Assigning non-root resonances

In the previous section all the root resonances (H and N) of the 3D peaks were assigned. The next step is to also create and assign resonances for the non-root dimensions of the 3D peaks. To do so, use M: Assignment: Pick & Assign From Roots, and in {Windows & Spectra} double click on the table cells related to |Assign Non-root dim?| for the spectra HNCACB and HNcaHA:

Note: The choice is made here to start assigning the resonances of the intra residual peaks first. In case we choose all spectra that contain sequential connectivities for assigning non-root resonances we have to merge resonances originating from the same atom, but which occur in more than one spectrum and would be assigned to different resonance objects. We avoid this extra step by starting from the spectra that contain the intra residual peaks.

In the {Link Peaks} tab, click [Assign All Non-root Resonances] and confirm. Inspection of the HCN and HHN windows should show that resonances have now been assigned in the non-root dimensions of the HNCACB and HNcaHA spectra, whereas those in the other spectra have been left untouched. Note that in the HNcaHA, some peaks are located in the region between 4.77 and 4.90ppm in the second 1H dimension. These peaks have not been assigned to resonances because the min water and max water parameters in {Tolerances} were set to exclude these regions. After curating the peaks in the water region, the non-root resonances of the remaining peaks can be assigned manually, or by setting the min water and max water parameters temporarily to 999 and clicking [Assign All Non-root Resonances] once more in the {Link Peaks} tab. All non-root resonances in the HNCACB and HNcaHA should now have been assigned. To add non-root atom types to non-root resonances, check the box "Set Non-root Atom Types". When doing this:

#NOTE: Analysis added all the HA's to the spinsystems, which is not what we want, this has to be checked!! This didn't happen for the CA/CBs. Could be an issue with the experiment type.

The project with cleaned peak lists and assigned resonances has been saved as NapD_5.

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