Processing 3D NMR Spectra

Additional considerations/procedures for processing 3D NMR data with nmrPipe and nmrDraw.

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Processing 2D Data 

Because our 3D data is typically sensitivity-enhanced, you must first run the program se_varian, before you run the regular varian program (see Processing 2D Data). 

Once you are in the directory containing the directory which contains your unzipped fid (if that made sense), enter 'se_varian' onto the command line.  Enter the name of the directory which contains the raw fid that is to be processed (ex. noesyhsqc_13C_ali.fid).  Enter 'y' for default processing.  Enter 'phase 2' for phase parameter for SE processing.  Enter 'no' for reverse order of phase and phase2 arrays on output.  This creates the file fid.se in the directory that contains the raw fid file.

Enter the directory which contains the fid and fid.se files.  Use the program varian as described in the Processing 2D Data section, except change the name of the input file from ./fid to ./fid.seRunning the varian program will create a directory called 'data' containing 2D planes of the 3D data(ex. files like test001.fid).  Process one of these 2D data sets using nmrDraw (as described in Processing 2D Data), making note of the phasing numbers.  

The following is a generic 3D processing script which needs to be modified for your experiment.  It performs the following:  3D processing with linear prediction in Y and Z dimensions by

(1) processing the directly-detected X-axis

(2) processing of the indirectly-detected Z-axis

(3) prediction and processing of the indirectly-detected Y-axis

(4) the inverse processing, prediction, and re-process the Z-axis.
 
xyz2pipe -in data/test%03d.fid -x  -verb            \
#| nmrPipe  -fn POLY -time                           \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 3 -c 0.5  \
| nmrPipe  -fn ZF -size 2048                        \
| nmrPipe  -fn FT -auto                             \
| nmrPipe  -fn PS -p0 29.0  -p1 0.0 -di             \
| nmrPipe  -fn POLY -auto -ord 1                    \
| nmrPipe  -fn EXT -x1 860 -xn 1600 -sw            \
| pipe2xyz -out spec2/test%03d.ft3 -x

xyz2pipe -in spec2/test%03d.ft3 -y -verb            \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0  \
| nmrPipe  -fn ZF -size 256                         \
| nmrPipe  -fn FT -auto                             \
| nmrPipe  -fn PS -p0 -90.0 -p1 180.0 -di           \
| pipe2xyz -out spec2/test%03d.ft3 -y -inPlace

xyz2pipe -in spec2/test%03d.ft3 -z -verb            \
#| nmrPipe  -fn LP -fb -pred 32                      \
| nmrPipe  -fn SP -off 0.5 -end 0.98 -pow 1 -c 1.0  \
| nmrPipe  -fn ZF -size 256                         \
| nmrPipe  -fn FT -auto                             \
| nmrPipe  -fn PS -p0 -90.0 -p1 180.0 -di           \
| pipe2xyz -out spec2/test%03d.ft3 -z -inPlace

Modify the pink text based on your experiment and processing information.  Name your modified script, make it executable, and run it.  This will create a spec2 directory (contains file like test001.ft3).  Use a modification of the following script to compile all these files into one.

xyz2pipe -in test%03d.ft3 -x > noesyhsqc_ali.ft3

followed by the following command to convert the nmrPipe formatted file(file.ft3) to a Sparky formatted file (file.ucsf).

pipe2ucsf noesyhsqc_ali.ft3 noesyhsqc_ali.ucsf

You can also convert from nmrPipe to nmrView using the following command:

xyz2pipe  -in test%03d.ft3 | pipe2xyz -nv -ov -out noesyhsqc_ali.nv