qNLS

Made by

Copyright (C) 2014 Troels E. Linnet, SBiNLab, Copenhagen University

Copyright (C) 2014 Kaare Teilum, SBiNLab, Copenhagen University

Asses quality of NLS for coMDD processing.

A python script to quickly evaluate effect of co-processing several 2D spectra together.

The analysis can be performed in 10-15 minutes time, and is a valuable guide to determine which limit one should set the sampling fraction level to.

This script is for the intended use, where several experiments is recorded together, and where the modulation of the peaks are expected only to be in the peak intensities. That means, that all spectra should share the same frequency information, but not same amplitude.

Data requirement

First record one full experiment, for example the reference spectrum.

Process the spectrum with NMRPipe, to produce:

fid (original file)

fid.com which produces test.fid

nmrproc.com which produces test.ft2 from test.fid

The script expects that names of files in the directory are:

fid

fid.com

test.fid

nmrproc.com

Outline of script

Put a link to qNLS.py somewhere in your PATH

In the folder, write: qNLS.py -sf 20 15 10 5

Where sf is the sampling fractions in percent.

The script then proceeds as follows:

1. Loop over the sampling fraction level:

• Produce nls.in ; Numper of points in direct and in-direct dimensions, and sweep-width (Hz) are read from test.fid with nmrglue. ; In 00_ref.fid, write nls.in at 100 sf level ; In 01.fid, write nls.in according to the sampling fraction level
• Produce nusschedules with 'nussampler' from MddNMR within each *.fid folder
• Binary read the orginal fid file, and write out a truncated fid file in each *.fid folder according to the nusschedule. ; The individual fid file only contains the in-direct FIDs determined and ordered from the nusscedule. ; The 00_ref.fid then contains the full fid, but where the in-direct FIDs have been shuffled according to the full nusscedule.
• Then write proc.sh, which is command file with environment settings to MddNMR. These settings can be modified by parsing input commands to qNLS.py
• Then write fidSP.com and recFT.com. These are spectrum processing parameters, and these are read from the initial files of fid.com, and nmrproc.com.
• Then produce files for coMDD processing.
• Then coMDD process.
• Then analyse and produce figures.

Options to script

Get help by writing:

qNLS.py -h

-h, --help show this help message and exit

-N [N] Number of repeated spectra. -N 1

-sf sf [sf ...] list of sampling fractions in percent: -sf 24 20 16 12 8

-T2 [T2] T2: spin-spin relaxation time, the expected time constant characterizing the signal decay in in-direct dimension (s): -T2 0.1.

-FST_PNT_PPM [FST_PNT_PPM] MDD param: Define from where the region of interest starts in the direct dimension [ppm]: -FST_PNT_PPM 11

-ROISW [ROISW] MDD param: Define sweep-width in ppm, to subtract from FST_PNT_PPM: -ROISW 5

-SRSIZE [SRSIZE] MDD param: Size of sub-region (ppm): -SRSIZE 0.1

-CEXP [CEXP] Toggle R-MDD / MDD mode. For a dimension, with "y" time domain shape in the dimension is expected to be autoregressive.

In other words, we assume that the FID in the dimension is a complex exponent.

CEXP=y may be used, for example, for HNCO and HNcoCA experiments, but not for the NOESYs: -CEXP yn

-MDDTHREADS [MDDTHREADS] MDD param: Maximal number of parallel processes: -MDDTHREADS 16

-NCOMP [NCOMP] MDD param: Number of components per sub-region: -NCOMP 25

-NITER [NITER] MDD param: number of iteration in mddnmr: -NITER 50

-MDD_NOISE [MDD_NOISE] MDD param: Noise in mddnmr: -MDD_NOISE 0.7

Software depencies

python module depencies for the script

nmrglue, to read spectrum as numpy array

matplotlib.pyplot, to produce figures

scipy.optimize, to fit histogram

numpy, for data arrays

If problems, try see this wiki page: http://wiki.nmr-relax.com/Epd_canopy

MddNMR

The following programs should be in your PATH.

Try write in your terminal "which mddnmr4pipeN.sh", to see if they are available.

MddNMR

mddnmr4pipeN.sh

setHD

queMM.sh

NMRPipe programs

showApod

Citations for software

MddNMR

Orekhov, V.Y. and V.A. Jaravine

Analysis of non-uniformly sampled spectra with Multi-?Dimensional Decomposition.

Prog. Nucl. Magn. Reson. Spectrosc., 2011

doi:10.1016/j.pnmrs.2011.02.002

Kazimierczuk, K. and V.Y. Orekhov

Accelerated NMR Spectroscopy by Using Compressed Sensing.

Angew. Chem.-Int. Edit., 2011, 123, 5670-3

Download & Manual: http://pc8.nmr.gu.se/~mdd/Downloads/

Link to discussion: https://groups.google.com/forum/#!forum/mddnmr

nmrglue

J.J. Helmus, C.P. Jaroniec

Nmrglue: An open source Python package for the analysis of multidimensional NMR data |

J. Biomol. NMR 2013, 55, 355-367

http://dx.doi.org/10.1007/s10858-013-9718-x

Homepage: http://www.nmrglue.com/

Link to discussion: https://groups.google.com/forum/#!forum/nmrglue-discuss

The code is develop at Github: https://github.com/jjhelmus/nmrglue/

Documentation: http://nmrglue.readthedocs.org/en/latest/index.html

Trouble shooting

coMDD in MddNMR needs some standard packages to be present on system.

On redhat 6, these are the packages to install.

> yum compat-libf2c-34

> yum install glibc.i686