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Institut de Biologie StructuraleGrenoble / France

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

NMRlib 2.0: IBS pulse sequence tools for Bruker spectrometers

A combination of python setup scripts and Bruker pulse sequence programs for easy use and sharing of protein NMR experiments.

Presentation

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.

* Some of the experiments (highlighted by a ’star’) provided in NMRlib use standard Bruker sequences, and therefore require an up-to-date Bruker PROSOL table for their use.

Content

Currently, 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 a few basic experiments (1H-13C and 1H-15N HSQC, 15N T1, T2 and HETNOE, ...), as well as 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.

Click on the image to get a detailled description of the library.

Setting up an experiment: how does it work?

For the setup of a new experiment, a python script is executed (by clicking on the corresponding button) that performs the following actions;

- It reads a standard Bruker parameter set (HNCOCAGP4D), in order to define the correct routing of the spectrometer.
- The corresponding pulse sequence is loaded.
- All relevant acquisition parameters are defined.
- All relevant processing parameters are set.
- Some security checks are eventually executed.

Use of PROSOL and 1H, 15N and 13C pulse calibrations

NMRlib pulse sequences are meant to use a reduced Prosol relation file that only contains the hard pulse power levels (plw1, plw2, plw3, ...) and the corresponding 90° pulse lengths (p1, p3, p21, ...).

The "Set pulse width" tool present on the main NMRlib GUI window allows to set manually the hard pulse widths. These values are set automatically upon loading any NMRlib experiment. Note that 1H, 15N and 13C calibration experiments are provided that measure and store automatically the 90° pulse lengths.

Easy 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".

How to create your own tools ?

- Setup your favorite experiment, record it, process it with optimized parameters and simply click on the floppy disk icon ...

Disclaimer

All pulse sequences and python scripts have been tested on Bruker Avance III HD spectrometers and TopSpin version 3.2 to 3.5 pl7 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.

Contacts

These tools have been developed at the Institut de Biologie Structural (IBS) in Grenoble. They are free of charge for academic users, industrial users can contact us to get a quotation for this product.
Please, send your comments and suggestions to Dr. Bernhard Brutscher
(Bernhard.brutscher@ibs.fr) or Dr. Adrien Favier (adrien.favier@ibs.fr)

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