Make synthetic peak lists

Instructions

Synthetic or artificial peaks lists, i.e. peak lists that are not made by direct inspection of spectrum intensities, can be made in several ways. This HowTo will show how synthetic peak lists can be made in two ways. The synthetic peak lists are created in the Peak: Peak Lists popup, in the {Synthetic Lists} tab, which is accessible through M: Peak: Peak Lists:

Synthetic peak lists based on chemical shifts or shift intersections

Under ‘From Shift Intersections’, it is possible to make a peak list based upon the intersections between chemical shifts that occur within the bounds of a given spectrum (the same spectrum that the peak list will belong to).

To predict peaks from chemical shifts:

• • Choose “Spectrum:”, “Shift List:” and “Mol System:” (Note: if resonances have been assigned to residues in the molecular system, select molecular system, otherwise leave this field to “any”)

  • To use resonances that are not assigned to atoms or atom types, check the box “Use unassigned?”

  • To only use intra residual connectivities (e.g. in a NOESY spectrum there is distance constraints both within and between residues), check the box “Intra residue and directly bound only?”

  • Now create the list by clicking [Predict from shifts]. The synthetic peak list should now be found under {Peak Lists}    

Synthetic peak lists based on chemical shifts and structure

Under 'From Shifts and Structure' it is possible to make a peak list based on the structure and the intersections between chemical shifts that occur within the bounds of a given spectrum. Distances in the structure are here used together with the chemical shifts to create a peak list for spectra in which through-space interactions are observed (e.g. NOESY). A synthetic peak is created for all the atoms that are closer in space in the structure or ensemble than the chosen cutoff ("Max Dist:"). Peaks involving atoms that are further away then the “Max Dist” value will not be made.

To create the peak list:

• • Choose “Spectrum”, “Structure:” (if exists), “Max Dist” and other parameters of interest under ‘From Shifts and Structure’.

  • Click [Predict from structure] and the list should appear under {Peak Lists}