Introduction.

The MNMR package consists of a series of programs for doing analysis of 2D, 3D, 4D, etc. NMR spectra of proteins. The programs enable the user to do Fourier transform, baseline correction, phase correction, projections, extractions, and to do contouring on different media. A set of library functions is included to read and write slices from spectra processed with this package.

Most of the code was written at Carlsberg Laboratory, Dept. of Chemistry, by Mogens Kjær, Kim V. Andersen, Christian Rischel. Suggestions and code was also provided by Frank van de Ven, University of Nijmegen. The HSVD code was provided by R. de Beer et al.

New facilities in 980316

The manual has been translated into HTML.

MCNTSeparate number of tick marks can now be specified on the two axes.
cplotBetter control of size and colors in the Encapsulated PostScript driver.
MVREADThis program reads in a VNMR processed file into MNMR.

New facilities Since 940201

MFFTAdded code for real FFT, real HSVD, time domain water filter, shifting of spectra, and skipping FFT (FvdV). Intensity cutoff for HSVD. Added code for reading of multidimensional FID files from Varian spectrometers.
MCNTBetter handeling of borders.
RELAXFour programs added for the study of relaxation parameters.

New facilities Since 930601

MFITCode changed.
MFFTComments can be specified in input as # <text>
MCNTComments can be specified in input as # <text>
NMRIOA check is made to see, if the spectrum file has zero length.
MBASEThe program generates a taxi file, so the progress of the baseplane fitting can be followed.

New facilities Since 930401

MFITProgram to fit Lorentzian peaks.

New facilities Since 930115

MFFT:The HSVD/HLSVD code has been inserted in all versions distributed, as the code is now public domain.

The following commands have been added/modified: BC, NOREFL, BLANK, CT, RUBOUTC, and RUBOUTD.

A log file is created in the current directory. This will reflect the progress of the calculations. The percent value in the file is not always correct, i.e. it can get larger than 100 %.

MLOAD: Loads the FID into an MNMR file.

MPROJ: The program can calculate a skyline projection.

MVIEW: The phases found with MVIEW is supposed to be compatible with the phases specified for MFFT. Minor changes in the user interface.

MNORM: Normalizes a spectrum.

New Facilities Since 921001

MFID:This program was missing from the manual. It is used to simulate n-D spectra.

MRANGE:Extract a range from a spectrum.

Various bugs corrected.

New Facilities Since 920701

M3DCNT:The program makes it possible to display a 3D spectrum in three dimensions. It is possible to rotate the spectrum, and study individual planes, in each of the three dimensions.

NMRIO:The input/output module can now read multidimensional Felix spectra. Some (untested) code has been added to read compressed Felix data.

New Facilities Since 920201

MFFT:Code for linear prediction has been added. We do not have a distribution agreement for the LP code, so you have to write to the authors to get the source code.

A new FFT algorithm is used. This is 30-40% faster.

MSLICE:This is a new program used to extract slices. The data in the slice is written out in ASCII format.

MADD:Adds two spectra together.

MMEAN:Prints out some statistics for the data points in a spectrum, e.g. mininum, maximum, mean value.

Conventions used in MNMR.

Program Names.

The program names in the MNMR package all have the following format:
<Machine ID>m<name>

where the machine id is a two-letter code, identifying the type of the host machine, and the software optimization level. Currently, this can be:

PrefixArchitecture
IOOptimized version for SGI.
IDDebug version for SGI.
TOOptimized version for the Stardent 1500 series.
TDDebug version for Stardent 1500 series.
SOOptimized version for Sun Sunos.
SDDebug version for Sun Sunos.
LOOptimized version for Sun Solaris.
LDDebug version for Sun Solaris.
QOOptimized version for x86 Linux.
QDDebug version for x86 Linux.

The use of Submatrices.

Figure 1

All data (2D, 3D, etc.) are stored in submatrix format. The layout of the submatrices is shown in Figure 1. This format makes it easy to access slices in all three dimensions.



Last updated: 18-Mar-1998
Questions/comments: mk@crc.dk