Copyright (C) V. Orekhov, Swedish NMR Centre, Gothenburg University, 2004-2006 README file ######### About mddNMR v. 1.3 This is pre-release of the software that allows performing MDD calculations as described in the papers: 1. Luan T, V. Jaravine, A. Yee, C.H. Arrowsmith, and V.Y. Orekhov, Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition. J. Biomol. NMR, 2005, 33: p. 1-14 2. Tugarinov, V., L.E. Kay, I. Ibraghimov, and V.Y. Orekhov, High-resolution four-dimensional H-1-C- 13 NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J. Am. Chem. Soc., 2005. 127(8): p. 2767-2775. 3. Orekhov, V.Y., I. Ibraghimov, and M. Billeter, Optimizing resolution in multidimensional NMR by three-way decomposition. J. Biomol. NMR, 2003. 27(2): p. 165-173. 4. Jaravine, V., I. Ibraghimov, and V.Y. Orekhov, Removal of a time barrier for high-resolution multidimensional NMR spectroscopy, Nature Methods, 2006, 3(8): p. 605-607. Please cite at least one of these papers when using the software. ########## Content of the package mddnmr1.3_*.tgz mddnmr1.3_*_example1.tgz fid_example1.tgz mddnmr1.3_*_example2.tgz mddnmr1.3_*_example3.tgz fid_example3.tgz After untaring them you will have the program directory and the mdd MDDEXAMPLES directory : 1. mddnmr1.3 with the following Copyright copyright statement Readme this file bin link to one of the following two directories prg_mddLinux directory with programs for Linux platform prg_mdd_MAC directory with programs for MAC com directory with C-shell, gawk, and Tcl scripts, as well as template Makefile for the HNCO example 2. MDDEXAMPLES three MDDEXAMPLES of processing of 4D HMQC-NOESY-HMQC, 3D HNCO, 3D NOESY-HSQC A key element of the package is a stand-alone program mddnmr1.2c that performs MDD decomposition. Description of the program arguments and formats of input and output (ASCII) files is given in the file ReadmeFiles (in MDDEXAMPLES/4D_NOESY). Role of the other programs and scripts is to link input and output of the mddnmr1.2c program with nmrPipe, which is used for handling the FID's from a spectrometer, Fourier transforms, spectra presentation, etc. ########## Installation The software for Linix (Intel x86) and Mac OS X 10.3 ( G4/G5 processors) is distributed as several compressed Unix tar archives 1. Please read the text in the file Copyright. 2. Note: To run this software you must have functioning nmrPipe package (Delaglio, F., et al., 1995, J. Biomol. NMR, 6, 277-293). 2. in the directory mddnmrx.x (e.g. mddnmr1.3) run command ./Install 3. To install examples unfold corresponding Unix tar archives. tar xzf ) this will create directory MDDEXAMPLES 4. Assuming that the package is installed in '/mddnmr1.3' (full path), add the following lines setenv MDD_NMR /mddnmr1.3 set path=( $path . ${MDD_NMR}/bin ${MDD_NMR}/com ) ########## Procedure This is pre-release of the software and instructions are limited to description of a couple of examples that are found in directory MDDEXAMPLES. --------------------------------------------IMPORTANT------------------------------------------- | Disclaimer: at this time we can not guarantee the usage of the software outside the scope | of the presented examples. !! BIOPACK SUPPORTS ONLY THE EXAMPLE 2 and 3 BELOW, i.e. 3D HNCO | (or similar 3D triple-resonance experiment with constant-time t2 (e.g.15N) evolution). ------------------------------------------------------------------------------------------------ 1. 4D NOESY --------------- NOTE: the NOESY example was prepared before the Aug 2006 incorporation of Non-uniform sampling into BioPack, thus the sampling is implemented as a stand-alone procedure. processing 4D Methyl NOESY spectrum described in the paper (Tugarinov, V., L.E. Kay, I. Ibraghimov, and V.Y. Orekhov, High-resolution four-dimensional H-1-C-13 NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J. Am. Chem. Soc., 2005. 127(8): p. 2767-2775). Experiment: All needed files and README file with short description for setting up the 4D Methyl NOESY experiment are found in directory MDDEXAMPLES/4D_NOESY/EXPERIMENT. Note, this experiment cannot be set up using BioPack. Processing of the 4D Methyl NOESY: In the directory MDDEXAMPLES/4D_NOESY check content of the lek4dInit.sh file, which is file with parameters and settings for the processing. Change directory to MDDEXAMPLES/4D_NOESY and read the Readme file 2. ubidemo ------------ processing 3D HNCO recorded using BioPack (Aug 2006 and later). See also Jaravine, V., I. Ibraghimov, and V.Y. Orekhov, Removal of a time barrier for high-resolution multidimensional NMR spectroscopy, Nature Methods, 2006, 3(8): p. 605-607. Experiment: See the paper and instructions in BioPack Processing: change directory to MDDEXAMPLES/ubidemo, follow instructions in the README file. 3. azurin3dNOESY ------------ processing 3D 1H-15N NOESY-HSQC spectrum of azurin (14 kDa) described in the paper Orekhov, V. Y.; Ibraghimov, I.; Billeter, M., Optimizing resolution in multidimensional NMR by three-way decomposition. J. Biomol. NMR 2003, 27, 165-173. Experiment: See the paper and instructions in BioPack Processing: change directory to MDDEXAMPLES/azurin3dNOESY, follow instructions in the Readme file.