The MFIT program fits Lorentzian peaks in 2D spectra using non-linear least-squares fitting. 'Lorentzian' means the real part of the discrete Fourier transform of an exponential decay (see for instance J.Mag.Res. 79, 78-89 for the exact form). The peaks must me phased correctly and have no appreciable baseline. Only exponential window functions should be used in transforming the spectra to be fitted. To use the full information of the experimental data, the FIDs should preferably be zero-filled to double length in both dimensions (ZERO = 2 * SINESIZE), or twice the next power of 2 if the length of the FID is not a power of 2.
As output MFIT produces a file fitparam.dat with the fitted parameters and the uncertainties of some parameters, and a spectrum with the fit subtracted.
The MFIT program is called as follows:
<Machine ID>mfit < inputfile
All commands to MFIT are read from standard input, and in the case above, this has been redirected to the file: inputfile.
The following is a list of all commands accepted by the MFIT program. All commands are given in upper-case, and no abbreviations or comments are allowed. The commands DATAFILE and REPORT must be given; other commands are optional.
Format:
DATAFILE <name> <expno> <procno> <disk> <user>
Description: See the description of this command for the MCNT program.
Format:
REPORT <name>
Description: The report file contains information about the peaks to fit: the area of spectrum points to use and initial guesses on the position and intensity of the peaks. The format is that of a Pronto 3D crosspeak-report with coupling constants and integration limits. The latter define the spectrum area to fit around each peak. All peaks in the report are fitted.
By far the easiest way to create such a file is of course to use Pronto 3D. To do it manually, the format is the following:
5 lines of comments (skipped by MFIT)
1 line for each peak, containing the following fields (in order):
Peak number
Position dim0 (in ppm)
Position dim1 (in ppm)
Integral
Class (not used by MFIT)
Jdim0 (not used by MFIT)
Jdim1 (not used by MFIT)
Integration range around peak position dim0 (in Hz)
Integration range dim1 (in Hz)
Assignment (not used by MFIT)
The following are excerpts from a crosspeak report generated by Pronto:
Spectrum: T2, 5 ms nmr1 cr ugc01.1x256 key dim0 dim1 int class Jdim0 Jdim1 int dim0intdim1 Assignment 100 10.022 -0.420 9.35e+03 ? 0 0 85.2 55.5 Gly-63: H,H 187 8.026 3.610 0 ? 0 0 86.6 36.9 :
The last line does not define a true peak; rather, it specifies an area with overlapping peaks (see also the command DUMMYATOM below). The data in such areas are simultaneously fitted to all the true peaks in the area. MFIT will terminate abnormally if an area with no true peaks is specified.
Format:
DUMMYATOM <name>
Description: A region with overlapping peaks is described by specifying a new peak assigned to a non-existing atom. This command specifies the name of the atom. The region with overlapping peaks is defined by the integration limits of the new peak. In the example given in the description of the REPORT command, the command DUMMYATOM P should be given. In Pronto, the peaks defining overlap regions must be assigned to a dummy atom which has been given this name. Furthermore, the dummy atom must be assigned to a dummy spin system to produce the correct output.
Initial guesses for peaks widths in ppm are specified by
WIDTHS <width0> <width1>
Default values are width0=0.04 ppm and width1=0.15 ppm (set up for H-N spectra).
Format:
NEXP <size0> <size1>
Number of complex points in the FID, equal to the argument to the SINESIZE command of the MFFT program. Default value is NFFT[dim]/2 (see the description of NMRIO) which is correct if the FID has been zero-filled to double length.
Format:
NFILLED <size0> <size1>
The number of complex points including zero filling in the FFT in both directions. Not necessary if the spectrum has been transformed using MFFT.
Format:
AMPSCALE <scale>
This command scales the spectrum, to have expected changes in the amplitude of the spectrum of the same order of magnitude as the changes in peak positions and widths. Default value is 1000.
Format:
RESIDUAL <name>
Name of spectrum with fit subtracted. Is placed in the same directory as the original spectrum and has the same size. Default is 'residual'.
Format:
START_INTENS <factor>
Factor by which to multiply the integrals in the Pronto cross peak report to obtain intial guesses on the integrals. Often it turns out that the non-linear fitting routine converges more easily if this value is not 1 but for instance 10. Default value is 1.
Format:
FIX_OVERLAP
This command fixes the position of peaks in overlap regions (specified as explained above), reducing the number of free parameters in the fit and thereby improving the probability of convergence to the correct minimum.
Format:
FIX_ALL
As FIX_OVERLAP, but for all peaks in the spectrum. This can be an advantage when dealing with very faint peaks.