3D Spectrum Display Window

Here you will find a description of various ways to visualize/analyze 3D data using the Virtual NMR Spectrometer, and the functions associated with the corresponding display windows.
The buttons that will open these panels are located in the 3D-Data Processing Window.

3D-Cube Representation of a 3D Spectrum:
This panel represents a 3D spectrum as a cube, where the data are shown as contours drawn for a user-selected contour levels (red=positive, blue=negative).

  1. Slider for negative contours: This slider allows interactive level-selection for blue contours that represent negative values in the 3D spectrum. Drag the slider with the mouse or click on the left or right side of it to move the slider in the desired direction. Clicking on the blue region will move the slider in fast steps, clicking on the edges (< or >) will move it in smaller steps. The lower limit of the absolute value achievable using the slider is set to 1/100-th of the min value of the data, to prevent overloading the plot/memory with data when the level approaches zero. You can specify the desired level manually (see 2, 4) -- this could be useful if you want to set the contour level smaller than what the slider settings permit.
  2. Current negative-contour level: This text-edit box displays the current level that is used for drawing negative contours and allows the users to manually set the desired contour level.
  3. Slider for positive contours: Same as in 1 but for positive contour levels (red).
  4. Current positive-contour level: Same as in 3 but for positive contour levels.
  5. CLOSE: Click on this button to close the window.
In order to rotate the 3D cube on the screen, select the Rotate 3D tool in the Tools on the top bar of the spectrum display window:

2D-Slice Display Window:
This panel displays a 2D slice of the 3D spectrum (cube) along the user-specified direction (axes) and at a user-specified position in the cube.
  1. Dimension Selection: This pull-down menu sets the direction of the slice plane, by defining the axis perpendicular to the plane: F1 means that the plane will be perpendicular to F1 hence parallel to F2-F3 axes, F2 means selection of a plane in the F1-F3 direction, etc.
  2. Slice in current direction: This slider allows interactive selection of the position of the slice/plane along the selected dimension axis (1).
  3. Slice Number: Shows current value and allows manual input of the slice position in terms of the number of the corresponding point in the data set. For example, if the spectrum contains 32 points in the F2 direction, the slice position in this direction can be any number from 1 to 32. Any input here will automatically update the current slider position (2) and the slice frequency (4) and vice versa.
  4. Slice Frequency [ppm]: Shows current value and allows manual input of the slice position in terms of the frequency (in ppm) along the corresponding frequency axis (e.g. F2). Input here will automatically update the current slider (2) and slice (3) position. The input frequency value will be rounded to the nearest discrete position in the spectrum.
The rest of the buttons/functions here are the same as detailed in the description of the Spectrum Display Window.

2D-Projection of 3D Spectrum Window:
This panel displays a 2D projection of the 3D spectrum along a user-specified direction (selected using a pull-down menu, see picture below). The projection is calculated as a Fourier Transform of the "first" data plane (in a given direction) from the 3D raw-data set. The plane is treated as a separate experimental 2D data set and all proper processing options/parameters are applied as specified in the corresponding columns (e.g. D3 and D2 if the F1 direction is selected) in the 3D-Data Processing Window. This projection is not affected by phase correction along the third dimension (e.g. F1) and hence could differ from what can be seen throught the corresponding face of the 3D cube.

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Page designed by David Fushman. Last modified 01/31/2004.