The RELAX sub-package (currently) consists of 4 programs for processing crosspeak integrals which have been calculated using MFIT or Pronto. The programs have been written with 15N-relaxation measurements in mind, but may be used in other connections as well (such as measurements of hydrogen exchange rates). The integrals from several spectra can be fitted to a sum of exponential decays using EXPFIT and a NOE value can be calculated using CALCNOE. Subsequently, these results can be fitted to the Lipari-Szabo model using TAUC and LIPASZAB.
The EXPFIT program fits data to one or two exponential decays, with or without a baseline offset. The fitted parameters as well as their uncertainties are written to a file. The data is taken from output files of MFIT or from Pronto crosspeak reports.
The EXPFIT program is called as follows:
<machine ID>mexpfit <inputfile
All commands to EXPFIT are read from standard input, and in the case above, this has been redirected to the file inputfile.
Commands to the EXPFIT program:
Format:
DATAFILE <filename>
Specifies the name of the files to which the fitted values for all peaks will be written.
Format:
PARAM_FILES <filename>
The EXPFIT program assumes that the data are located in several files with identical names but in different directories. This command specifies the name of the files. Default is fitparam.dat (MFIT output). EXPFIT compares the peak assignments in the files, and integrals with identical assignments in different files are taken as belonging to the same decay curve.
Format:
PRONTO_REPORT
Identifies the input files as Pronto crosspeak reports.
Format:
TIME <t> DIR <dirname>
This command tells EXPFIT in which directory the data recorded with delay t are located. To ensure compatibility with the LIPASZAB program, the numbers should be given in seconds.
Format:
MODEL <name>
Specifies to which model the data should be fitted. Possible choices are
| Name | Formula |
|---|---|
| ONE_EXP | y = A0*exp(-t/A1) |
| ONE_EXP_OFFSET | y = A0*exp(-t/A1) + A2 |
| TWO_EXP | y = A0*exp(-t/A1) + A2*exp(-x/A3) |
| TWO_EXP_OFFSET | y = A0*exp(-t/A1) + A2*exp(-x/A3) + A4 |
Default is ONE_EXP.
It should be easy to add new models. The form of the model including derivatives should be added to $MNMR_DIR/mfit/expfuncs.c, and $MNMR_DIR/mfit/relax.h as well as $MNMR_DIR/mfit/egetarg.c should also have suitable additions.
Format:
GUESS a1 a2 ...
Specifies initial guesses at the parameters A0, A1 ..., to be used in all fits. Please notice that the decay constants are specified as times, not rates, and that the choice of units must be consistent with the TIME ... DIR commands. This command should be given after the MODEL command.
Format:
DECAY_FILES <suffix>
EXPFIT can generate individual ASCII files of all decays. If the DECAY_FILES command is given, a file with delay times and integrals listed is produced for each peak. The file name consists of the assignment of the peak with spaces replaced by underscores, followed by the specified suffix.
Format:
XMGR_FILES <suffix>
This commands works essentially like the command DECAY_FILES above, but provides a particulary convenient interface to the program XMGR. XMGR is a free X-windows plotting program (which we highly recommend that you get if you don't have it already). When this command is given, XMGR input files for each decay curve including the fit are produced. If you have XMGR installed, the curves will be drawn on the screen by typing xmgr <filename>.
For XMGR afficionados: The XMGR input files are ASCII files which may be modified. The files produced by expfit begin with the contents of the file $MNMR_DIR/mfit/template.xmgr proceded by the data, and end with the contents of the file $MNMR_DIR/mfit/commands.xmgr. These files may be modified to suit your needs (see the XMGR manual for particulars of the command language).
Format:
PLOT
This command works exactly like the command XMGR_FILES above, except that the plots will be generated by XMGR and sent to your printer. The XMGR files generated by EXPFIT will be deleted after use. Before using this command you should probably make some files using XMGR_FILES and have a look at some of them, since PLOT may send a large number of plots to your printer.
Sample input file for EXPFIT:
DATAFILE T1.dat PARAM_FILES cp.rep PRONTO_REPORT XMGR_FILES .xmgr TIME 0.050 DIR 201 TIME 0.250 DIR 202 TIME 0.450 DIR 203 TIME 0.650 DIR 204 TIME 0.850 DIR 205 TIME 1.100 DIR 206 TIME 1.500 DIR 207
The CALCNOE program calculates Nuclear Overhauser Effects using one or several determinations of crosspeak integrals in spectra with and without proton saturation. If several spectra of each type are provided, an uncertainty on the calculated NOE is found.
The CALCNOE program is called as follows:
<machine ID>mcalcnoe <inputfile
All commands to calcnoe are read from standard input, and in the case above, this has been redirected to the file inputfile.
Commands to the CALCNOE program:
Format:
DATAFILE <filename>
Specifies the name of the files to which the fitted values for all peaks will be written.
Format:
PARAM_FILES <filename>
See description under the EXPFIT program.
Format:
PRONTO_REPORT
See description under the EXPFIT program.
Format:
NOSAT DIR <dirname>
Specifies a directory with data from spectra recorded without proton saturation.
Format:
SAT DIR <dirname>
Specifies a directory with data from spectra recorded with proton saturation.
The TAUC program calculates an overall tumbling time tauC using the average T1/T2 ratio and the Lipari-Szabo model (J. Am. Chem. Soc. 104, 4546-4559 (1982)) with chemical shift anisotropy included. In addition, a value may be calculated on the basis of average T1, T2 and NOE values. An uncertainty of the determined tauC is calculated using a Monte Carlo procedure and the uncertainties of the relaxation parameters.
The TAUC program is called as follows:
<machine ID>mtauc <t1filename> <t2filename> <noefilename>
The last argument is optional. The files specified must be generated by EXPFIT and the optional NOE file by CALCNOE. The decay times read in the files are the second parameter in the model (works with models ONE_EXP end ONE_EXP_OFFSET in EXPFIT).
T1/T2 values that are more than a specified number of standard deviations away from the average are omitted and a new average is calculated. The number of standard deviations to use is defined as OUTLIER_CUTOFF in the file $MNMR_DIR/mfit/relax.h. The number of iterations in the Monte Carlo procedure is defined as MC_ITERATIONS. These numbers can be changed and the program recompiled.
The LIPASZAB program fits relaxation measurements for individual peaks to the Lipari-Szabo parameters S2 and tau with a specified overall correlation time tauC. Uncertainties of the fitted parameters are calculated using a Monte Carlo procedure. Usually, T1, T2 as well as NOE values are used; however, T2 values can be omitted to investigate the effects of exchange broadening.
The LIPASZAB program is called as follows:
<machine ID>mLipaSzab <inputfile
All commands to LIPASZAB are read from standard input, and in the case above, this has been redirected to the file inputfile.
Commands to LIPASZAB:
Format:
DATAFILE <filename>
Specifies the file to which the fitted parameters are written.
Format:
TAUC <t>
Specifies the overall correlation time in units of seconds.
Format:
T1 <filename>
Specifies the file with T1 values.
Format:
T2 <filename>
Specifies the file with T2 values.
Format:
NOE <filename>
Specifies the file with NOE values.
In the present version, no extensions of the Lipari-Szabo model are implemented. It is possible to make such extensions by modifying the files $MNMR_DIR/mfit/model.c and $MNMR_DIR/mfit/LipaSzab.c, following the instructions at the top of the latter file.