Data Processing with nmrPipe

H. Zhou updated Oct 2010

Data Format and Conversion

Saved Varian data (.fid folder) typically contains four files:

• fid (raw FID, binary)
• procpar (parameter file, text)
• text (user added comment/notes, text)
• log (log file containing messages, including error messages, during the acquisition, text)

All raw NMR data from Varian or Bruker instruments need to be converted using the program varian or bruker into nmrPipe format before processing.

The default data conversion script is named fid.com. The defualt nmrPipe processing script is named nmrproc,com. Both are text files and can be edited, after they are created (see below), with any text editors. A nice graphic text editor is nedit, installed on all our spectrometer workstations. Type:

• nedit fid.com &

or:

• nedit nmrproc.com &

to edit the scripts.

There are two ways to create the data conversion script.

1: Open a Linux terminal window, and change directory to inside the .fid folder that contains the raw data:

• cd noesy2d.fid
• varian&

2: From with nmrDraw

• cd noesy2d.fid
• nmrDraw&
• Right button click menu item Proc->Convert varian

Once the program opens, click Read Parameters. It reads the procpar file from the .fid directory and opens a separate window with the conversion script inside. Most of the parameters are automatically set, except a few (often highlighted in yellow) that may need manual correction. Generally, the following may need adjustment:

• Adjust the Observe Freq MHz for the 2nd dimension (2nd column). For 2D 1H-1H NOESY, COSY done at 500MHz, select ~499.0MHz 1H (sfrq). For 2D 1H-13C HSQC/HMBC etc, this should be 125MHz 13C (dfrq).
• Adjust acquisition mode in the 2nd dimension according to the actual detection mode. For phase-sensitive NOESY, select Complex. For absolute-value mode COSY, select Real under 2D Mode (above Temperature) which turn the Acquisition mode to Real and the -aq2D parameter into Magnitude.
• After adjustment, click Save Script, then Execute Script. The script is saved as fid.com. A output file named test.fid (in nmrPipe format) is generated.
• Once done, click Quit. Move on to data processing.
• The script fid.com can be run anytime from the terminal, by typing: fid.com

Content of a 2D NOESY data conversion script (fid.com)

#!/bin/csh
var2pipe -in ./fid -noaswap  \
  -xN              1324  -yN               248 \
  -xT               662  -yT               124 \
  -xMODE        Complex  -yMODE        Complex  \
  -xSW         4422.822  -ySW         4861.449  \
  -xOBS         499.858  -yOBS         499.858  \
  -xCAR           4.140  -yCAR           4.140  \
  -xLAB             H1x  -yLAB             H1y  \
  -ndim               2  -aq2D          States  \
  -out ./test.fid -verb -ov
sleep 5

call to C-shell. Always the 1st line

fid as the input file
Real+Imaginary data points numbers
Complex data point numbers. Half of complex #
Quadrature detection mode
Spectrum width along X and Y in Hz
Transmitter frequency along X and Y
Center of each dimension (carrier) ppm value
Axis label
Number of dimensionality

Output file

Data Processing

Once Varian data is converted into nmrPipe format (with a new file named test.fid for 2D data), you can process it. A processing script can be generated either from within nmrDraw or by copying over a template script. By default, the script has a name nmrproc.com.

#!/bin/csh
 
nmrPipe -in test.fid \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 0.5    \
| nmrPipe  -fn ZF -auto                               \
| nmrPipe  -fn FT                                     \
| nmrPipe  -fn PS -p0 56.0 -p1 5.6 -di                 \
#| nmrPipe  -fn EXT -left -sw -verb                    \
| nmrPipe  -fn TP                                     \
| nmrPipe  -fn LP -after \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 0.5  \
| nmrPipe  -fn ZF -auto  -size  512                 \
| nmrPipe  -fn FT                                   \
| nmrPipe  -fn PS -p0 44.2 -p1 0 -di                \
| nmrPipe  -fn TP \
   -verb -ov -out test.ft2

call to C-shell. Always the 1st line

input file: test.fid
cosine-bell apodization
Zero-filling to at least double size
Fourier transform
Apply zero and first order phasing
#line is commented out. Keeps left half of spectrum