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PHASING

Phasing

There are a few different tools for phasing, including automatic phasing routines that use Simplex optimization, phasing of the entire spectrum using the mouse, and applying specific numerical phase values.

Summary of phasing commands:

AP – Auto Phase. Automatically adjusts zero- and first-order phase.
QA – Quick A Phase. Automatically adjusts zero- order phase only.
QP – Quick Phase. Automatically adjusts zero- and first-order phase.
PA – Phase A. Input zero-order phase correction to be applied.
PB – Phase B. Input first-order phase correction to be applied.
PC – Phase C. Input second-order phase correction to be applied.
PHSubroutine for phasing using the mouse. Left & right mouse buttons control A and B phase parameters.
PH2D – Similar to PH, but allows phasing of 2D data while looking at the sum of chosen slices.
PE – Phase in expanded mode; useful for fine-tuning phase correction
PS – Phase using Saved values
phase – Manual phase correction. This command can take the following arguments:

seta n – where n is a numerical value to which the zero-order correction parameter will be set
setb n – where n is a numerical value to which the first-order correction parameter will be set
setc n – where n is a numerical value to which the second-order correction parameter will be set
correct – apply phase correction using the values previously set
The pivot point for correction performed this way is always the far left edge of the spectrum

Often the best first step in phasing is to make initial phase correction using only zero-order correction, until the phase is close to correct. This is most easily done either with QA (automatic phasing, zero-order only) or with PH, using only the left mouse button to apply zero-order correction. Adjust phase until the spectrum has approximately the correct phase, then use PH to make final adjustments. This avoids the possibility of inadvertently entering too large a value for the first order phase correction, resulting in an undulating baseline.

Spectral baselines can be improved and phasing simplified by adjusting data acquisition parameters so that the first-order phase correction needed is close to zero. This is done by adjusting the delay before the first data point is acquired (DE in Nicolet or Bruker software).

Automatic phasing — There are several ways to phase a spectrum with NUTS. The first way is to use the QP (Quick Phase) or AP (Auto Phase) command which adjust the zero- and first-order phase corrections. The 2 commands use slightly different algorithms, and one may work better than the other for any specific spectrum. These routines work well if there is a lot of baseline (no peaks) at the ends of the spectrum, if there is no DC offset for the spectrum and if the baseline is reasonably good. There is also an automatic phasing command (QA) which adjusts the zero-order phase only, which is best used to give a good starting point for additional phasing. If the phase obtained is not perfect using the automatic routines, manual phase adjustment becomes necessary. Automatic phasing does not work very well when the spectrum contains very narrow lines (eg., a 13C spectrum). A simple way around this is to process the spectrum with 3-4 Hz of linebroadening, FT and phase. Then recall the spectrum, reduce the linebroadening, FT and phase manually using the previously determined phase parameters.

PH – Mouse phasing — The spectrum phase can be adjusted using the mouse. The user can start the mouse phasing routine from the menu selection Process / Phasing / Phasing by Mouse or with the PH command.

On entering the phasing routine a “reduced data point” display of the data will be shown to make screen updates faster. The values of 0-, 1st- and 2nd-order phase corrections (A, B and C, respectively) are shown on the left side of the screen, along with the current setting of the pivot point, which by default is the first data point in the spectrum.

The pivot point can be changed while in the PH routine. Hold down the left mouse button, place the cursor where the pivot point should be, and type P.

When the left mouse button is depressed, dragging the mouse left and right adjusts the zero-order (or A) phase of the spectrum.

When the right mouse button is depressed, dragging the mouse left and right adjusts the first-order (or B) phase of the spectrum.

The second-order phase, while usually not needed, can be adjusted using the mouse wheel. Some practice is needed to use this!

Note that the values of zero-, first- and second-order correction are updated during phasing.

When the phase is properly adjusted, the user types the <ENTER> key and the new phase adjustments for the spectrum are applied, and the PH routine is exited. Under some conditions there is a slight difference in the phase for the full data point spectrum and the “reduced data point” display. Repeating the PH command will usually correct the problem.

PH2D – Mouse phasing of 2D data — This operates in the same manner as PH, in terms of mouse buttons and setting of the pivot point. However, instead of displaying the current slice, the sum of selected slices is displayed. The reason for this is that each slice of a 2D spectrum often contains a single peak, so it is not possible to determine 2 phase correction parameters while viewing a single slice.

The command syntax is

ph2d i j <n> <m>

where i, j, n and m are slice numbers. At least 2 slices must be entered; a third and fourth slice number are optional (as indicated by the angle brackets < >).

Slices are most easily selected using the cursor to determine slice numbers associated with chosen slices. It works best to select slices containing peaks near both ends of the spectrum, and perhaps also in the middle.

As with PH, the phase correction determined during this process is applied when <ENTER> is typed to exit the phasing subroutine.

PE – Phase in Expanded mode — Fine adjustment of phase correction parameters may be best done while viewing only a small region of the spectrum. The first step is to select 2 regions of the spectrum, preferably well-separated.

Enter Zoom, use the cursor to select a region, and type 1.

Select a second region, and type 2. Then exit Zoom.

Type PE to begin phasing. Press and hold the left mouse button, and the chosen region 1 is displayed. While still holding down the mouse button, move the mouse left and right to adjust the phase. Release the mouse when the region is phased.

Next, press and hold the right mouse button, and phase the second region in the same manner. Repeat as needed.

When finished, use <ENTER> to exit the PE subroutine.

To apply the correction to only the displayed slice of a 2D spectrum, and not to all slices, use “PE this” to start the phase routine.

 

PS – Phase from Saved values — This allows previously determined phase correction parameters to be applied to subsequent spectra. First, start with a spectrum that is correctly phased, and save the phase parameters with the command “ps save“. To apply this phase correction to subsequent spectra, use the command PS. To apply the correction to only the displayed slice of a 2D spectrum, and not to all slices, use “PS this“.

Specifying numerical phase values — The spectrum phase can also be adjusted manually from the keyboard. The amount of phase correction for the A, B and C phasing parameters (zero-, first- and second-order corrections, respectively; the pivot point is at the far left end of the spectrum) can be entered from the command line, with the PA, PB or PC commands which display the Processing Parameters dialog box or from the View menu. After values for A, B and C phase correction have been entered, the phase correct command will apply those phase corrections each time the command is issued. That is, phase correct adds to any phasing which has already been done. The total amount of phase correction done to the spectrum will be noted in the View / Processing Parameters dialog box and will be saved with the spectrum when the file is saved to disk.


Last updated: 2/16/08.