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Working with Pseudo3Ds

Working with Pseudo3Ds

You can open a pseudo 3D spectrum like any other spectrum - simply drag it into the program, or use Spectrum / Load Spectra.... Analysis will treat your pseudo 3D spectrum as a regular 3D spectrum with a time dimension axis. When you open it in a SpectrumDisplay module, the module will probably be called something like 3D_HNT where H and N refer to 1H and 15N axes and T to a time dimension axis. Be default, the time dimension axis is placed in the z-dimension. You can scroll through the different planes to inspect them, but because the spectrum is being treated as a 3D, you won't be able to pick peaks in each plane. Any peaks you pick will be treated as 3D peaks and their position will depend on the intensities in the time dimension axis (you will be able to see this if you flip the y and z axes with YZ).

In order to pick 2D peaks in each of your planes, you will need to split your pseudo-3D into 2Ds. right-click on your spectrum in the sidebar and select Split planes to SpectrumGroup. This will create a set of 2D spectra which will be written in .ndf5 format in the same directory where the original pseudo-3D was (it therefore needs to be writeable by you!). The spectra will automatically be place into a new SpectrumGroup.

Once you have your individual planes in a SpectrumGroup, you can double-click on the SpectrumGroup in the sidebar to set various parameters. In the Series tab, for instance, you can set your time domain values (which are often not available from the raw spectrum data) and reorder your spectra. You can then select all the spectra in the spectrum group and open them in a SpectrumDisplay by dragging them into the Drop Area. By using Tab, Tab you can cycle through the different spectra/planes in turn to inspect, peak pick etc. (Remember that Tab+A will show all spectra in a SpectrumDisplay and Tab+Z with switch them all off.)