BioPack Calibration

BioPack calibration will run a series of experiments and find the optimum values for various parameters and then update your HCN probefile with these values. Now whenever you load in a new experiment (either by typing in pulse sequence name or by selecting it from the menus) it will automatically have these calibrated values. All you should have to do is collect a 1D spectral check and then setup your aquisitioin parameters.

If you are only checking some samples, maybe running Nhsqc spectra to compare different solution conditions or proteins, it is not necessary to go thru the BioPack calibration procedure. But if you are setting up a series of 3D experiments for assignment purposes, you should probably do a full BioPack calibration on your sample. It may take 2 hours to run a full calibration if you have a good concentration. If you have poor signal to noise, the calibration could take 6 hours, and you may want to just check specific pulses instead. The pw90 calibrations only take several minutes.

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.
  • Or simply select the pw90 calibrations.

Reinit BioPack and Reset Users HCN Probefile

A user can reset their HCN probefile back to the system probefile, which is calibrated on Sac7d-VM protein, and reinitialize their copy of BioPack using the following procedure.
  • Type “BPrmlocalfiles” and answer yes to any questions.
  • Quit Vnmrj and then restart Vnmrj
  • Select from the Menus -> Experiment -> ActivateBioPack -> copy probefile from vnmr1 (not vnmr)
  • Follow onscreen instructions.

Deuterium Decoupling Calibration

  • First press the Instructions button for 2H decoupling calibration and read what it says. The 800 has a 2H decoupler on channel 4. Follow the directions. You will have to recable the magnet leg as described in the instructions. Also, please read the info on this page.

HCN Probefile

BioPack uses a file to store parameter values. Whenever a new experiment is loaded into a workspace, these parameters are retrieved and used to generate any shaped pulses needed for the experiment. These parameters will supersede any parameters in the .par file (in parlib directory) but not any parameters that are set from within the pulse sequence setup macro (in /vnmr/maclib).
~/vnmrsys/probes/HCN/HCN - users HCN probefile
/home/vnmr1/vnmrsys/probes/HCN/HCN - systemwide probefile

The probefile can be edited directly with a text editor (e.g., to set tof) or edited using the vnmrj software. To do the latter, click on the the “Probe” button at the bottom of the Vnmrj window. Check the “edit probe” box and select from the popupbox the nucleus (i.e., H1 for proton parameters) whose parameters you want to edit. In the window that appears, enter the value of whatever parameter you want to change (i.e., “tofH2O” for tof) and Save.

BioPack Calibration by vnmr1 (system administrator)

  • vnmr1 should periodically perform a full BioPack calibration on Sac7d-VM protein to check for drift of amplifiers, etc.
  • 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.
  • Click here for more information on BioPack calibration by vnmr1.