Calculate the scalar coupling between HN and H_alpha.
This function does not take into account periodic boundary conditions (it will give spurious results if the three atoms which make up any angle jump across a PBC (are not “wholed”))
Trajectory to compute J3_HN_HA for
- modelstring, optional, default=”Bax2007”
Which scalar coupling model to use. Must be one of Bax2007, Bax1999, or Ruterjans1999
- indicesnp.ndarray, shape=(n_phi, 4), dtype=int
Atom indices (zero-based) of the phi dihedrals
- Jnp.ndarray, shape=(n_frames, n_phi)
Scalar couplings (J3_HN_HA, in [Hz]) of this trajectory. J[k] corresponds to the phi dihedral associated with atoms indices[k]
The coefficients are taken from the references below–please cite them.
Schmidt, J. M., BlÃ¼mel, M., LÃ¶hr, F., & RÃ¼terjans, H. “Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles.” J. Biomol. NMR, 14, 1 1-12 (1999)
VÃ¶geli, B., Ying, J., Grishaev, A., & Bax, A. “Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.” J. Am. Chem. Soc., 129(30), 9377-9385 (2007)
Hu, J. S., & Bax, A. “Determination of Ï and Î¾1 Angles in Proteins from 13C-13C Three-Bond J Couplings Measured by Three-Dimensional Heteronuclear NMR. How Planar Is the Peptide Bond?.” J. Am. Chem. Soc., 119(27), 6360-6368 (1997)