University of Wisconsin–Madison

Pulse Programs – Agilent

About this NMR pulse program library

The main emphasis of this pulse program library is directed towards protein and nucleic acids NMR spectroscopy of isotope enriched proteins in solution.

All pulse programs are written and tested on Varian VNS consoles running VnmrJ 2.1B and have been optimized for running on ColdProbes.

Note. This page is currently under construction, new material is being added every day.


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.


How to use this Library

Each pulse sequence is saved as a tar file. Each tar file contains the pulse program, parameter files,  a macro to load the pulse sequence, VnmrJ customized pages, a manual page.

To install an experiment onto your machine:

  1. download the tar file
  2. cd to your vnmrsys directory (or go to the /vnmr directory to install the experiment in the main directory)
  3. untar the file from within this directory, using the command:tar xvf  <path>/<tar_file>
  4. compile the pulse program using the seqgen command

To load an experiment onto your vnmrj:

  1. if you have BioPack properly installed and calibrated:
    • simply type the name of the experiment into the VnmrJ command line to load the experiment
  2. if you do NOT have BioPack installed:
    • load the parameter files and update the spectrometer dependent parameters by hand. The critical parameters typically are:
      1. power levels, hard pulse widths and compression factors:
        • tpwr, pw, compH,
        • pwC, pwClvl, compC,
        • pwN, pwNlvl, compN
      2. offsets:
        • tof, dof, dof2
      3. parameters for decoupling during acquisition:
        • dm, dmm, dseq, dpwr, dmf, dres,
        • dm2, dmm2, dseq2, dmf2, dres2

The experiments

Pulse programs for PROTEIN samples:

    • gNhsqc_2fb – sensitivity-enhanced 15N-HSQC
    • TROSYgNfhsqcA – fast 15N-HSQC with TROSY option
    • gTRACT – estimate effective correlation time of a protein by measuring the relaxation rate of 15NHamide alfa and beta states
    • gNfhsqcZZ_3DA – Nz exchange experiment based on the fast 15N-HSQC pulse sequence
    • ghnco_LRA – Long-range HNCO experiment to detect NH-OC H-bonds in proteins
    • CCLS/DCLS – A set of 13C-filtered 15N-HSQC experiments developed at NMRFAM for the studying of multi-protein complexes (available soon)

Pulse programs for large PROTEIN samples:

    • gNtrosyA – 2D N,H 15N-TROSY experiment with Nietlispach modification to suppress unwanted anti-TROSY components without any extra loss in sensitivity
    • gChmqcnoesyChmqc_3D – 3D C,C,H 13C-HMQC NOESY 13C-HMQC experiment for selectively labeled proteins

Pulse programs for Nucleic Acids samples:

Click HERE for useful macros for VnmrJ.


Problems, Questions, Suggestions, Requests ?
Drop me line: Marco