University of Wisconsin–Madison

Pulse Programs – Bruker


About this NMR pulse program library

This pulse program library provides protein and nucleic acid solution NMR experiments for use in standard methods of spectral characterization, ligand binding and structure determination. Additional emphasis is given for isotopically enriched samples.

All pulse programs are written and tested for Bruker NMR spectrometers running Topspin 1.3 – 3.2 or XWin-NMR 3.5, with optimized parameters for CryoProbes.

Note: This page is currently under construction, with new material being added periodically.


Disclaimer

These pulse programs are provided “as is” for your information. If used incorrectly these programs may potentially damage your instrument! Users employ the pulse programs at their own risk. Neither NMRFAM nor University of Wisconsin-Madison are liable for any physical or other damage incurred during the use of the pulse programs. This web site may contain proprietary software, design, original art, and possibly other copyrighted, trademarked, or proprietary content. Such use in this web site does not limit the original owners rights to any content used in this web site.


How to use this Library

Each pulse program is provided as a text file. Future versions of this library will include parameter sets and macros for particular pulse programs.

To use pulse programs, download the text file into the Bruker pulse program directory:

<path>/exp/stan/nmr/lists/pp/user

where <path> is equivalent to the Topspin or XWin-NMR install directory (e.g. for Topspin 3.2.5 place these in /opt/topspin3.2.5/exp/stan/nmr/lists/pp/user).

The logical channels for each nucleus in these pulse programs have been encoded to circumvent discrepancies between the hardware wiring of different spectrometers. As such, the file NUCS.incl should also be downloaded into the pulse program directory. Once saved, edit this file for nuclei channel assignments (i.e. f1 for 1H, f2 for 13C, etc.) specific to your spectrometer.


The experiments

HSQC0– In the download zip file, there are 6 pulse sequence files, 3 for non-constant time (HSQC1, HSQC2 and HSQC3) and 3 for constant time (HSQC1, HSQC2 and HSQC3) and an instruction file on how to set up the experiments. (Kaifeng Hu, William M. Westler, and John L. Markley, Simultaneous quantification and identification of individual chemicals in metabolite mixtures by two-dimensional extrapolated time-zero 1H-13C HSQC (HSQC0), (2011) J. Am. Chem. Soc., 133(6), 1662-5.)

Pulse programs for PROTEIN samples (compatible with Bruker’s prosol automatic pulse calibrations):

  • pr_artsy_deut_fam – ARTSY-2D TROSY for measuring 1DNH RDCs on perdeuterated proteins
  • pr_artsy_prot_fam – ARTSY-2D TROSY for measuring 1DNH RDCs on protonated proteins
  • pr_artsy_3D_deut_fam – ARTSY-3D TROSY for measuring 1DNH RDCs on perdeuterated proteins
  • pr_brct3dj_fam – 3D version, 2D 13C-HSQC modulated in 3rd dimension by 1JCH (for RDCs)
  • pr_diffusion_fam – 1D self diffusion measurement by stimulated echo using incremented gradient pulse duration
  • pr_hnco_nh_fam – 3D HNCO 1JNH coupled in the 15N dimension (antiphase) (for RDCs)
  • pr_hcaconJ_fam – 3D HACACON for 1JCAHA  (antiphase coupled – for RDCs)
  • pr_hncajch_fam – 3D HNCA for measuring couplings in CA dimension (e.g. 1JCAHA and RDCs)

Legacy site containing old xwinnmr pulse programs (download, unzip, and open index.html in a web browser)

Pulse programs for NUCLEIC ACID (NA) samples:

Required .incl files for Bruker pulse programs (e.g. for Topspin 3.2.5 place these in /opt/topspin3.2.5/exp/stan/nmr/lists/pp/user):

Required prosol relations files (e.g. for Topspin 3.2.5 place these in /opt/topspin3.2.5/conf/instr/spect/prosol/pulseassign):

Useful macros for Topspin/XWin-NMR:

  • Xnucref – unified scale referencing for X-nucleus indirect dimension of n-dimensional spectra

Problems, Questions, Suggestions, Requests ?
Drop us a line: Larry for NA pulse programs or Gabriel for protein pulse programs (including legacy) and the NA_artsy.