InSane: raw NOE data



Steps 3 and 5 of the automatic NOESY crosspeak assignment algorithm requires access to raw NOE intensity data. Currently, Wit!P can read only 13C and 15N edited 3D spectra from Felix .mat data files (1st dimension: edited proton, 3rd dimension: C or N). The spectrum open command of the NMR module is used to make the data accessible to the program:
NMR> spectrum open foobar.mat
spectrum>
Typically, the open command is followed by commands that set the noise level and reference information necessary for the conversion of points to ppm and vice versa:
spectrum> noise foobar.mat 2.2e4
spectrum> reference foobar.mat C 150.856 4620 23.195 54.6
spectrum>  reference foobar.mat N 60.795 4620 59.0 123.02
Reference information for the two proton dimensions is read from the spectrum file and does not need to be specified. If no reference is given for C or N, the reference information of the third dimension in the file will be used. The noise level will be used in the filtering step 3 of the crosspeak assignment algorithm: NOE intensity below a fixed multiple (usually 1) of the noise level will be regarded as insignificant. A reasonable value of the noise level may be obtained by visual inspection of the spectrum (e.g. in Felix), or automatically by
spectrum>  noise foobar.mat automatic
Note that the automatic determination of noise works by examination of random samples of data, and will give slightly different results each time the command is used. For better reproducibility, it is recommended to define the noise level explicitly (from visual inspection, or from the average of several runs of the automatic method). If no noise level is set, 1.e4 will be used.

The spectrum info command may be used to list some of the information contained in the header records of the spectrum:

spectrum> info foobar.mat
3D spectrum foobar.mat, 4097 bricks, reality: 1, squeeze: 0
1 heterosexual file, 4097 bricks per segment
noise level:  2.200e+04
npnts     :    512    256    128
nbrck     :     16     16     16
reference:
axistype  :        ppm        ppm        ppm
refsf     : 5.9991e+02 5.9991e+02 1.5086e+02
refsw     : 8.0000e+03 5.9997e+03 4.6200e+03
refpnt    : 2.5650e+02 1.2850e+02 2.3195e+01
refppm    : 4.8050e+00 4.7700e+00 5.4600e+01
ppm: [-1.85,11.46] [-0.21,9.75] [29.52,59.91]
chemical shift range for Carbon: [29.52,59.91]
chemical shift range for Nitrogen: [76.99,152.99]


A.Widmer, NIBR/CPC/CSG-SB