Processing with NMRPipe

See here for processing corrupted datasets

This consists of at least three procedures:

Conversion into NMRPipe
Processing (FT etc)
Conversion into programme format of choice

It is best (and easiest) to use nmrDraw as a GUI interface to generate scripts (not like the good old days!)

For help type: nmrPipe -fn <function> -help
Any comments/recommendations email:michael.osborne@umontreal.ca

Getting Started

Open a terminal shell
Change to the directory your nmr data (e.g. for yggxfinalcnoesy.fid for varian data) is stored:
cd /home/osbornem/variandata/yggxfinalcnoesy.fid
this way you will not need to search for the correct file

type nmrDraw

you will see the following window

Conversion to NMRPipe format

Note:

The raw data file is found automatically if you are in the right directory. Or you can search for the data
Output files - no need to change
Output name of the script (a text script). Again no need to change
To continue click on READ PARAMETERS

Information about the data has been read from the spectrometer files. E.g. Total points etc
However: you may need to CHANGE some parameters since the scripts are not perfect.
In this case the Y axis is the indirect 1H and the Z-axis is the 13C we need to change the circled values
To alter this it is best to left click on the Observation frequency for Y or Z and choose the correct nucleus. E.G for Y (1H)

Which will give a corrected script e.g.

Do the same for the Z axis (this time choose C13)
Then click on save script and answer yes
then click on run script - this will run your script (fid.com by default)

OR you can EXIT nmrDraw (Q) and run the script in a terminal e.g.
./fid.com

your script will look something like this:

some explanations:

var2pipe - converts varian to pipe format. Note '-in XX' is the varian raw data file.
-noaswap - atomically determines if data is little or big endian format
xN/yN/zN - number of total points (i.e. real + imaginary) in different dimensions
xT/yT/zT - time domain size, must enter complex number for a complex acquisition and real the total number of points should be entered. This seems frightening, but is only really important when using LP, and defining windows. For info on ACQ Mode and DAT type see below
x/y/zMODE - defines the manner data was recorded: note prams xT/Y/Z and FT are dependent on this. The following table will help

              oooooooooooo   oooooooo ooooooooooo ooooooooooooooo
              ACQ MODE       DATA AND NEEDS SIGN NEEDS NEGATION
              KEYWORD        FT TYPE ALTERNATION OF IMAGINARIES
              oooooooooooo   oooooooo ooooooooooo ooooooooooooooo

              Complex        Complex No          No
              States         Complex No          No
              States−TPPI    Complex Yes         No
              DQD            Complex No          No

              Complex−N      Complex No          Yes
              States−N       Complex No          Yes
              States−TPPI‐N Complex Yes         Yes

              Rance−Kay      Complex Sometimes   Sometimes
              Echo−AntiEcho Complex Sometimes   Sometimes

              Real           Real     No          No
              TPPI           Real     No          No
              Sequential     Real     Yes         No
              Bruker         Real     Yes         No
              oooooooooooo   oooooooo ooooooooooo ooooooooooooooo