NMR experiment and processing tool catalog for liquids
(Solution-state NMR version : Favier & Brutscher, J Biomol NMR 2019, 73:199
Solid-state NMR version : Vallet, Favier, Brutscher & Schanda, Magn. Reson. Discuss., https://doi.org/10.5194/mr-2020-25, in review, 2020.)
The NMRlib package contains a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.5–4.0) 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.
Upon installation, NMRlib comes with both solution- and solid-state NMR experiments. The installed probe is automatically detected, which opens either the solution- or solid-state NMR branch of the library.
Solution-state NMR experiments
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.
Solid-state NMRlib experiments
Currently, more than 140 pulse sequences are implemented for homo- and heteronuclear experiment from 1D to 4D. The library comprises 1H-, 13C- and 15N-detected experiments for biomolecular resonance assignment (protein backbone and side chains, sugars), distance restraints (1H-1H, 13C-13C), molecular dynamics (relaxation, dipolar-coupling measurements, conformational exchange).
The library contains also an extensive set of calibration tools for transfer steps (cross-polarization ; homonuclear transfers such as BSH-CP, DREAM, RFDR ; INEPT etc).
Safety checks furthermore assist the user in experiment setup.
- 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.
- From the TopSpin command line execute :
xpy <installation directory absolute path>/nmrlib/py/setNMRlib
for example :
(to be executed on each spectrometer).
- Restart the TopSpin software.
- 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.
The installation steps are also described in the video "install.mp4" provided in the archive.
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".
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.
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 papers. For the solution-state NMR branch cite : A. Favier and B. Brutscher, J Biomol NMR 2019, 73:199-211. ; for the solid-state NMR branch cite : A. Vallet, A. Favier, B. Brutscher & P. Schanda, Magn. Reson. Discuss., https://doi.org/10.5194/mr-2020-25, in review, 2020. ;
For industrial users : please contact Rime Kerfah (firstname.lastname@example.org) at NMRBio (link) for a quotation of the NMRlib licence.
The automatic probe type detection (solid or liquid) does not work yet for this topspin version. On the main panel of NMRlib, the button "Select your probe" allows you to define your installed probe manually.