Covariance NMR
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.
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]
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.
Last modified: Jun. 2006