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Institut de Biologie StructuraleGrenoble / France

Contact person(s) related to this article / FAVIER Adrien

NMRlib 2.0 : IBS pulse sequence tools for Bruker spectrometers


NMRlib has been developed in the biomolecular NMR group of the Institut de Biologie Structural in Grenoble. For any questions or comments concerning NMRlib, please contact either Adrien Favier or Bernhard Brutscher .

Presentation

A detailed description of NMRlib can be found here

(Favier & Brutscher, J Biomol NMR 2019, 73:199)

The NMRlib package contains a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2–4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further parameter adjustment. NMRlib is magnetic-field independent, and thus particularly helpful for laboratories operating multiple NMR spectrometers. NMRlib is easily per-sonalized by adding, deleting, or reorganizing experiments. Additional tools are provided for data processing, visualization, and analysis.

The main features of the IBS pulse sequence tools are the following :

  • Complex NMR experiments can be recorded in an automated way. The user selects the experiments by simply browsing into a Jython emulated frame. All spectrometer dependent parameters are set automatically. A dialog window allows the user to define a few sample dependent parameters, and to select between different options.
  • Shaped pulse parameters (pulse length, power level, and frequency offsets) are calculated within the pulse sequence. If necessary, the spectroscopically relevant parameters (excitation offset and band widths in ppm) are made accessible to the users via constants.
  • The NMR experiments can be easily shared between several NMR instruments (via an NFS mounting point for example). This allows easy maintenance and further development of the library.
  • The IBS pulse sequence package also contains tools that allow you to create your own templates that will be automatically included in the GUI starting from a successful NMR experiment. The created python scripts can then be used on other spectrometers or shared with other users.

NMR experiments in NMRlib

The library has been developed mainly for protein NMR, but it can be easily extended to other fields of applications. Currently, the library comprises NMR tools for sample quality control, resonance assignment, and the measurement of structural and dynamic NMR parameters. In particular, NMRlib contains most of the fast NMR experiments (SOFAST-HMQC, HET-SOFAST, BEST-HSQC, BEST-TROSY, HADAMAC, ...) developed during recent years at IBS. In addition, it also contains tools for pulse calibration, setup of composite pulse decoupling, and advanced data processing.
NMRlib is regularly updated with new developments. So, have a look back at this site in the future.

Latest developments

09/2019 The BEST-TROSY HNCA, HNcoCA, and iHNCA experiments now contain options for CB decoupling during CA chemical shift editing using GOODCOP/BADCOP pulses.

Installation of NMRlib

  •  Download the archive using the request form on this web page.
     Unzip the file on your spectrometer disk, or alternatively at an NFS mounting point if you want to share NMRlib between several spectrometers.
  •  Execute the setup python script (setup.py) from a shell terminal.
  •  You will be asked to update your "Manage Preference Directories".
  •  Restart the TopSpin software.
  •  From the TopSpin command line execute : edpy setNMRlib (to be executed on each spectrometer).
  •  To activiate the IBS tool buttons click on the arrow sign in the TopSpin tool bar as illustrated in the figure below :
Alternatively you can enter "nmrlib" in the Topspin command line.
Corresponding shell commands:

cd
unzip NMRlib.zip
cd NMRlib
python setup.py

You can test the library on your protein by running a large set of experiment in 1D, 2D or 3D mode by clicking on "Spectro tests".

Disclaimer

All pulse sequences and python scripts have been tested on Bruker Avance III HD spectrometers and TopSpin version 3.2 to 4.0 using Linux host computers. The NMRlib program is provided as is, and the authors of the program disclaim all liability whatsoever, and offer no warranty, express or implied, as to the damages, direct or indirect, that may result from downloading, use of the program and exploitation of the results thereof.

Rules for the use of NMRlib

For academic users, the use of the NMRlib software package is free of charge. Please fill in the form below to receive a link for the download of NMRlib.

Please acknowledge the use of NMRlib for you research by citing the following paper : A. Favier and B. Brutscher, J Biomol NMR 2019, 73:199-211.

For industrial users : please contact Rime Kerfah (kerfah@nmr-bio.com) at NMRBio (link) for a quotation of the NMRlib licence.

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