Spectrometer Calibrations for Administrator

Probe Files

Probe files are used to store pulse length calibrations and such. There may be system probe files in /vnmr/probes and user probe files in ~/vnmrsys/probes
  • There are 2 probe files on the 500: penta and HCN
  • On the 800 there is only the HCN probefile
  • The “penta” probefile is used for ChemPack (small molecules)
  • The “HCN” probefile is used for BioPack (proteins and nucleic acids)


Shim map files are used to store information for gradient shimming. There may be system shimmaps in /vnmr/gshimlib/shimmaps and user shimmaps in ~/vnmrsys/gshimlib/shimmaps
  • ChemPack users’ shimmap defaults to penta_lk_someDateOrAnother
  • BioPack users’ shimmap defaults to H1_map, which is appropriate for aqueous samples in 10% D2O
  • A system shimmap for 100% D2o samples (such as the lineshape standard) is H2_map

BioPack Calibration by vnmr1

  • vnmr1 should periodically perform a full BioPack calibration on Sac7d-VM protein to check for drift of amplifiers, etc.
  • Also, updates to BioPack may be installed periodically, and these may require a new calibration.
  • Check the spectrometer log book for when updates have been applied and add entries as necessary

BioPack Calibration Procedure

  • Setup tab -> Calibrations page
  • Select the type of calibration you want to perform, such as a full calibration starting from your HCN probefile values.

Creating a New HCN Probe File for BioPack

Here is the procedure I have used to create a new probe file when new parameters have been defined by Varian.
Setup -> Proteins -> Activate BioPack
choose Create New Probe File
load ghn_co if not already done
adjust parameters.
sw=14ppm, sw1=20*dfrq, sw2=40*dfrq2
d1=1 for 500; d1=1.5 for 800
at=.064, waltzB1=8ppm
rof2=2, alfa=6.6
tpwr=53 for 500; tpwr=56 for 800
set pw and pw90 to previous values (not critical here)
Use previous values in old probe file (in directory vnmrsys/probes/HCN_xxx) to set
  • gzcal
  • dpwr, dmf, dpwr2, dmf2
  • tpwrsf, pwClvl, pwC, dof, compC, pwNlvl, pwN, dof2, compN
on 800 also copy over H2 parameters
set BPspinlock according to printout
set gzlvl1=13000; gzlvl2=13000
Setup -> Proteins -> Manage Probe File -> Udate with these values
Setup -> Water -> AutoCalibration -> PreSat (to find tof)
run 1D of hn_co after settting tof to above value
set center ppm (cr=sw/2-rfl; rl(4.72p)
then set dof to 174ppm; dof2 to 118ppm (use dofcal and dof2cal macros)
again do Setup -> Proteins -> Manage Probe File -> Udate with these values
Setup Tav -> CalibrationsPage -> Full