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Institut de Biologie StructuraleGrenoble / France

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

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 clicking on a button. 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 and buttons starting from a successful NMR experiment. The created python scripts can then be used on other spectrometers or shared with other users.

Content

Currently, the IBS library 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.
The IBS library will be regularly updated with new developments. So, have a look back at this site in the future.

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 HNCO parameter set, 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

The IBS sequence tools 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, ...).

Important point: The getallprosol macro should be executed once before setting up an experiment of the IBS library. This macro defines the correct 90° hard-pulse lengths for the 1H, 13C and 15N channels, by executing a command such as getprosol 1H 9 10W 15N 35 300W 13C 12 200W
Note that the getallprosol macro can also be used together with a pulse sequence of the Bruker library using the Prosol relation file triple.

If the pulse calibrations have not yet been determined for a given sample and spectrometer, this can be achieved in a fast and automated way, using the PULSE CALIBRATION tools of the IBS library.

Easy installation of IBS library

Before starting: setup an n experiment (from the Bruker library), and write the parameter set with the name HCN
wpar HCN all (to be executed on each spectrometer)

  • 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 the IBS library 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 IBS_lib_setup (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:

    You are ready to browse through the IBS library and execute the experiments by clicking on the "IBS templates" button.

Corresponding shell commands:
cd
unzip archive.zip
cd IBS_templates
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 using the button (’Setup a series of exp.’).

How to create your own tools ?

  • Setup your favorite experiment, record it, process it with optimized parameters and simply click on the button "TemplateMaker" ...
  • Click on "Buttonmaker", and add your own button.
    (edpy ButtonMaker)

Disclaimer

All pulse sequences and python scripts have been tested on Bruker Avance III HD spectrometers and TopSpin version 3.2 using Linux host computers. The authors and IBS are not liable for any loss or damage arising from the use of this software package.

Contacts

These tools have been developed at the Institut de Biologie Structural (IBS) in Grenoble.
Please, send your comments and suggestions to Dr. Bernhard Brutscher
(Bernhard.brutscher at ibs.fr) or Dr. Adrien Favier (adrien.favier at ibs.fr)

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