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2D

 

NUTS Help

Working with 2D data

This section describes the processing and display of 2D data.   Topics and commands covered:

Quick intensity plots and contour plots
Setting the chemical shift reference
Setting contour levels
Setting colors for contour levels
Turning on/off gridlines
Selecting individual slices for display
Viewing slices
Summing slices
Creating projections
Placing projections or 1D spectra along the edges of a contour plot
Making 2D plots come out square
Stacked plots
Symmetrize
Tilt
Transpose data
Save
Substitute one slice for another
Zero diagonal
Processing TPPI, hypercomplex and echo-antiecho data

See also:

Arrayed Mode processing with NUTS Professional version
Processing 2D data — step-by-step processing descriptions for different types of 2D data
Examples of 2D spectra using codeine
Sample macros
Sample data files
Displaying 2D data
Displaying horizontal and vertical lines on a contour plot, to aid in interpretation
Setting chemical shift reference
Editing 2D data
comparing multiple 2D spectra
2D nomenclature

Macros have been supplied which perform the basic types of 2D processing (magnitude, TPPI and hypercomplex).  These macros simply string together linked command sequences (Links) so that the entire processing can be performed with a single command. The user should have a basic understanding of the commands in the Links and the macros because some parameters vary from experiment to experiment or with different spectrometers. The macros have comments and, combined with the explanation below, should contain sufficient information.

IP — Intensity Plot

If the currently displayed data is a 2D data set, this command displays the data as a two dimensional intensity map. NUTS can also draw contour plots (CP), which look nicer, but take longer to display. The intensity plot is faster because its speed is limited by the graphics display process, while the contour plot is calculation-limited. The intensity map is recommended for initial viewing of the data, determining the levels to be displayed, setting shift references and Zoom frequency limits, etc., leaving the contour plot for the final display, for viewing details and plotting. Show me how to display 2D data.

The SS (set 2D scale) command should be executed before IP or CP so that the scale is reasonable for an initial display.

The levels of data represented by the different contour levels are determined as multiples of the MH parameter.  For versions compiled after Dec, 2001, the contour threshold can be changed interactively in several ways.  The coarsest adjustment is made using the scroll bar along the right edge of the screen.  Page Up and Page Down keys, Arrow Up and Arrow Down keys and the “<” and “>” keys apply finer adjustments.

The MH value can also be set explicitly.  To lower the first contour level to be displayed, type MH and set it to a smaller value.

The number of levels, the MH multiplier for each level and the color for each level are set in the NUTS.INI file.  The maximum number of levels is 10.  The multiplier for each level can be set while NUTS is running using the LV command.   Contour level colors can be changed from within NUTS using the CR command.  Changes made using LV and CR are not saved for future NUTS sessions.  To make the changes persistent, edit the nuts.ini file.

NUTS provides the option of displaying horizontal and/or vertical projections or a 1D spectrum along each axis.  These options are available from the Borders menu or by using the proj command.   See illustration.

By default, both positive and negative contour levels are displayed. The user can switch to just positive by typing C+ (plus) or to just negative levels by typing C- (minus). To display both, type C0 (zero).  (In versions of NUTS older than Sept, 2001, this is done with the single-letter commands +, – and 0, respectively.)  The colors for each level are set separately in the NUTS.INI file, or can be set within NUTS with the CR command.

The intensity map or contour plot can be interrupted before finishing drawing by typing <escape>. This command halts the Windows screen paint operation, allowing the user to change parameters such as frequency limits or minimum height, or to plot the spectrum, without having to wait for the 2D display to be completed. The mouse can be used to define a Zoom region even though the screen paint operation is incomplete, because NUTS “knows” where the peaks are. Once the parameter change is completed, the screen paint is re-started.

CP — Contour Plot

If data set A is a 2D data set, this command displays the current data as a two dimensional contour plot. This is a nicer display than the intensity plot, but takes longer to draw. The intensity plot is recommended for initial viewing of the data, determining the levels to be displayed, setting shift references and Zoom frequency limits, etc., leaving the contour plot for the final display for viewing details and plotting. The colors and contour level spacing are set in the NUTS.INI file and cannot be changed after NUTS is started. See description of the NUTS.INI file for explanation of how these parameters are set.

C+, C- and C0 — Display positive, negative or all contour levels

By default, both positive and negative contour levels are displayed. The user can switch to just positive by typing C+ (plus) or to just negative levels by typing C- (minus). To display both, type C0 (zero).

Setting the chemical shift reference

The coordinates of a peak in the 2D plot can be displayed by holding down the left mouse button, just as for 1D spectra. The cursor location is given in the lower right corner of the screen. The slice number and shift value in Hz and PPM is given for the vertical (2nd) dimension. The point number and shift value in Hz and PPM is given for the horizontal (1st) dimension. While holding down the left mouse button, typing O brings up a dialog box allowing the user to set the offset (chemical shift reference) in both dimensions.

Note that the 2 checkboxes on the right should not be checked when working with 2D plots.

Because of the poor digital resolution of most 2D data, and the fact that NUTS will read the cursor location as the nearest actual data point, setting chemical shift reference with the cursor will often result in the crosspeaks not lining up with the high resolution 1D spectra placed along the edges of the contour plot.  The easiest way to fix this is to adjust the Offset parameters explicitly.  The “offset” in each dimension is defined as the number of Hz from the center of the spectrum to 0 ppm.  Using the cursor, you can determine the frequency difference, in Hz, between the crosspeak and the corresponding peak in the 1D “border” spectrum, best measured using an expanded display.  Bring up the parameters dialog box by typing O1 (for horizontal dimension) or O2 (for vertical dimension).  Change the appropriate offset parameter by the measured difference.  If it is determined that the values of these corrections are always the same, this process can be automated using a macro.  See example.

After 2D parameters have been changed, use the UH (Update Header) command to save the changes.  (Caution:  When processing in Arrayed Mode, the UH command should NOT be used if any processing has been performed since the data set was saved, as the updated header will be written to the original file, and parameters may not be compatible.)

While holding down the left mouse button, press and hold the right mouse button. The slice corresponding to the cursor location is displayed. As the mouse is moved vertically, the slice is updated in real time. The Page Up and Page Down keys can be used to scale the slices. Users with a single-button mouse can press the period key in place of the right mouse button.

Two dimensional Zoom works in the same way as for 1D spectra. Typing ZO or double clicking the left mouse button enters the Zoom routine, indicated by the cursor changing to a small crosshair labeled “ZO”. Hold down the left mouse button and drag the mouse to highlight a region for expansion. Typing control-E or clicking the right mouse button jumps to expanded display of this region. Control-F and control-E toggle between fill and expanded display, as does clicking the right mouse button. Typing <Enter> exits the Zoom routine.

Exit the 2D display mode by typing 1D(In versions older than Sept, 2001, 2D display is exited by typing <ENTER>.)

Outside of the 2D display mode, individual slices can be displayed by specifying the slice number with SL, and the View (VW) command allows stepping through slices. To view slices in the second dimension requires that the data set first be transposed with the TD command so that the dimension of interest becomes the horizontal dimension.

2D Peak Picking and 2D Volume Integration are performed within the Define Peaks (DP) subroutine.

LV — Set contour levels

This command allows the multiplier for each level to be set while NUTS is running.   These changes are not saved when NUTS is closed.  Permanent changes must be made in the nuts.ini file, along with the number of levels and the color for each level.  Note that the maximum number of levels is 10.   See also 2D display.

CR — Set contour colors

This command allows the color for each level to be set while NUTS is running.   Colors are set as numerical Red, Green and Blue values.  See Setting Colors.  Changes made with CR are not saved when NUTS is closed.  Permanent changes must be made in the nuts.ini file, along with the level multipliers for each level.

Ctrl-G — Toggle on/off display of grid lines

This command will display gridlines on an intensity or contour plot.  The command is a toggle, so entering it a second time will remove the gridlines.  The lines are drawn at the position of the major tick marks on the axis, and cannot be moved or their spacing changed by the user.  Users who want gridlines displayed always can add a line to the nuts.ini file which is
GRIDLINES = TRUE
which makes display of gridlines the default condition.  (Gridlines are shown on 1D data as well, but this is probably not very useful.)

SS — Set 2D data Scale

Examines all slices of a 2D data set and sets the automatic scaling factor which is used in commands such as View data (VW), stacked plots (SP), intensity plots (IP) and contour plots (CP). SS should be performed before attempting to display 2D data to get reasonable scaling. This command also identifies the largest positive and negative peaks in the data set and sets their difference to 100%. This value is then the basis for the Minimum Height (MH) parameter, which is used to set the scale for 2D Intensity Plots (IP).

SL — Set Slice

This commands allows the user to select which slice of a 2D data set will be available for processing. When a 2D data set is read by NUTS, the first slice is displayed and is available for data processing. The user should avoid saving a slice as a file under the same name as the 2D file (Save command from menu or SA command ) as the 1D file will replace the 2D data set. Use the Save As menu command or SB keyboard command to save the processed 1D file under a different name.

VW — View 2D data slices

Steps through slices of a 2D data set. Set starting slice with SL.  While in Arrayed Mode and in the View routine, subcommand Z will zero all data points in the currently displayed slice.

To view a series of 1D files, they must first be converted to a 2D file.   See description under Stacked Plot command.

Subcommands:

I or N – Increment to next slice
D or R– Decrement to previous slice
Z – Zero the displayed slice.
<Enter> – exit VW

SU or sum — Sum slices

Sums a specified range of slices of a 2D data set.  By default, all slices are summed.  If executed in the “non-2-letter” command mode, it is possible to specify a subset of slices.  The command takes 2 arguments, which are the first and last slices to be included in the sum.  For example, this command would sum slices 5 through 20, inclusive:

sum 5 20

Note that the sum becomes the current data (1D) set.  If in arrayed mode, save the data before performing the sum.  See sample macros.

It is possible to add two 2D files by running a link such as

ga b1 gb b2 b+ sc in

Note this is NOT done in the arrayed mode.  The link will ask for the names of the 2 data sets to be added, and for a name to use for the resulting sum.  See commands b1, b2 and b+ for details.

Similarly, one 2D data set could be subtracted from the other – just change the b+ command in this link to b-.

SUM — Sum planes

The sum command can also be used for summing of planes in a 3D data set in a manner analogous to summing slices of 2D data. When the second argument of the “sum” command is “planes”, all planes of a 3D data set are summed into a single 2D data set. The command also takes additional optional arguments allowing the user to specify the starting and ending planes to sum. The original 3D data set is destroyed and replaced by a new 3D data set which has only one plane. The command must be used in the 3D arrayed mode.

sum planes <start> <end>

PJ — Projection

Calculate the “skyline” projection of the current 2D data set along the horizontal axis. The projection consists of the largest value in the 2D data set at each data point. When the procedure is complete, the projection is displayed as a 1D file which can be saved with SA. To return to the 2D data set, it must be reopened with GA.

A projection can be created from a subset of the entire data set by first expanding the displayed region using Zoom. The desired limits can be entered using the F subcommand within Zoom or using the mouse. Use Ctrl-E to display the expanded region. PJ will create a projection of the displayed region.

Placing projections on contour plots

NUTS provides the option of displaying a horizontal and/or vertical projection along any side of a 2D intensity or contour map. These projections are automatically scaled such that the tallest peak in the displayed region is set to a height of one-tenth of the total display size. Display of projections along the Top, Right, Bottom and Left sides of the plot are toggled on/off with the  commands P1, P2, P3 and P4, respectively. (Note that in versions of NUTS older than Sept, 2001, this is done with the single-letter commands 1, 2, 3 and 4.)  These commands are also available from the Borders menu, or from the command line (see below).

The projections can be scaled independently with the EP command or by choosing Edit Display Parameters from the Edit menu, which allows a scaling factor to be entered for each projection.  (Note that this same dialog box allows margins to be set for each side of the 2D plot.  Values are entered as fraction of total display.)  Each projection can also be clipped, allowing the vertical scale to be increased to show small peaks while limiting the height of larger peaks.  This option is available from the Display menu. As always, what is displayed on the screen is what will be plotted.

Using high resolution spectra as projections

It is often preferable to use a high resolution 1D spectrum instead of the actual projections due to the better digital resolution.  The 1D spectrum must already exist, saved to disk, and must have been processed.  The file is selected from the Borders menu.  The 1D file need not have exactly the same spectral window as the 2D plot. The appropriate region will be displayed, based on the chemical shift scale.

Scaling and clipping are performed in the same manner as for actual projections, described above.

Once a 1D file has been selected in this manner for use as a projection, the commands P1, P2, P3 and P4, respectively will toggle on/off display of the projection on top, right, bottom and left sides of the plot. (Note that in versions of NUTS older than Sept, 2001, this is done with the single-letter commands 1, 2, 3 and 4.)  If it is desired to display instead the actual projection, rather than a separate spectrum, the file must be removed from this projection “buffer” with the XC command.

These can also be defined from the command line or in a macro.

PROJ (or PROJECTION) – specify projection file and position

This non-2-letter command allows display of projections on the edges of contour plots to be turned on and off, and also allows a file to be specified for use as each projection.  The command takes 2 or 3 arguments. The first argument defines which side projection is the focus of the command.  Allowed 1st arguments are:

Top Projection

-1
-top
-t

Right projection

-2
-right
-r

Bottom projection

-3
-bottom
-b

Left projection

-4
-left
-l

The second required argument determines whether or not the specified projection is shown:

-on
-off

A third optional argument defines a file name to use for the specified side projection spectrum.

XC — Clear projections

Removes any file which has been defined for use as a projection on the edges of a 2D plot.

SQUARE2D — Force plots to be square

This command allows the user or a macro to turn on the forcing of square 2D plots. When used without arguments, it toggles the current value of the variable to force printing of square 2D plots.
The command also accepts two possible arguments:
square2d on
square2d off

SP — Stacked Plot

Plots slices of a 2D data set on the screen. A series of 1D spectra can be plotted if they are first stored as a 2D file (see instructions).

Before executing SP, read in the first slice of the 2D file with GA and use SS to set the scaling. The entire plot can be scaled vertically in the same ways as 1D spectra. The vertical scale can also be set by typing A or from the Display menu, which brings up the Amplitude Change dialog box (same as AC command). Press Enter to exit from the stacked plot.

Show me how to use SP.

When SP is executed, a new set of menu choices is displayed. Under the Display menu is an option to whitewash the stacked plot. The command is a toggle, so executing it a second time undoes the whitewash. Equivalently, whitewash can be toggled by typing W. Depending on the type of data, whitewashing may or may not be desirable. The whitewashed spectrum contains many more “draw” operations, so will take longer to draw on the screen and to plot. In most cases, a whitewashed plot is too large to copy as a metafile to other applications, and it must be copied as a bitmap instead. (See copying spectra for further information).

The offsets in both x and y dimensions can be changed by typing O or choosing Offset from the Display menu. The X-offset can be changed from 0 to 100% and the Y-offset from 1 to 10. These offsets can also be set in the Nuts.ini file, so that the user’s preference is always set as the default.

Because drawing the stacked plot can be slow, the draw operation can be terminated by typing Q.

A subset of the entire data set can be plotted by using 2D Zoom from an intensity plot (IP) or contour plot (CP) to select a region to be plotted. From the 1D display of a slice, type ZO to enter Zoom, then F to bring up the dialog which allows setting of frequency limits for expansion. The limits must be set in both dimensions by points, Hz or PPM. Failure to set the limits in the vertical dimension will result in only 2 slices being displayed. Click OK to close the dialog box. Type Ctrl-E to expand to the limits you have set. Now typing SP will display a stacked plot of the selected region. To plot the entire spectrum, first type Ctrl-F to select the full display.

Note that it is necessary to explicitly set values for the first and last slice to be displayed, followed by Ctrl-E, and that this operation needs to be repeated if the horizontal expansion is changed. Failure to do this will cause NUTS to display only 2 slices.

Once the stacked plot is displayed on the screen, it can be plotted with PL.

SY — Symmetrize 2D data set

This is applied to symmetrical homonuclear 2D data, such as COSY experiments, in which the data are ideally symmetrical about the diagonal, f1=f2. Symmetrization is used to remove artifacts from the 2D spectrum to improve its appearance. Noise and other artifacts which do not occur symmetrically on both sides of the diagonal are eliminated. The data set must be square (that is, the same number of points in both dimensions).

The SY command examines the entire 2D data set, comparing each point to its symmetrically related partner across the diagonal. Then both of these points are replaced by the smaller (absolute value) of the 2 points.

This process can take a minute or more, depending on the size of the data set. It also involves multiple TD operations, saving temporary files in the process, so there must be sufficient disk space available.

The SY command can be used to symmetrize J-resolved data about the horizontal axis, with the command

SY tilted

This should be done after tilting.

Ref: R.Bauman, G.Wider, R.R.Ernst and K.Wuthrich, J.Magn.Reson., 44, 402-406, 1981.

TD — Transpose Data

This command is available only in the 2D and Pro versions of NUTS. The TD command swaps the 1st and 2nd dimensions and their associated parameters.   See also: processing 3D data.

SC — Save dataset C

Used in macros or links.  This command asks for a new file name for File C and saves the current data to File C as the first slice of a 2D data set. Subsequent SC commands save the current data set to File C as successive slices of a 2D data set. When this command is used in a Link (the preferable method), File C is closed when the link finishes. When this command is used manually, the operator must use the Close File C ( CC ) command when finished writing to file C. An opened File C will be closed automatically when the NUTS program is exited.

When used in a Link, the SC command asks for the name for File C on the first pass only. On each additional pass through the link, the SC command saves the current data set to the already opened File C as the next slice.

UH — Update Header

Writes parameters into the header of a 2D file. This should be executed after parameters have been changed to insure the changes are saved with the file. For example, after setting the chemical shift reference or after editing the variable delay list for relaxation data, UH will save the changes.

Caution:  When processing in Arrayed Mode, the UH command should NOT be used if any processing has been performed since the data set was saved, as the updated header will be written to the original file, and parameters may not be compatible.

S2 — Save 2D data set  (Used in non-arrayed mode only)

This command can only be executed when the current data file A is a 2D data set. A dialog box prompts for a file name. The command functions differently depending on whether a new file name is supplied or the current file name is chosen. If a file name different from the current file A name is entered, the entire 2D data set is copied into the new file exactly as it currently exists on disk and the new file becomes data file A. If the file name supplied is the same as the current file name, the entire 2D data set is saved as it currently exists on disk EXCEPT for the currently displayed slice, which is saved as it is currently displayed. This allows modifications on individual slices to be saved permanently.

One situation for which this is useful is for touch-up phasing of a series of kinetics or relaxation data following automated processing. The 1D spectra must first be converted into a 2D data set.

Another use is when one slice of a 2D data set gets corrupted. A simple way to “fudge” the data so that it can be displayed without artifacts is to overwrite the corrupted slice with its neighboring slice, since adjacent slices should be similar. Let’s assume that slice 10 is corrupted and we will replace it with a copy of slice 11. To do this, display slice 11 and place it in the Add / Subtract buffer by typing AL. Be sure that the Add / Subtract multiplier (AM) is set to 1, its default value. Next, display slice 10 and zero the entire slice by typing ZE. Then type AS, + and <Enter> to add the contents of the Add / Subtract buffer ( which is slice 11 ). Slices 10 and 11 are now identical. With the modified slice 10 displayed, use the S2 command to save the modification, specifying the file name to be the same as the current file name. This entire procedure must be repeated for each slice which needs to be modified, because the S2 command updates only the currently displayed slice.

In arrayed mode, simply use SA (or File/Save) to save the file.

Substitute — Slice substitution (Arrayed Mode only)

This command allows one slice of data to be copied over (replace) another slice.  This is useful when a slice has been corrupted.  Note that this requires NUTS to be placed into the “non-2-letter” command mode (with 2F).

For 2D data,

substitute  target_slice   source_slice

For 3D data, it is possible to perform this slice substitution either for a single plane of the 3D data, or for all planes.  To operate on a single plane, the plane is specified as the first argument:

substitute  plane   target_slice   source_slice

If the substitute command has just two arguments, then all planes of a 3D data set will have the source_slice copied to the target_slice.

ZeroDiagonal 

A non-two-letter command which takes either one or two arguments.  This is used with homonuclear 2D data to eliminate (zero out) all data points including and around the large diagonal peak.

If only one argument is given, then the command takes a 2D data set and zeros the diagonal over a range which is plus and minus the number of points specified by the argument.  If two arguments are given, then the 2D data set’s diagonal is zeroed plus the first argument number of points and minus the second argument number of points. Usage:

ZeroDiagonal [+ points] [-points]

See also: Removing the dispersion component of a residual solvent peak.

TL (or Tilt) — Tilt of 2D data (arrayed mode only)

TL (or Tilt) is used to rotate a 2D data set, such as J-resolved data.

The default rotation is a counter-clockwise rotation of 45 degrees, based on Hz, so NUTS first calculates the Hz/point in both dimensions.

In the non-2-letter command mode, arguments can be supplied to apply the tilt differently.

An argument of C or CC is used to define the direction of the tilt to be clockwise or counter-clockwise, respectively.

An second argument is taken as the number of points to tilt per slice (fractional points allowed).

If the TILT command is given with an argument which is not C or CC then the argument is taken as the number of points to tilt per slice (fractional points allowed) and the tilt will by default be in the counter-clockwise direction.

For example,

tilt c 0.1

would rotate clockwise 1 data point every 10th slice.

An invalid first argument is used as the number of points to shift and any second argument is ignored. The center slice (slice number_of_slices divided by 2) is taken as the center and is left unshifted.

The SY command can be used to symmetrize J-resolved data about the horizontal axis, with the command

SY tilted

This should be done after tilting.

TPPI — Time Proportional Phase Incrementation

TPPI is a method for achieving quadrature detection (distinguishing positive and negative frequencies) in the indirect dimension of a 2D experiment. This allows data to be acquired as phase sensitive.

Processing TPPI data requires a Real Fourier transform (as opposed to the normal complex FT).

A detailed explanation of a macro for processing TPPI data is available.

Hypercomplex 2D data

(method of States, et. al. )

An example of processing hypercomplex data is available, including step-by-step explanation, and sample macros.

The alternative to TPPI for obtaining phase-sensitive 2D data is to acquire 2 FIDs (with a 90 degree phase shift; ie., a quadrature pair) for each t1 point. After FT of each FID in the first (t2) dimension, the imaginary part of each is discarded and the real parts are combined to form real and imaginary halves, and a complex FT is performed in the second (t1) dimension.

NUTS uses the commands TR and TI (“tag” real and imaginary halves, respectively) to select which half of the data will be saved. (Usually, only TR will be used to save the real half of each spectrum. However, the TI command is provided in case the need arises to save the imaginary half. This could be the case depending on how the phase cycling was done in the experiment.) These commands are followed by the command ST ( save “tagged” data) instead of the usual SC command. This is done in processing the first (t2) dimension only. The Link for the first dimension processing then looks like

GA BC EM FT PS TR IA GA BC EM FT PS TR ST IN

The first time TR (or TI) is encountered, the selected part becomes the real half of the final complex pair. The second time one of these commands is encountered, the selected part becomes the imaginary half of the complex pair. The ST command then saves the data as a complex interferogram in t1. The IA ( Increment counter for file A ) command must be included before reading in the second FID.

The above Link is appropriate for data which have been saved as a single file, with the pairs of FIDs occurring sequentially. Some spectrometers save the 2 halves of the data as 2 separate files. For this case, the Link for processing in the first dimension must be modified as follows:

GA BC EM FT PS BC TR GB BC EM FT PS BC TR ST IN

so that slices are read alternately from the 2 different files, designated as A and B.  Or, use the interleave command to form a single file.

The second dimension processing is normal, using FT to perform a complex transform. If phasing is needed in the second dimension, PS can be included in the link or performed after, using a link such as

GA PS SC IN

performed after the appropriate phasing parameters are determined.

Interleave  (Arrayed Mode only)

This is a non-2-letter command which interleaves two data sets into a new data set. This is used for hypercomplex data that was saved on the spectrometer as 2 separate files, creating a single file containing all the data.  This command works only for the Complex Arrayed Mode. The two data sets must have the same number of points and slices. The resulting data set is not automatically saved.  Syntax:

Interleave FileName1 FileName2

TR — Tag Reals

Used in processing hypercomplex (States type) 2D data.

The TR command is used to discard the imaginary half of each pair of spectra acquired for a given t1 value. The real halves are then used to construct a complex t1 interferogram. The ST command then stores the interferogram as complex data ready to be processed with a complex FT in the t1 dimension.

For complete description and examples of use, see hypercomplex (States type) 2D data.

TI — Tag Imaginaries

Selects the Imaginary half of the data to be saved and discards the Real half. Intended for use in processing hypercomplex ( States type ) 2D data. (N.B. Normally, the TR (Tag Reals) command is used, but TI is provided to give the user maximum flexibility in data processing.)

ST — Store Tagged data

Used in conjunction with the TR (tag reals) (or TI (tag imaginaries)) command to process hypercomplex (States type) 2D data. The TR command is used to construct a complex t1 interferogram. The ST command then stores the interferogram as complex data ready to be processed with a complex FT in the t1 dimension.

For a complete description and example of use, see hypercomplex (States type) 2D data.

The next 4 commands work only in Arrayed Mode, and on data sets having an even number of slices.  These commands facilitate processing of echo-antiecho gradient data which must be processed by adding or subtracting pairs of slices. (An example is Varian g_hsqc data, which uses the C2 command.)  Each command operates on a pair of slices, n and n+1.  The real halves of the 2 slices are either added or subtracted, and the sum becomes the real half of a single processed slice.  The imaginary halves of the 2 slices are either added or subtracted, and the sum becomes the imaginary half of the processed slice.  So, in each case, the processed data has half as many slices as it started out with.

Echo-antiecho 2D data

These phase-sensitive gradient experiments are run such that each slice contains both sine and cosine terms in t1.  To process these data, we FT and phase slice 1 and slice 2, then calculate the sum and the difference of them. Because the 2 slices are, respectively, (cos t1 + isin t1) and (cos t1isin t1), the sum gives you just cosine, and the difference gives you just sine.  Together, they comprise a complex “FID” in the indirect dimension.

This add/subtract process is handled with command C2 which works in Arrayed Mode only, but can be accomplished in non-arrayed mode using a combination of commands.  See details.

C1 — Combine Mode #1

This command adds the reals and imaginaries of even and odd slices and gives back a data set with half the number of slices.

C2 — Combine Mode #2

This command adds the reals and subtracts the imaginaries of even and odd slices and gives back a data set with half the number of slices.  Used in processing echo-antiecho data.

C3 — Combine Mode #3

This command subtracts the reals and adds the imaginaries of even and odd slices and gives back a data set with half the number of slices.

C4 — Combine Mode #4

This command subtracts the reals and subtracts the imaginaries of even and odd slices and gives back a data set with half the number of slices.

GC — Get data set C

Opens the dialog box for loading a file. The last name used for File C, if any, will be the default selected name. Data set C is used in 2D processing.  This is rarely used, as GA is “smart” enough to detect when the file is 2D.

OC — Open file C

(rarely used)  This command allows the user to open a 2D file and move to the last slice of data. Further Save to file C ( SC ) commands add the currently displayed data set to the end of file C. When finished the user should close file C with the CC command.

The better way to accomplish the same thing is with a Link which contains SC and IN commands, and automatically takes care of opening and closing the 2D file.

CC — Close file C

(rarely used)  If a File C has been opened for writing data into, this command closes File C. This could be used to manually combine 1D files into a 2D data set, but this is more easily performed with a Link such as GA SC IN. When using such a Link, the IN command takes care of closing File C when the complete 2D data set has been processed.

 

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Last updated: 3/6/06.