mdtraj.compute_J3_HN_HA¶
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mdtraj.
compute_J3_HN_HA
(traj, model='Bax2007')¶ 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”))
Parameters: traj : mdtraj.Trajectory
Trajectory to compute J3_HN_HA for
model : string, optional, default=”Bax2007”
Which scalar coupling model to use. Must be one of Bax2007, Bax1999, or Ruterjans1999
Returns: indices : np.ndarray, shape=(n_phi, 4), dtype=int
Atom indices (zero-based) of the phi dihedrals
J : np.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]
Notes
The coefficients are taken from the references below–please cite them.
References
[R5456] Schmidt, J. M., Blümel, M., Löhr, F., & Rüterjans, 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) [R5556] Vögeli, 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) [R5656] Hu, J. S., & Bax, A. “Determination of Ï and ξ1 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)