mdtraj.compute_J3_HN_CB

mdtraj.compute_J3_HN_CB(traj, model='Bax2007')

Calculate the scalar coupling between HN and C_beta.

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_CB for

model : string, optional, default=”Bax2007”

Which scalar coupling model to use. Must be one of Bax2007
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_CB, 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

[R25]Hu, J. S., & Bax, A. “Determination of ϕ 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)
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