NMRFAM 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.


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 15NH amide 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

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2017 NMRFAM Introductory Structure Determination Workshop (6/4-9, 2017), Madison WI

2017 NMRFAM ADVANCED Structure Refinement Workshop ( 8/6-9, 2017), Madison WI 

"The Future of NMR-Based Metabolomics, Current Opinion in Biotechnology (2017), pp. 34-40

Telluride School on Biomolecular Structure and Dynamics;Theory and Experiment (July 24-31, 2017) 

AMPERE NMR School (June 25th - July 1, 2017: Zakopane, Poland)

Documents on the use of the Bruker-Axs Nanostar,SAXS instrument and analysis of SAXS data are now available.

NMRFAM-SPARKY Distribution - the popular NMR analysis program SPARKY recompiled (including updated python and Tcl/Tk) with incorporation of PINE-Sparky, enhancements to import/export to the structural analysis program CYANA, and other useful python extensions.

ADAPT-NMR Enhancer: Complete Package for Reduced Dimensionality in Protein NMR Spectroscopy

RNA-PAIRS: RNA Probabilistic Assignment of Imino Resonance Shifts

PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis 


Donate to NMRFAM. US tax-deductible donation can be made to NMRFAM
Please write check payable to "UW Foundation, Account 112152802"  
And mail to: 
Attn: Sarah Lynn Traver Saunders
Associate Administrative Program Specialist 
University of Wisconsin-Madison 
433 Babcock Drive 
Madison, WI 53706 
Tel: 608-265-2507 or email 


1st: Lai Bergeman 
Rm 171; Phone 262-3173

2nd: Milo Westler
Rm B160; Phone 263-9599

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Rm B224; Phone 265-3303

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