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).
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:
- 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
- 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.
- Slider for positive contours: Same as in 1 but for positive contour
- Current positive-contour level: Same as in 3 but for positive contour
- CLOSE: Click on this button to close the 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.
The rest of the buttons/functions here are the same as detailed in the description of the Spectrum Display Window.
- 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,
- Slice in current direction: This slider allows interactive
selection of the position of the slice/plane along the selected
dimension axis (1).
- 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.
- 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.
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.