2D NMR

Index

• The 2D buttons
• PL 2D - 2D plot
• Crop/UCrop - Crop and Un-crop
• CP - Contour Plot
• Phase - 2D Phase
• Integration
• Calibrate
• Processing
• Saving part of the spectrum
  

The 2D buttons

This block of button is made active when a multi dimensional NMR file is loaded.



  Toggle between 1D mode and 2D mode

PL 2D - 2D plot

In this mode (the default mode) the intensity of each points is represented by a colored box. If only positive intensities are plotted, the color scale is from red (low intensity) to blue (high intensity). if only negative intensities are drawn, the color scale is reversed (blue is low intensity and red corresponds to high intensity). When both positive and negative intensities are drawn, the color scale is split in two. The positive intensities range from red to yellow green, and the negative intensities from blue to blue green. Use the  button (positive + negative contour levels) to select positive , or negative  contour levels. The spectrum has to re-plotted after a change in level-mode.


 
 

Standard 2D plot with super imposed 1D track.
 

With the    and    buttons, the lowest level can be selected. Down always means 'go to zero'. Thus the lowest level is always given as an absolute value.

For 3D files, one can use the plane up  and plane down  to go one plane up or down. The buttons and , are for undoing and redoing the selection of a plane.
 

With the  option of the mouse, one can select specific 1D spectra from the 2D spectrum. The row or column that has been selected is indicated by a dotted line, and the 1D spectrum is plotted on top of the 2D spectrum. There are three selection modes. With , rows (spectra parallel to the X axis) are selected. With  , columns (spectra parallel to the Y axis) are selected, and with  , both rows and columns are selected . With the  buttons, one can select the next or the previous 1D spectrum.  are the Undo and Redo buttons for the record section. 'Undo' button, one can undo the previous 1D spectrum selection. With the 'Redo' button, the spectrum is selected again.

Select Sum rows/columns



To select an accumulation of rows or columns, use the  Mouse Option. When the left mouse button is pressed, it indicates the first of the rows (or columns) and when the left mouse botton is released, this marks the last row (or column). The rows (or columns) are now accumulated, and displayed as one track. The first and last row (or column) are both marked with a dotted line.

Crop/UCrop - Crop and Un-crop

When a part of the spectrum is enlarged with the zoom option, the total spectrum is still kept in memory. This enables the scrolling and panning through the spectrum. However, the resolution (in channels/colored boxes) is still the same. This means that the appearance of the spectrum get worse when a larger zoom factor is used. With the  option, the selected part of the spectrum is made the whole spectrum, and the resolution improves. The highest resolution is reached when 1 colored box corresponds to 1 channel. With  (un-crop), the spectrum is reset to is maximum size.


Part of the spectrum before crop -> after crop.

CP - Contour Plot

This  CP = 'Coutour Plot' button option renders the spectrum as a contour plot, or uses the colored block representation, depending on the position of th CPM = 'Contour Plot Mode' button.  = Colored blocks,  = Contour Plot, and  = Contour Plot without skipping channels, no matter the X-and Y increment values..



Contour plot with super imposed 1D track. The contour parameters can be modified with the contour parameter popup, that can be activated via the menu items 'Param' -> 'Contour Parameters'. The first part enables you to do manually, what the 'crop' option does interactively. It selects which part of the spectrum to display. With the X and Y increment, channels can be skipped for faster contouring. An increment of 1 means, use all channels, 2 means skip one channel out of two, etc.



The rest of the options define the contour levels.

• Level mode:
• Explicit- Explicitly define each level. If this option is selected, the user is asked to specify these levels, when the contour parameter popup is closed.
• Use factor - Use the factor given in the 'Factor for Use factor mode' box. The next level is computed by 'factor * previous level', starting at the lowest level.
• Equidistant - Use the distance given in the 'Distance for Equidistant mode' box. The next level is computed by 'distance + previous level', starting at the lowest level.
• Log-range - Calculate a range of levels, positioned at a logarithmic distance, from the lowest level to the level specified in 'Highest level for Log-range mode'.
• Level colors:
• All levels same color - One color mode.
• Pos/Neg levels - Two color mode. Plot the positive and negative levels each in their own color.
• Automatic - Assign each level its own color.
• Show levels :
• Positive - Calculate only positive levels.
• Positive and negative - Calculate positive and negative levels.
• Negative - Calculate only negative levels.
• Number of levels: The number of levels to calculate. When 'Show levels' is 'Positive and negative' half of this number is drawn positive and the other half negative.


 

Phase - 2D Phase

The button enters the 2D phase mode. The screen shows four regions. Region one is the original 2D spectrum, and the other three are initially empty, but are intended towill contain 1D spectra that are simultaneously submitted to the phase procedure.


Screen split up in 2D phase mode. Three of the regions have a green border, and one has a red border.  This last one is connected to the scroll bars when the zoom options is active.



To place spectra into the three 1D regions, one first has to select appropriate spectra. This is done by using the bookmark option.



After three spectra have been selected, select one of those and press one of the 'Add to PhaseBlock' buttons. When the first spectrum is added, a number of options can be set.


 

• Pre-run AU command on data - The first option asks if the AU command should be run on each spectrum. This can be useful if unprocessed data is loaded. For example, a Window and a Fourier transformation can be performed before spectra are loaded.
• Reset phase parameters - This option asks if the phase parameters should be reset. The answer is yes, unless previous phase parameters are applied with the AU command..
• Use Hilbert transformation - Use this option if there are only real data (imaginary data are zero). This option will restore the imaginary points, using a Hilbert transformation.

After the 1D spectra are loaded into the regions, one can zoom in on the most interesting parts of the spectra. When the zoom option is active, the appropriate viewports (=regions) are activated automatically. One does not have to use the 'Select viewport' buttons. After this, use the normal phase procedures. All spectra will be phased simultaneously. When done, press the 'Phase' button again, and you are back in the normal 2D mode.

Integration

Script: <result> = integral ( <left> , <right> { , <bottom> , <top> } )

When the 'Integrate' option of the mouse-popup is selected, the cursor can be used to select a region (peak) that will be integrated. Alternatively, the peakpick routine can be used. However, this routine only selects non-overlapping peaks, or sees overlapping peaks as one peak. There are tree integration modes.  In the first mode  (box mode) a green box marks the area that is integrated. In the second mode, floodfill mode, the whole area inside the lowest contour line is integrated. The last mode (convex floodfill) is an extension of the floodfill mode. All dents and holes in the area, marked by floodfill, are filled.
 



Box integration. The whole area inside the box will be integrated.



Flood-fill integration. Only the area inside the closed contour lines (marked with green squares) will be integrated.



Convex flood-fill integration. Same as flood-fill integration, only the integration area is made convex (Well, not really convex, but all holes and dents are filled).
 

Integration 2D options

Get popup menu via Utilities->Integration 2D options

• Integration Mode:
• Box
• Flood-fill
• Convex flood-fill
• Levels for peak-picking
• Reference distance
• Reference peak intensity -A distance (R) is calculated as:  reference_distance * (reference_peak_intensity ^ 1/6) / ( peak_intensity ^ 1/6 )
• Use box for offset correction - If this option is set to 'Yes' the border values of the selected region are considered the offset and subtracted from the total intensity.

 
 

 Integration 2D bookkeeping

Get popup menu via Utilities->Integration 2D

Add - Add the last integration box to the list. Peaks are marked AA, AB,  ... ZZ.

Edit -  Edit the selected integration box . The numbers are the left, right, bottom and top channel numbers. An optional user label can be added.

Remove - Remove the selected integration box from the list.

Reset - Remove all integration boxes from the list.

Plot - Redraw all integration boxes.

Hide - Hide the integration boxes.

Show - Undo the hide operation.

Read - Read integrals from a file that was created with the write command.

Write - Write the box coordinates of the integrals, and the corresponding labels, to file.

Grab Mouse Integrate - Set left mouse button in the 2D integration mode. The area, that is selected with the mouse, is put into a box and integrated. However, it is not added to the list of peaks. This must be done manually with the 'Add' button.

Grab Mouse Peak Pick - Set left mouse button in the 2D peak-pick mode. 

• Peak Pick Find - Find all peaks within the area selected with the mouse. The routine looks for closed contours on the lowest contour level. Positive or negative peaks are selected, based on the selection made in  'Integration 2D options'
• Peak Pick Remove - Remove all existing peaks inside the region that was selected with the mouse.
• Peak Pick Merge - Merge the two peaks (inside the region selected with the mouse) into one peak.

Print Integrals - Print the integrals from the list with label, box coordinates and intensities.

Print Integral + Reference - A distance (R) is calculated as:  reference_distance * (reference_peak_intensity ^ 1/6) / ( peak_intensity ^ 1/6 )

Print Peak Center - Prints max-intensity-position.

Re-calculate Integrals - Use this option after the 'offset correction' mode has been changed.

Options - Popup  ''Integration 2D options' .

Edit peak borders and user-label.

Calibrate

To calibrate a 2D spectrum, first select from the mouse menu the function 'Calibrate'  . Then select a reference peak in the 2D spectrum



Now press mouse button 1. Two dialog boxes appear one after the other. In the first one you can set the calibration value for the X axis, and in the second on the calibration value for the Y axis.

Grid

The button that is marked '#' can be used to toggle a grid. This option works also in the 'Contour Plot' mode.


2D spectrum with grid.

Processing

When a newly created 2D file is loaded for the first time, all parameters, with the exception of the spectrometer frequency and the spectral width, are unset or are not active. If, for example, the user applies a Fourier transformation with 1x zero fill (FT 1), the result is reflected in the parameters. When an other record is loaded, and the AU button is pressed, all processing steps that are marked with 'Do' are executed . In this case the 'Do Fourier' setting executes the Fourier transformation with 1x zero fill for the new record. Alternatively, parameters can be edited by hand. The 'Param' menu gives al list of all the parameters. The 'Edit all parameters' option will give access to all parameters in all dimensions.


The 'Edit all parameters' option.

When all parameters are set to the user's liking, the Scrip button can be used to display a 'Run Script' popup menu. This popup window has a text area in which a script can be created, edited or loaded. The option 'Create script from parameters' uses the current parameters to create a script, that essentially will perform an AU command for all records in that dimension. Before the script is created, the user is asked to supply an output file name and to select a processing direction.


The 'Run Script' popup menu.

Saving part of the spectrum

To keep only the most interesting part of a 2D spectrum, one can restrict the output during the procesing steps, or one can use the 'Save as...' option in the File Menu. Fist select the part that you want to sve in the 2D spectum by zooming or cropping. Then, use 'Save as...'



The selection will be written to the file that is entered in 'New filename'. If the original data is complex,  the new data can be set to real or complex with the mode option. Automatic means that only the real data will be written, unless a Fourier transform does not yet have been performed on it. The selection is given in data points (channel numbers). This popup menu will create a script in the script-editor, and running this script will create and load the new file.

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