mdtraj.chemical_shifts_shiftx2

mdtraj.chemical_shifts_shiftx2(trj, pH=5.0, temperature=298.0)

Predict chemical shifts of a trajectory using ShiftX2.

Parameters:

trj : Trajectory

Trajectory to predict shifts for.

pH : float, optional, default=5.0

pH value which gets passed to the ShiftX2 predictor.

temperature : float, optional, default=298.00

Temperature which gets passed to the ShiftX2 predictor.

Returns:

results : pandas DataFrame

Dataframe containing results, with index consisting of (resSeq, atom_name) pairs and columns for each frame in trj.

Notes

You must have ShiftX2 available on your path; see (http://www.shiftx2.ca/).

Chemical shift prediction is for PROTEIN atoms; trajectory objects with ligands, solvent, ions, or other non-protein components may give UNKNOWN RESULTS.

Please cite the appropriate reference below.

References

[R23]

Beomsoo Han, Yifeng Liu, Simon Ginzinger, and David Wishart. “SHIFTX2: significantly improved protein chemical shift prediction.” J. Biomol. NMR, 50, 1 43-57 (2011)