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Hello all, I am working with a varian spectrometer and did a 2D experiment with a 3D pulse sequence and I need help with the conversion as well as the processing script with NMRpipe.

In slightly more detail, the pulse sequence is for a C1-N2-C3 correlation, assuming C1 being the first indirect dimension, C3 being the direct dimension.

When I do a N2-C3 correlation, processing with NMR pipe was straighforward(the interface reads it correctly). However I did a C1-C3 correlation and this is my problem. And auto-read parametersresults in a 1D, and I tried manually entering the 2 other dimensions and my scripts looks as follows:


var2pipe -in ./fid \
 -noaswap  \
  -xN              2084  -yN                 1  -zN                40  \
  -xT              1042  -yT                 1  -zT                20  \
  -xMODE        Complex  -yMODE        Complex  -zMODE        Complex  \
  -xSW       104166.667  -ySW         3200.000  -zSW         5027.020  \
  -xOBS         201.134  -yOBS         201.134  -zOBS         201.134  \
  -xCAR          54.000  -yCAR         120.000  -zCAR          54.000  \
  -xLAB            C13x  -yLAB            N15y  -zLAB             C13  \
  -ndim               3  -aq2D          States                         \
  -out ./data/test%03d.fid -verb -ov


Upon running this script though there is an error and the following is the output (note the error at the end)

Varian Format: Short Floating-Point Complex Data, 4 Bytes per Point.
Varian Sizes:  2084 Total Points per FID, 40 FIDs, 1 Experiment.

Varian Four-Byte Float Format --> NMRPipe Conversion.
Input File: ./fid
Output Template: ./data/test%03d.fid
3D Sizes: (2084 Real+Imag)(1 Real+Imag)(40 Real+Imag)

Segmentation fault

Does anyone have experience with this and knows the solution for this? If yes, could you please share it here.

Thanks in advance. PBjang

asked Jul 16 '13 at 03:36

PBjang's gravatar image


2 Answers:
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I am not an expert...since the mode is complex for N15 too, shouldn't yN be 2? (I know it is 2D..but just for the sake of a logical header).. I may be wrong


answered Jul 16 '13 at 07:57

nmr2rmn's gravatar image


updated Jul 16 '13 at 07:57

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Hi thanks for the reply. Just found the answer. This is somewhat similar to relaxation-weighted experiments. I had to do the following steps in order to solve this problem.

  1. Consider it only a 2D experiment.
  2. Set the parameters of the Z-axis to be Y and ignore the Z-axis.

My conversion script then looks like this

 var2pipe -in ./fid \
 -noaswap  \
  -xN              2084  -yN                40  \
  -xT              1042  -yT                20  \
  -xMODE        Complex  -yMODE        Complex  \
  -xSW       104166.667  -ySW         3200.000  \
  -xOBS         201.134  -yOBS         201.134  \
  -xCAR          54.000  -yCAR          54.000  \
  -xLAB            C13x  -yLAB            C13y  \
  -ndim               2  -aq2D          States  \
  -out ./test.fid -verb -ov

and its all fine.

thanks Santhosh


answered Jul 17 '13 at 01:39

PBjang's gravatar image


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