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Working with Peaks and Peaklists

Peaks and Peaklists are available in Cara to be compatible with other programs such as XEASY. They are also used for integration of peaks. Peaks and Peaklists can be used only with the Tool > Open Spectrum, MonoScope, HomoScope and PolyScope. Later we will learn about the more advanced feature of CARA called Peak inference which uses Spins, ResidueTypes and SpectrumTypes to infer the position of peaks. Now lets learn to work with peaks.

  1. Start Cara and use the Tool > Open Spectrum to
  2. Open an NMR spectrum
  3. Prepare an expansion as shown in SpectrumNavigation
  4. Position the crosshairs using the mouse or keyboard on top of a signal in the NMR spectrum. Use the x- and y-slices to help with positioning.
  5. Use the right-click context menu to pick peak. Alternatively, use the shortcut pp.
  6. Select a peak by clicking on it. If you are unhappy that the crosshairs are not centered on the peak, use View > Center to peak to force the cursor to position the crosshairs at the exact position of the peak when you click near it. Select multiple peaks by pressing Shift while selecting a region with click-drag. Shift-click selects a peak without moving the crosshairs.
  7. Three ways to move a peak:
    • first select peak, then move the crosshairs via keyboard to a new position and finally use the right-click context menu move peak or the keyboard shortcut mp.
    • first select peak, then move the mouse cursor to the new position and press Shift-right-click to move the crosshairs and finally use the right-click context menu move peak or the keyboard shortcut mp
    • first position the crosshairs at the new position, then select the peak using Shift-click and finally use the right-click context menu move peak or the keyboard shortcut mp.
  8. Use View > Undo or the Shortcut zz to undo this change.
  9. Delete peaks selected via the right-click context menu or the shortcut dp.
  10. Export the peaklist by using Peaks > Export Peaklist .... This is useful for external programs such as XEASY. CARA however keeps the peaklists in the repository.
  11. Import an XEASY peaklist via Peaks > Import Peaklist ... If the DIM attributes in the header are not set, the peaklist might be oriented incorrectly. Use Peaks > Rotate Peaklist ... to correct this.
  12. Calibrate an XEASY peaklist onto the spectrum by selecting a peak, and moving the crosshairs with the keyboard or shift-right-click to the signal in the NMR spectrum. Use Peaks > Calibrate Peaklist ... or the shortcut cl. Alternatively, you can first position the crosshairs at the new position and then select the peak with Shift-click and finally apply Peaks > Calibrate Peaklist ... (shortcut cl).
  13. You can use the integrator functionality to pick peaks in regions with moderate overlap. See the BatchIntegration tutorial for more details.
  14. You can display a list with all peaks in associated with the spectrum by selecting View-Show List or use the keyboard command "sl" to turn on/off the peaklist display

    The PeakList serves as a navigator (to find a peak) and as an editor (to modify peak information).

    You can navigate to a peak in the spectrum by double-clicking on the peak in the PeakList.

    Conversely, you can click on a peak in the spectrum and highlight its entry in the PeakList with the keyboard command "sp" (show peak).

    Each peak in the list has the following attributes:

    • ID (a unique integer created when the peak is picked)
    • Coordinate along each dimension in ppm
    • Volume and amplitude (see BatchIntegration for more on amplitude/volume)
    • Label, a text which can be displayed next to the peak symbol in the spectrum
    • Color (see ColorCode for more on this)
    • Probability

    By right-clicking in the PeakList navigator, and selecting "Show assignments" the coordinates can be replaced by the assignments if available (atomname and residue). Assignments of peaks can be modified by right-clicking a peak and selecting "Edit assignments". Each dimension of the peak can be associated with a spin in the SpinBase? by entering the SpinId.

    You can add additional columns to the PeakList with user-defined Peak attributes. Look in the header of the LUA script HetNoe.lua for an example of how this is done.

    Tools > Open Spectrum is for directly accessing data for simple operations or a quick check of data. However to integrate the information from multiple spectra and make use of the advanced features of CARA you will need to set up a Repository.

NEXT: The Repository

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