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Visualising 3D Spectra

Visualising 3D Spectra


Many 3D spectra are based upon a 2D spectrum and it is easiest to understand how 3D spectra are visualised by using one of these as an example. So we might start with a 2D 1H-15N HSQC spectrum. In an experiment such as an HNCO, you now add a third dimension which is a carbon dimension. You can image each HSQC peak being lifted up into the third dimension by the amount of the carbon chemical shift. What you then end up with, is essentially lots of 'blobs' (3D peaks) 'floating' in a 3D cube. Now that is not a very useful way of looking at a 3D spectrum. So instead we look at at individual planes out of that cube. In each plane you will see a different peak. You can do this in several ways - either by taking 1H-13C planes at different 15N positions, or by taking 1H-15N planes at different 13C positions (15N-13C planes at 1H positions is, of course, also possible, but in practice not done very often).

If a plane only contains one or two peaks, then most of it will just be empty space. So a lot of time we don't bother looking at the whole plane, but just a thin strip either side of the peak of interest. It is then possible to take several such strips, essentially extract them out of the 3D cube, and lay them next to one another. This is referred to as strip plot. Note that one axis in such a strip plot, usually the y-axis, is shared by all strips. But the x and z positions are unique to each strip.

3D spectra in CcpNmr Analysis

A 3D spectrum is shown as a plane from the 3D cube. The x and y axes are labelled in the same way as 2D spectra. The ppm position for the z-axis is shown along the bottom of a 3D spectrum display (V3.0.0) or in the top left corner of the spectrum display (V3.0.1). You can move through the planes using the arrows either side of the z-axis position, or you can type a ppm value directly into the box.
Next to the ppm box the plane count is shown. By default one plane is shown at a time. Increase this value if you want to visualise several planes at once.
For V3.0.1, click on the z-axis ppm position to bring up the arrows and plane count and click elsewhere in the display to hide them again.

If you would like to display your spectrum with a different arrangement of axes, then you can type XY, XZ or YZ to swap those axes. A new module with the new axis arrangement will open up. For more information on flipping spectra and how to set default axis arrangements see Flipping Spectra.

You can add or remove strips from a display by using the + and - buttons in the toolbar. Note that each strip has its own X and Z axis, but that the Y-axis is shared between the strips. For more information on how to use strips in Analysis, go to Working with Strips