VNMRJ 2.1B – Quick overview and BioPack features

VNMRJ 2.1B interface is a much more intuitive user interface than the VNMR6.1C. The Java interface is a

layer on top of the conventional VNMR so all commands and macros from the old interface are still valid

in VNMRJ 2.1B. As a matter of fact VNMRJ 2.1B as shown in Fig. 1 is essentially allows one to use it much

like 6.1C or earlier version (but for the absence of menus).

Figure 1

It is, however, useful to familiarize with VNMRJ 2.1B features and use them to both ease and speed up

the operation of the spectrometer. The focus from here on is based on BioPack/VNMRJ interface.

Figures 2 , 3, and 4 show the initial sample setup panels in VNMRJ. After proper sample positioning in

the magnet (see Sample Positioning document) the sample temperature , locking, and shimming are

implemented from the panels in the Setup folder.

Command Line

Text out (dg)

Figure 2

After selecting the temperature by entering the number or using the slider hit the Regulate temperature

button. Selecting the check box control temperature from this panel only avoids accidental temperature

changes with go in different experiments.

Locking is the next step and there is no separate acqi window for this function. The graphics area

displays the lock signal. The lock tools are selected from the Lock panel (Figure 3). The sliders can be

used to change values or clicking the left/right buttons on the mouse will also do the same.

Click on the Setup folder

Select Spin&Temp

Set the temperature here

Figure 3

One could do gradient shimming from the lock panel by clicking the Gradient Autoshim on Z button. It

would use the last used gradient map. A new map can be made with the Setup Gradient Shimming

button. This loads gmapsys experiment and associated panels for making a new map.

The manual shimming tools are also available in Shimming Panel (see Figure 4). Both axial and non-spin

shim buttons are available. With every sample, particularly in Shigemi tubes, it is better to touch X, Y, XZ,

YZ, and then Z1 and Z2 before making a new map.

Click on the Setup folder

Lock panel

Clicking here enables

lock/unlock

Figure 4

Experiment selection:

The pull-down menus on the top Menu Bar allow one to navigate through the various functions that one

would want to select. An experiment is selected from the experiment menu. In Figure 5, the way an

experiment is selected in VNMRJ is illustrated.

Click on the Setup folder

Select Shim Panel

Figure5

The walk-through menu system gives flexibility to group NMR experiments based on a common type,

such as water suppression experiments 1D, 2D, etc…, Protein triple resonance experiments, Protein

HSQC experiments and so on. Selecting Presat from this menu will setup Presat experiment (Figure 6).

This is the experiment one would first start after proper sample placement in the magnet (see Sample

Positioning document) , tuning and shimming. Once the experiment is selected the following steps are

carried out.

(See Fig.6 for the following points)

(1) Select the Find Best Saturation Frequency button. This would array tof and satfreq (diagonal

array) and find the best saturation frequency for the solvent at the selected temperature.

(2) Calibrate pw360 on proton by clicking on the the pw360 button. The experiment will start with

pw array and enter the number of the array when the signal goes to zero.

(3) Then update the probe file value for proton by clicking the Update probe file with this pw90

button.

Menu Bar

Figure 6

BioPack Calibrations:

Now the system is ready to do a full BioPaack calibration. Assuming that the probe file (usually named

HCN) has a close enough starting values for carbon and nitrogen pulse widths, one proceeds to the

Globals & Probe file panel in Setup folder (Figure 7). If not, it is advised that the probe file be first

updated with a known set of values and do the calibrations.

(See Fig. 7 for the following points)

(1) If the probe in use is a cold probe then first set dsp=’I’ from the command line and click the

ActivateQcomp option button. Otherwise this step is not needed and just set dsp=’r’.

(2) If the probe is a cold probe then click the Automatic Gradient (WURST) Shaping radio button.

Although, gradient shaping is useful in RT probes to it is not necessary as the gradient recovery

is very fast in these probes. But one should be warned that if the probe is calibrated with

gradient shaping then in all experiments it should be used (gradienshaping=’y’) otherwise the

gradient calibrations will be wrong in that experiment.

(1) (2)

(3)

(3) If BioPack Power Limits is checked and values are entered then during calibration BioPack will

use these settings to create decoupling patterns.

(4) The default Carbon spin lock value is generally correct for the given spectrometer frequency. But

it is useful to check it.

Figure 7

The next step is to initiate calibrations from the Calibrations panel. Figure 8 illustrates the various

options in this panel.

(See Fig. 8 for the following points)

(1) Here there are 5 options. The very first time it is suggested that the first option (Full Using

Probefile Values) is initiated. A detailed description of all the options can be easily viewed in the

text page by clicking the Describe Options on this Page button.

(2) For just a N15 labeled protein there is a separate option for that – This option does a sub set of

the full calibration omitting carbon experiments. A similar button for C13 only labeled protein is

also available (it is buried behind the pulled down menu in this figure).

(1)

(2)

(3)

(4)

(3) There are buttons for H2- calibration depending on the channel used for decoupling. For new

samples the flipback pulses can also be calibrated separately.

(4) After calibration a set of 1D or 2D experiments (NH and CH planes) can be acquired

automatically to see the general feasibility of experiments with a given sample.

Figure 8

It is now straightforward to select any BioPack experiment from the Experiment menu from the

Menu Bar (Fig. 5) and select the number of transients and increments in the indirect dimensions

(Fig. 9) and start the experiment. All the other parameters like pulse widths, powers, delays, and

decoupling conditions are automatically retrieved from the calibrated probe file. Pulses sequence

specific parameters and flags are in the Pulsesequence panel (see Fig. 9).

(1) (2)

(3)

(4)

Figure 9

BioPack installation procedure is described in a separate document – BioPack_Install.

Start here for setting parameters

Set ni,

phase

p

Set ni2,

phase2

p Calibrated Parameters

come from probe file

(HCN)

p