Couplings and RDCs

rdc2d measures one-bond scalar couplings (J) and residual dipolar couplings (D) from the separation between paired component spectra. It is a peak-tracking analysis: a residue's peak appears at a slightly different position in each component, and the difference in the coupling dimension gives the coupling.

You record two conditions — isotropic (gives J) and aligned (gives J + D) — and for each you supply the two doublet-component spectra (already combined, e.g. IPAP α/β, or HSQC/TROSY):

using NMRAnalysis

rdc2d(isotropic = ["expt/1", "expt/2"],
      aligned   = ["expt/11", "expt/12"])

The four spectra become the planes of a peak-tracking experiment. Add a peak for each residue (A, marking its position in each plane), and the per-residue analysis reports:

\[J = \mathrm{sep}(\text{isotropic}) \times \text{scale}, \qquad J + D = \mathrm{sep}(\text{aligned}) \times \text{scale}, \qquad D = (J + D) - J\]

where $\mathrm{sep}$ is the position difference between the two components in the coupling dimension, converted to Hz.

Arguments

• isotropic, aligned: each a two-element vector of the component spectra [A, B]; a component can also be given as a Bruker experiment number.
• scale: the fraction of the coupling that the measured separation represents — 1 for IPAP (separation is the full coupling) or 0.5 for HSQC/TROSY (separation is half).
• coupling: the dimension the splitting is measured in (:F1 or :F2). Defaults to the heteronuclear dimension.

Sign convention

The coupling sign is flipped automatically when the coupling dimension is ¹⁵N (negative gyromagnetic ratio), so $^1J_\text{NH}$ comes out around −93 Hz. List the two components in the same order for both the isotropic and aligned conditions; if J appears with the wrong sign, swap the pair (this corrects both J and D).

Output

The peak-info panel shows J and D (± uncertainty) for the selected residue. Save to folder writes them to results.csv, and the summary plot shows D against residue number.