2.3. Spectral Data Processing

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2.3 Spectral Data Processing

Chenomx NMR Suite can import spectral data from a number of common sources. These include:

Agilent fid files and phasefiles
Bruker fid and 1r files
JEOL .jdf files
JCAMP-DX .jdx, .jcm and .dx files
NMRPipe .fid and .ft2 files
Mestrelab .mnova files (uncompressed format only)

Before you analyze a spectrum with Chenomx NMR Suite, you must properly process your raw spectral data using either the Processor module or one of the alternate software packages described in the next section. Note that the following steps can be partially or completely automated when using the Processor module.

Zero-fill your data, using the smallest power of 2 that is at least twice as large as the number of points acquired in the original spectrum (e.g., for 16000 points in the original spectrum, use zero-filling of 32K points).

To do this in Processor, select Automatic in the import dialog under zero-filling.

Do not apply any transformations like sine bell or Gaussian functions to your spectra.

For the best results, you must properly phase and baseline correct all of your spectra.

For the best results, your spectra should have CSI linewidths of no more than 1.5 Hz. Use an appropriate combination of shim correction and line broadening to adjust the linewidths.

Data Processed with Other Software

If you prefer to process your spectra using a third-party software package, you need to ensure that the Fourier-transformed (frequency domain) data from your processed spectra is available for Chenomx NMR Suite to import. The processed data from the following software packages are supported:

VNMR and VNMRj (Agilent phasefile files)
XWIN-NMR (Bruker 1r files)
Delta (JEOL .jdf files)
NMRPipe (.ft2 files)
ACD/Labs software package. Export to the JCAMP-DX format (.jdx files).
Mestrelab .mnova files (uncompressed format only)

Spectra processed by most of these software packages requires no additional preparation before they can be imported. However, if you have spectra that were processed in older versions of VNMR or VNMRJ and you would like to retain your processing when you import them into Chenomx NMR Suite, you will need to copy each spectrum's phasefile into its fid folder.

To manually copy an Agilent phasefile into the fid folder

Open the spectrum in VNMR and process the spectrum.
Change experiments or quit VNMR, making note of the experiment number in which you have opened the spectrum (e.g., exp2).
In a Solaris terminal window, copy the datdir folder into the mydata.fid folder where mydata.fid is your Agilent spectrum. mydata.fid is the folder that you need to access to open the spectrum using Chenomx NMR Suite.

Use the following commands:
```
                cd ~/vnmrsys/data/mydata.fid
                cp -r ~/vnmrsys/expn/datdir .
              
```
where expn is the experiment number noted previously, and mydata.fid is the fid folder you want to access with Chenomx NMR Suite. In this example, expn would be exp2.

Note that it is possible to automate this process using VNMR if this is something you expect to do often. Consult your VNMR documentation for further information on automating tasks.

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