Simple 1D processing in vnmr

From NMR Wiki

Contents 1 Open file 2 Apply simple FT 3 Phase the spectrum 3.1 Autophasing 3.2 Manual phasing 3.3 Fine-tuning phasing 4 Apply baseline correction 5 Reference the spectrum 6 Define plot region 7 Plot spectrum 8 Multi-fid data

Open file

Open file (type in vnmr command line):

rt('file_name')

rt - retrieve, file name does not have to have .fid attached

File must reside in the current working directory.

Apply simple FT

Apply simple processing:

ft f full vsadj

ft - apply Fourier tranform
f - show full 1D spectral window
full - stretch spectrum on full screen
vsadj - adjust vertical scale so that tallest peak fits display window height

Phase the spectrum

Autophasing

Try automatic phasing

aph

List of automatic phasing commands: aph, aph0, aphx. These commands apply different algorithms to calculate values of lp and rp parameters.

All three commands can be tried and seen which one gives better result.

Manual phasing

If autophasing fails, you have to phase manually.

Type ds to switch into the interactive display mode

Move cursor to the left part of spectrum, click and hold left mouse button.

Drag mouse up or down to make peaks in left part appear phased, release left mouse button.

Move cursor to the right part of spectrum click and hold right mouse button.Drag mouse up or down to make whole spectrum well phased.

Now hit Return(the last button in the bottom row)

If you still see huge baseline distortion - it is possible that phase parameters lp(left phase) and rp(right phase) are too large. You can check what they are by typing:

lp?
rp?

Typical values for lp = -180 ... 0; rp = -360 ... 360.

If rp or lp are too large - reset them:

lp=0 rp=0

Then repeat manual phasing procedure shown above.

Fine-tuning phasing

This part is relevant if peaks that you want to look at are less intense then the major peaks in spectrum. If there is a slight misadjustment of phase - baseline around very tall peaks may be still quite distorted - so smaller peaks will appear on tilted or even nonlinear background.

Adjust vs(vertical scale) so that you can see peaks of interest.

One way to do it is to type:

vs=vs*5

Here vs is multiplied by 5 (use other number if you want)

You might want to repeat above multiplication by scrolling up in the command line and pressing 'Enter' until you clearly see the low intensity peaks that need to be phased

Now repeat manual phasing procedure so that baseline around very intense peaks looks symmetric.

Apply baseline correction

To apply baseline correction we need to tell the program which parts of spectrum contain peaks and which ones contain baseline.

First we might need to delete previously defined baseline regiouns by typing cz(clear integration reset points).

Now we'll need to define new reset points. To clearly see what parts of spectrum are baseline and what parts are defined as peaks, we'll need to enter Part Integral integral display mode.

Click buttons in this sequence: Main menu->DispMenu->Interactive

Now push second button from the left (it will be either Full Integral, No Integral or Part Integral)
This button switches between integral display modes. Keep clicking until this button displays Part Intergral and then push it again. Now vnmr should be in 'partial integral display' mode - that is only peak integrals will be shown.

Then push Resets button. In this mode (Part Integral and Resets integral over the baseline regions is shown with dotted line, and integral over the peaks - with continuous line. Now starting with left part of spectrum, click with left mouse button before and after each peak. (remember to go left to right).

Once all reset points are defined, i.e. enough baseline regions are shown to the program - hit Return button.

Finally type

bc

and that should apply baseline correction, baseline regions should be nearly flat.

Reference the spectrum

Find peak that you can use for chemical shift reference. Let's say it is H2O signal at about 4.7 ppm.

Zoom onto the peak to be used as reference: Main menu->DispMenu->Interactive

Now first button on the left in the bottom row will be either Cursor or Box. This button switches between cursor modes. Current cursor mode is displayed on top-right of the vnmr command line window.

Enter Box mode - you will get two cursors.

With left mouse button place left cursor before the reference peak (i.e. on the left of that peak) and place right cursor with right mouse button after the reference peak (on it's right), then hit Expand button.

Now vnmr zooms to the peak. If it is too small - adjust the vertical scale.E.g. by typing vsadj(adjust vertical scale automatically) or by typing vs=vs*2 or vs=vs/2 (you can use any other number too) until peak clearly shows.

In Cursor mode, click on the center of reference peak. After this you can have software to place cursor exactly on peak center by typing nl(nearest line)

Now (when cursor is put on peak center) click Ref button.
You will be promted:

New reference value (in ppm)?

Enter correct value and press 'Enter'

Define plot region

To precisely define the display region (let's say 6-16 ppm) type:

sp=6p wp=10p

sp(start of plot), 6p means 6 ppm, wp(width of plot)

Adjust vertical scale as desired.

Plot spectrum

There are many commands that plot various types of information on the spectrum.

The the following simple command plots line pl, scale pscale on the system printer:

pl pscale page

Command page sends plot to the printer.

Command below creates postscript file 'test.ps' in current directory:

pl pscale page('test.ps')

Multi-fid data

Spectra in arrays iterate from 1 not 0.

(D)isplay (A)rray data

da

(D)isplay (S)tacked (S)pectrum (H)orizontaly spectrum x-y

dssh(x,y)