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| D. Flemming Hansen >> Programs >> FuDA >> Inputfile | |
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The input file
A text input parameter file must be provided with the following parameters: | |
| SPECFILE [Mandatory] | This is the actual spectrum that contains all the experimental data. The spectrum file must be a nmrPipe cube. If you have your data as a set of 2D planes (test001.ft2,test002.ft2,...), then collect data into a cube with: xyz2pipe -in data/test%03d.ft2 | nmrPipe -ov -verb -out test.ft2. EXAMPLE: SPECFILE=test.ft2 |
| PEAKLIST [Mandatory] | The PEAKLIST parameter provides the program with a text file that in turn contains an assignment of peaks, i.e., name, {chemical shifts}.
The peaklist file contains a column with the assignment ( a string without spaces and tabs) and then on the
same line as the assignment a chemical shift (double; ppm) for each dimension of the spectrum. Lines starting with a hash "#" are ignored. A typical line of the peak
list file could be: 94N-HN 119.877 7.979 EXAMPLE: PEAKLIST=test.list |
| ZCOOR [Mandatory] | Describes the "Z-coordinate" of the spectrum. For a 2D spectrum, ZCOOR=2D, for a 3D spectrum ZCOOR=3D, while for an arrayed spectrum the ZCOOR parameter is equal to the parameter defined in your spectrometer parameter file (procpar for varian). Thus, assume that you have preformed a nitrogen T1 experiment with the parameter "time_relax" arrayed to describe the relaxation delay, then set ZCOOR=time_relax. The program will now use the value of time_relax to compile plot-files and other output files.
EXAMPLE: ZCOOR=time_relax |
| DELAFACTOR [Default=1.] | Provides a factor that is multiplied to every Z-coordinate point. Assume that you have recorded a nitrogen T1 experiment with a parameter "ncyc" that describes the number of cycles used for each relaxation delay. Then "ncyc" actually reports indirectly on the relaxation by a certain factor ( e.g. 5 milliseconds).
EXAMPLE: DELAYFACTOR=0.0050372 |
| NOISE [Mandatory] | Provides the standard noise of the experimental spectrum (SPECFILE).
EXAMPLE: NOISE=1200. |
| PARAMETERFILE [Default=(varian,procpar)] | Provides a parameter file, from which information is read about the SPECFILE, e.g., the parameter ZCOOR is read from the parameterfile in the case of a 2D
EXAMPLE: PARAMETERFILE=(bruker;/home/flemming/sommer/frisk/time.inp) |
| BASELINE [Default=N] | This parameter specifies whether a base-plane (line) should be fitted on top of the correlation. Allowed values are "N" and "Y". For example if a correlation is located in the vicinity of a strong solvent signal, you might need to fit also a offset baseplane, however, under normal circumstances it is strongly advised that you phase-correct your spectrum correctly and not use the baseplane fitting.
EXAMPLE: BASELINE=Y |
| VERBOSELEVEL [Default=1] | Specifies how much crap is written to the screen during the fitting procedure. Integer values between 0 (no output) to 5 ( a LOT of output) can be specified.
EXAMPLE: VERBOSELEVEL=5 |
| PRINTDATA [Default=Y] | Specifies whether output files and individual plotting files for every correlation are generated. Allowed parameters are "N" and "Y". The output files are names exactly as the name of the PEAKLIST. Thus, in the example of the PEAKLIST, all output files will start with "94N-HN".
EXAMPLE: PRINTDATA=N |
| LM [Default= (MAXFEV=250;TOL=1e-10)] |
Provides two specific parameters for the LM fitting procedure, i.e., the number of function evaluation (MAXFEV) and the tolerance (TOL).
EXAMPLE: LM=(MAXFEV=500;TOL=1e-4) |
| FITEXP [Default=Y] | Only apply to analyses of arrayed 2D spectra. After the line-shape has been fitted and intensities estimated for each plane of the arrayed spectrum, a single exponential decaying function is fitted to the delay v.s. intensity. Allowed values are "N" and "Y".
EXAMPLE: FITEXP=N |
| FITBIEXP [Default=N] | Only apply to analyses of arrayed 2D spectra. Same as FITEXP parameter, but now a bi-exponential decay ( A*Exp(lamda1*Trelax)+B*Exp(lamda2*Trelax) ) is fitted to the delay v.s. intensity.
EXAMPLE: FITBIEXP=Y |
| FIT180EXP [Default=N] | Only apply to analyses of arrayed 2D spectra. Same as FITEXP parameter, but now a exponential decay with value at infinity different from zero is fitted, A*exp(-x*delay)+B
EXAMPLE: FIT180EXP=Y |
| DEF_LINEWIDTH_F1 [Mandatory] | This is the default linewith along the first dimension (in ppm). For all correlations this linewidth will be used as a starting parameter for the least-squares fit, unless a specific "NOT_DEF_PEAK" statement is provided.
EXAMPLE: DEF_LINEWIDTH_F1=0.40 |
| DEF_LINEWIDTH_F2 [Mandatory] | This is the default linewith (width at half hight) along the second dimension (in ppm). For all correlations this linewidth will be used as a starting parameter for the least-squares fit, unless a specific "NOT_DEF_PEAK" statement is provided.
EXAMPLE: DEF_LINEWIDTH_F1=0.05 |
| DEF_RADIUS_F1 [Mandatory] | This is the default radius of the region taken out for fitting (along the first dimension and in ppm). For all correlations this radius will be used, unless a specific "NOT_DEF_PEAK" statement is not provided.
EXAMPLE: DEF_RADIUS_F1=0.30 |
| DEF_RADIUS_F2 [Mandatory] | This is the default radius of the region taken out for fitting (along the second dimension and in ppm). For all correlations this radius will be used, unless a specific "NOT_DEF_PEAK" statement is not provided. The complete region used for fitting includes all points X that satisfy, Sqrt( (X0-C0)^2/R0^2 + (X1-C1)^2/R1^2 + ... ) < 1 where {C0,C1,...} is the peak position given in the peak list, {R0, R1,..} are the radii along the individual dimensions. EXAMPLE: DEF_RADIUS_F2=0.05 |
| SHAPE [Default=GLORE] | The lineshape used for all correlations, unless a specific "NOT_DEF_PEAK" statement is provided. The SHAPE parameter takes the following parameter values: LORENTZIAN (Lorentz shape), GAUSSIAN (Gauss shape), GLORE (Mixture of Lorentzian and Gaussian), VOLUME (No line shape or fitting is performed; just integrate up the Volume). For SHAPE=GLORE, the lineshape is defined as LineShape(PeakPostition,LineWidth)=g*Gaussian(PeakPosition,LineWidth)+(1-g)*Lorentzian(PeakPosition,LineWidth). Please note that a Gaussian and Lorentzian are non-orthogonal, which means that the absolute intensity that you get from a fit of a GLORE lineshape is not to scale among different correlations. If you need to compare the intensity of two different correlations use either SHAPE=GAUSSIAN or SHAPE=LORENTZIAN. (In coming version of FuDA, we will try to scale the intensities and take care of this issue). For arrayed 2D spectra, where one is only interested in the relative intensity the GLORE shape will work perfectly well. EXAMPLE: SHAPE=GAUSSIAN |
| ISOTOPESHIFT [Default=N] | The isotopeshift used for all correlations, unless a specific "NOT_DEF_PEAK" statement is provided. The isotopeshift takes the following parameter values, N: No isotopeshift, (J1,J2): Fit a doublet [ratios of intensities are fitted as well] of peaks separated by a vector (J1,J2), (J1,J2,FIX): Fit a doublet of peaks separated by a vector, the values of J1 and J2 provided are not optimized in the least squares fit.
EXAMPLE: ISOTOPESHIFT=(-13,-6) |
| DISCARD_SLICES [Default=()] | This parameters is primarily used for analyzing 2D arrayed spectra. If, for some reason, you want to exclude some planes of your 2D array you can do so with the DISCARD_SLICES parameter. For example, DISCARD_SLICES=(1;5;6) will result in that plane no. 1, 5, and 6 are discarded and excluded from the least-squares fit.
EXAMPLE: DISCARD_SLICES=(2;4) |
| INCLUDE_PEAKS [Default=(all peaks)] | This parameter sets the peaks (correlations) to be included in the analysis. If the parameter is not specified, all correlations given in the PEAKLIST file will be used. NOTE: This parameter cannot be defined when also the parameter DISCARD_PEAKS is defined.
EXAMPLE: DISCARD_PEAKS=(18N-HN;24N-HN) |
| DISCARD_PEAKS [Default=()] | This parameter sets the peaks (correlations) to be excluded / discarded in the analysis. By default, this parameter is empty, i.e., no correlations are discarded. NOTE: This parameter cannot be defined when also the parameter INCLUDE_PEAKS is defined.
EXAMPLE: INCLUDE_PEAKS=(18N-HN;24N-HN) |
| OVERLAP_PEAKS [Default=()] | This parameter defines a group of overlapped peaks (correlations), i.e., peak that cannot be analyzed separately. You can define as many OVERLAP_PEAKS groups as your like, one line for each overlapped group of peaks. Note that the larger the group is the longer the least-squares fit takes and correlation between parameters might start to occur when extremely large overlap group (>10 peaks) are defined. NOTE: All OVERLAP_PEAKS group must be disjoint. This means that if you have one group defined as OVERLAP_PEAKS=(1N-H;3N-H;4N-H;9N-H), then you cannot have another group defined as OVERLAP_PEAKS=(4N-H;6N-H), since the correlation 4N-H is now present in two overlap groups.
EXAMPLE: OVERLAP_PEAKS=(18N-HN;24N-HN) |
| NOT_DEF_PEAK [Default=()] | SYNTAX: NOT_DEF_PEAK=(NAME=[name];[par0]=[val0];[par1]=[val1];....) The NOT_DEF_PEAK parameter is used to specify specific starting fitting parameters for a correlation [name] (name from the peaklist). Parameters that can be defined specifically with the NOT_DEF_PEAK parameters are: LINEWIDTH_F1 [real] (ppm) LINEWIDTH_F2 [real] (ppm) LINEWIDTH_F3 [real] (ppm) RADIUS_F1 [real] (ppm) RADIUS_F2 [real] (ppm) RADIUS_F3 [real] (ppm) SHAPE [string] LORENTZIAN/GAUSSIAN/GLORE ISOTOPESHIFT [string/array] N/([real],[real])/([real],[real],FIX) EXAMPLE: NOT_DEF_PEAK=(NAME=77N-HN;RADIUS_F1=0.30;ISOTOPESHIFT=-18,-5,FIX) |
| For more details on the input file, please see the "param.fuda" input file provided with the example of a nitrogen T1 experiment "dfh_puf1Nt1012.fid". | |
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