mdtraj.chemical_shifts_shiftx2¶
- mdtraj.chemical_shifts_shiftx2(trj, pH=5.0, temperature=298.0)[source]¶
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 – Dataframe containing results, with index consisting of (resSeq, atom_name) pairs and columns for each frame in trj.
- Return type:
pandas DataFrame
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
[1]Beomsoo Han, Yifeng Liu, Simon Ginzinger, and David Wishart. “SHIFTX2: significantly improved protein chemical shift prediction.” J. Biomol. NMR, 50, 1 43-57 (2011)