the data in the corresponding dimension can be truncated or zero-filled. The maximum number of points for complex data in each dimension is 216 = 65536. A specified value represents the number of points used by the Fourier transform without zero filling to the next power of two. (Key: npF1, ..., npF3)

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