Covariance NMR

Synopsis

Covariance NMR Spectroscopy provides a powerful approach to NMR correlation spectroscopy with resolution enhancement along the indirect dimension. The resulting spectrum is fully symmetric with the same resolution along the indirect dimension w1 (called w2') as along the detection dimension w2. The singular value decomposition (SVD) implementation of the matrix square-root operation makes covariance NMR computationally affordable and amenable to a wide range of routine applications in liquids and solids.

Software

You can download covNMR, which is the executable code of a C++ program running under Linux, or covNMR2.0.au (This AU program is new as of 06/19/06), which is a Bruker AU program.

covNMR:

covNMR software is an executable code that runs under Linux with or without NMRpipe software (Frank Delaglio, NIH) that implements covariance NMR.
It was tested on Redhat 7.3 and Fedora Core 3. It should work on most Linux systems.
Just put the covNMR in your path, type "covNMR -h" to get help for this program.


Example for covNMR as standalone program

covNMR -N1 256 -N2 2048 -QUAD1 1 -CALC 0 < input.ft2 > output.cov

where input.ft2 is the mixed time-frequency spectrum S(t1,w2), which is obtained by Fourier transformation of the 2D time-domain data only along t2,
N1, N2 give the number of complex points along t1 and w2, respectively,
QUAD1 1 indicates that the data were recorded using States-TPPI along t1,
CALC 0 indicates that the square-root of the covariance spectrum is computed using SVD (instead of regular diagonalization),
for more information and other options type "covNMR -h"

Example for covNMR in nmrPipe script

#!/bin/csh

bruk2pipe -in ./ser -bad 0.0 -noaswap -DMX -decim 24 -dspfvs 12 -grpdly -1  \
  -xN              4096  -yN              1024  \
  -xT              2048  -yT               512  \
  -xMODE            DQD  -yMODE    States-TPPI  \
  -xSW         6613.757  -ySW         6613.757  \
  -xOBS         600.133  -yOBS         600.133  \
  -xCAR           4.725  -yCAR           4.725  \
  -xLAB              1H  -yLAB              1H  \
  -ndim               2  -aq2D          States  \
  -out ./test.fid -verb -ov

sleep 5

nmrPipe -in ./test.fid       		        \
| nmrPipe  -fn SP -off 0.5                      \
| nmrPipe  -fn ZF -size 2048                    \
| nmrPipe  -fn FT                               \
| nmrPipe  -fn PS -p0 237.7 -p1 14.0 -di        \
| nmrPipe  -fn POLY -auto                       \
| covNMR   -N1 512 -N2 2048 -QUAD1 1 -CALC 0    \
| nmrPipe  -fn POLY -auto	                \
   -verb -ov -out ./output.cov

The final spectrum is in file 'output.cov'. The files input.ft2 and output.cov are in nmrPipe format, and can be viewed using nmrDraw (Frank Delaglio, NIH).

covNMR.au:

covNMR.au is an AU program by Wolfgang Bermel (Bruker Biospin). It was tested on TOPSPIN BioSpin 1.3, and it it should work on other TOPSPIN versions as well.
To use this AU program follow the following steps:
1. Copy the AU program to directory /usr/local/topspin/exp/stan/nmr/au/src/
2. On the TOPSPIN command line type "edau covNMR.au"
3. Compile it by pressing the save/exit/compile button
4. You may want to change "TDeff" in F1 to select how many increments in F1 you want to include
5. Execute by typing on the TOPSPIN command line "covNMR.au"
6. Answer a few questions (default options correspond to the direct covariance method with standard square-root processing)
7. Wait until small window appears saying 'covariance finished' appears (this can take between seconds and a few minutes depending on the data size and the computer performance)

Acknowledgement

This material is based upon work supported by the National Institute of Health under Grant No. RO1 GM066041.

References

The following papers should be cited for publications that use the software described below.

[1] R. Brüschweiler and F. Zhang, Covariance nuclear magnetic resonance spectroscopy. J. Chem. Phys. 120, 5253-5260 (2004). [read online]

[2] N. Trbovic, S. Smirnov, F. Zhang, and R. Brüschweiler, Covariance NMR spectroscopy by singular value decomposition. J. Magn. Reson. 171, 277-283 (2004). [read online]

For indirect covariance NMR spectroscopy cite:

[3] F. Zhang and R. Brüschweiler, Indirect covariance NMR spectroscopy. J. Am. Chem. Soc. 126, 13180-13181 (2004). [read online]

---

Last modified: Jun. 2006