Assignment

About

In general, NMR resonance assignment involves connecting an observed NMR signal to an atom or group of atoms and their type of interaction. For example, a NOE peak in a 2D homonuclear NOESY spectrum may be assigned to a NOE interaction between Val 27 Hα; Ala 30 H.

Assignment in CcpNmr Analysis (Analysis) can be done on different levels involving different procedures. What is important to know is that central to making assignments in Analysis is the resonance object: assignments of a peak to atoms is always done via resonances (Figure 1).

Figure 1. The central role of a resonance in assignment (see also Resonances and Spin Systems - Core Concepts). A peak dimension is first assigned to a resonance, and the resonance is then assigned to an atom type or atom. Resonances can be grouped into a spin system, which in turn can be assigned to residue types or residues in the molecular system.

Peak to resonance assignment

The first step in an assignment is to assign a peak dimension to a resonance. This is done by either assigning to an existing resonance or by creating a new resonance. Resonances are always numbered and displayed in square brackets, e.g. resonance [234] (Figure 2).

Figure 2. A 3 dimensional peak assigned to resonances. The chemical shifts of the peak affect the average chemical shifts of the resonances to which it is assigned.

Resonance to atom and spin system assignment

In a next step, the resonances can be assigned to:

• • An atom type. Typically a resonance is first assigned to an atom type, based on the type of atoms that can be observed in an experiment. For example, in a 3D HNCO, the 13C dimension of a peak would always be assigned to carbonyl ‘C’.

  • A specific atom. A resonance is assigned to an atom when it is known from which specific atom a resonance originates. For example, the above carbonyl atom type can be made to a specific carbonyl atom, e.g. Val 27 C.

  • A spin system. The resonance can be assigned either to a new spin system or an existing spin system (Figure 3). Spin systems are numbered and the numbers are indicated in curly brackets, e.g. spin system {34}.

Figure 3. A 3 dimensional peak assigned with resonances assigned to atom types. Two of the resonances are assigned to a Spin System.

Spin system to residue assignment

Next, a spin system can be assigned to (Figure 4):

• • A residue type. The residue type of a spin system can be assigned, e.g. based on the resonances that the spin system contains. For example, a spin system may be assigned to residue type Glycine, {34} Gly, without specifying which glycine in the sequence it is.

  • A specific residue. A spin system can be assigned to a specific residue, in a specific chain of the molecular system.  

Figure 4. A spin system assigned a residue type and residue in the Molecular System. The spin system contains a list of resonances, that are assigned to atom types and carry chemical shifts.

Tentative assignments

Tentative assignments allow the user to make a ‘possible’ assignment of a resonance or spin system to atoms or residues. Tentative assignments can be made when the user is not sure about an assignment, but is confident enough to make an assumption about the assignment. Note that a single resonance can be assigned to more than one atom using the tentative assignment function! This allows the user to keep track of ambiguities that still exist in assigning the resonance to a specific atom.