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Processing of NMR data in Topspin

Contents

• Downloading Bruker NMR data to a local computer

• Opening data in Topspin from the data folder on  a disk

• Processing of 1D NMR data

• Phasing

• Calibrating the chemical shift axis

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• Known glitches: Topspin on newer Macintosh computers does not open files

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Downloading Bruker NMR data to a local computer

• First, you download your data using Data Server v.5 and obtain a ZIP file (or other if you choose). As an example, my local folder here is NMR_Data
  
  

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• When I un-zipped it, I obtained a directory structure including my user name and the instrument name. I need to remove them, otherwise Topspin will not read the data.
  
  

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• I will copy only the folder enclosing NMR datasets (folders labeled with number) to my working directory (NMR_Data):
  
  

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• I moved my data folder to NMR_Data. Now I may delete the rest of the tree and the original ZIP file:
  
  

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• Here is my final result:
  
  

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  I will direct Topspin to this folder following Opening data in Topspin from the data folder on  a disk
  This has to be done only once - Topspin will remember location of the data.
  

 

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Opening data in Topspin from the data folder on a disk

Often it is possible to just drag-and-drop the NMR datasets into the Topspin window. However, it is recommended to add your working NMR data folder into the Data Browser panel in Topspin for a quick and reliable access. To do this I need to take the following steps:

1. I will make a folder for storage of all of my Topspin data, NMR_Data
   
   
2. Download my data files into NMR_Data and restructure as described here   Downloading Bruker NMR data to a local computer
   
   
3. Launch Topspin
   
   
4. Make a right click in the File Browser area to bring the contextual menu:
   
   

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5. In a contextual menu click "Add New Data Dir"
   
   

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6. Click three dots in the dialog box to search for the NMR_Data folder:
   
   

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7. Select NMR_Data folder and click Open :
   
   

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8. In Alias field, type in NMR_Data and click OK:
   
   

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9. Data tab of the File Browser window now has NMR_Data entry:
   
   
   

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   Any new data added to NMR_Data folder on my disk will appear in Topspin Data tab in NMR_Data.
   

 

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Processing of 1D NMR data

To process 1D NMR data, type ef on the Topspin command line. This command will perform apodization with exponential window and a Fourier transform.

 

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Phasing

Automatic phasing

• Type apk on the Topspin command line. The automatic phasing will work if tall peaks in your spectrum all have good absorptive shape.
• If you used water suppression - the apk will fail because water is distorted. You have to use manual phase adjustment (below)

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Manual phasing

This tutorial describes how to phase a spectrum in Topspin manually if automatic phase adjustment

Summary

• type ef to remove old phasing and reprocess data
• click Processing: Adjust Phase
• Set pivot on the peak at the left end of the spectrum
• Adjust zero-order phase correction (watch for continuing baseline pattern on the left)
• Adjust first-order phase correction (watch peaks and baseline on the right)
• Save phases
• To process again using saved phases: type ef then pk
  NOTE: A new dataset made of this one will inherit phases. You can phase it after acquisition by issuing ef; pk

 

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Calibrating the chemical shift axis

• Open a spectrum that contains a peak of a reference compound
• Zoom around the reference peak
• issue .cal on Topspin command line
• Left-click in a center of the reference peak

• Enter reference chemical shift in ppm and hit OK
  NOTE: For tables of chemical shifts you may look at UW Chemistry or SpectraBase or some other reputable source.
  
  Now the chemical shift axis in this experiment is calibrated:
  
  
  
  
  
  
• You can transfer this calibration to a different experiment if it was acquired on the same spectrometer.
  
  Open Procpar tab of the calibrated experiment and copy SR value to a clipboard
  
  
  
  
• Next, you display the target experiment and enter this value in its Procpar, SR field.
  
  
• Hit Enter and check your Spectrum tab: it will show a properly calibrated 1D.

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Known glitches: Topspin on newer Macintosh computers does not open files

Description: Topspin files downloaded to newer Macintosh computers cannot be open in Topspin.

Explanation: Newer OS X versions direct requests for data, by default, to the Apple iCloud storage and only after that - to a local disk system. Topspin becomes confused and cannot open the files.

Workaround:

1. Make a folder for storage of all of your Topspin data outside of your user folder: /Users/NMR_Data. Since it is outside of the normal user area, it is not affected by the iCloud glitch. To do this:
   • Open Finder window
   • hit Command-Shift-G (opens a dialog to enter an explicit path)
   • enter /Users, hit Go
   • hit Command-Shift-N (to make a new folder in /Users), enter your password (if needed), hit OK, enter NMR_Data as a folder name
     
     You created /Users/NMR_Data
     
     
2. Download your data files into /Users/NMR_Data
   
   
3. To properly structure your data and add the folder to Topspin Data Browser, see  Opening data in Topspin from the data folder on  a disk

 

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