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PHASING

PHASING

NUTS Help

Phasing Overview

NUTS offers several different tools for phasing, including automatic phasing routines that use Simplex optimization, phasing of the entire spectrum using the mouse, phasing using an expanded display of 2 spectral regions and applying specific numerical phase values.  

Follow the "Show Me" links to see a step-by-step illustration of the phasing commands, illustrated with screen captures.  

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 with PC.
PB Phase B. Input first-order phase correction to be applied with PC.
PC Phase Correction. Adjusts the phase of spectrum by the values in PA and PB.
PI Incremented phase. Applies phasing equal to PA and PB multiplied by the slice number.
PE Phasing Expanded. Mouse phasing routine using 2 expanded regions.
PH Phasing using mouse. Left & right mouse buttons control A and B phase parameters.
PS Phase Same. Applies previously determined phase correction to the current spectrum.
TP Total Phase. Displays values of phase correction which have been applied.
ZP Zero Phase. Sets both zero- and first-order phases to zero.

See also: Phasing 2D data, Auto-phase details 

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 or PE 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. (If that happens, use ZP to reset the phase and start over.)

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).

Users who prefer up/down mouse movements to left/right mouse movements can select this in the NUTS.ini file.

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 using PS, which applies the previously determined phase parameters.

The auto-phase routines were re-written and improved in March, 2003.  See details.

PH – Mouse phasing — The spectrum phase can also be adjusted using the mouse. The user can start the mouse phasing routine from the menu selection Process / Phasing by Mouse or with the PH command. This is usually applied to the entire spectrum at once, but can be used on an expanded region if that is the current display when the PH routine is entered.

On entering the phasing routine a "reduced data point" display of the data will be shown to make screen updates faster. 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.

By default, the phasing pivot point for the B correction is the left end of the spectrum display. However, the user can choose a different pivot point.  This can be done before entering the PH routine, or while in the PH routine. From the Nuts base level, hold down the left mouse button, place the cursor where the pivot point should be, and type P. While in the PH routine, place the cursor at the chosen pivot position, and (without pressing a mouse button) type P.  

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.

The coarseness of the mouse adjustment of phase can be reduced by 3x by holding down the Control key while phasing.  A default setting can also be made in the nuts.ini file.

Show me how to use PH.

The PH routine was modified to allow a second-order correction to be applied.  When second-order phase correction is applied, the pivot point is always the far left edge of the spectrum, for simplicity.  To use this, type 2 on the keyboard while in the PH routine.  Any mouse movement will result in application of second-order correction – Use Caution!  Pressing either mouse button returns to the normal mode of applying zero- and first-order correction.  

The values of zero-, first- and second-order correction are shown at the left edge of the screen during phasing.

PE -Phasing expanded regions — The spectrum phase can also be adjusted with the Phase Expanded (PE) routine, in which 2 regions of the spectrum are phased in turn. This is usually the best choice of phasing routine for larger data sets, especially to do a "touch-up" after automatic phasing, because it more easily allows careful examination of the phase. (Since the total phase is defined by 2 parameters, determining the correct phase in 2 spectral regions is sufficient to calculate the phase for the entire spectrum. This is similar to Bruker’s and Nicolet/GE’s cursor phasing process.)

To begin, two regions of the spectrum are selected using the Zoom routine. First, display the entire spectrum using Ctrl-F. Then, enter Zoom, select a region by holding down the left mouse button and wiping across the spectrum. Type "1" to select this as region #1.  (Don’t expand the display to the selected region, just hi
ghlight the chosen region and type 1.)  Then select another region and type "2". This defines the 2 regions to be phased.

Now, exit Zoom and enter the Phase Expanded routine with the PE command. Region 1 is displayed first by default. Press and hold the left mouse button and adjust the phase of region 1 with left and right mouse movements.  The pivot point (where linear correction is zero) is automatically set to the tallest peak in region 1.  Adjusting the phase with the left mouse button applies a zero-order correction to the entire spectrum. Then, press and hold the right mouse button and, likewise, adjust the phase of region 2. When both regions are adjusted properly, exit with an <ENTER>. The NUTS program will calculate and apply the proper A and B phase correction to the full spectrum. The selected regions will remain in effect until re-defined, they become invalid, or the NUTS program is exited. Typically, two regions with easy to phase peaks at opposite ends of the spectrum are selected for this operation. In some cases, care needs to be used to keep the B phase correction from getting too large (> 360 degrees) which results in an undulating baseline. You can check this by typing TP (Total Phase).  The B phase parameter should be small, and should definitely NOT exceed 360 degrees.  Should this happen, the Zero Phase (ZP) command can be used to reset the phases to zero so you can start over. 

The coarseness of the mouse adjustment of phase can be reduced by 3x by holding down the Control key while phasing.  A default setting can also be made in the nuts.ini file.

Show me how to use PE.

For a series of spectra acquired with the same spectrometer conditions, the phase correction is usually the same for each. After the phase correction has been determined for one spectrum, use the PS (Phase Same) command to apply the same correction to subsequent spectra. Some minor adjustment may be necessary, which can be done using any of the above methods.

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

Some filters on Varian and JEOL spectrometers create spectra which cannot be phased with only a zero and first order phase correction. The NUTS phasing routines were modified to include a second-order phase correction.  In the non 2-letter command mode, the PC (and PhaseCorrect) command can take 3 arguments. The first argument is the zero order phase amount, the second argument is the first order phase amount and the third argument is the second order phase amount.  This takes practice!

PI Incremented phase — Some solids multidimensional experiments (such as MQ-MAS) require a phase correction which is proportional to t1, rather than being the same for all slices. The PI command applies phasing equal to the values of PA and PB multiplied by the slice number.  PI can be used in the non-2-letter command mode to specify the phase correction on the command line.  If one argument is given, it is used as the A phase value when doing the phase incrementing. If two arguments are given they are used as the A and B phase values when doing the phase incrementing. If three arguments are given they are used as the A, B and C phase values when doing the phase incrementing. 

PI is also used in processing Bruker Sates-TPPI data.  These 2D data require inversion of every other slice, which can be done by setting PA to 180 and applying PI.

The PI command was modified to implement diagonal peak suppression in COSY data (ref: The NMR Newsletter, August, 2000).  If the first argument is "-cosy", the command does a special case of phase incrementing which allows the diagonal of a 2D data set to be phased to the desired addition three arguments as above.

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Last updated: 1/27/08.