NMR
API reference for the synth_pdb NMR-data modules.
synth_pdb.rdc — Residual Dipolar Couplings
Overview
Re-exports calculate_rdcs from synth-nmr.
RDCs encode the orientation of backbone N–H bond vectors relative to a global alignment
frame and are therefore complementary to local-distance NOE restraints.
Physics behind RDCs — see NMR Theory: Residual Dipolar Couplings.
calculate_rdcs(structure, Da, R)
| Parameter | Type | Default | Description |
|---|---|---|---|
structure |
biotite.AtomArray |
— | Protein structure containing backbone N and H atoms |
Da |
float |
10.0 |
Axial component of the alignment tensor in Hz (typical: 5–25 Hz) |
R |
float |
0.1 |
Rhombicity of the alignment tensor, \(0 \leq R \leq 2/3\) |
Returns: dict[int, float] — mapping res_id → RDC (Hz). Proline residues and any
residue missing a backbone amide H are automatically excluded.
Example
import biotite.structure.io.pdb as pdbio
from synth_pdb.rdc import calculate_rdcs
structure = pdbio.get_structure(pdbio.PDBFile.read("my_peptide.pdb"), model=1)
rdcs = calculate_rdcs(structure, Da=15.0, R=0.2)
for res_id, rdc_val in sorted(rdcs.items()):
print(f"Res {res_id}: {rdc_val:+.2f} Hz")
synth_pdb.chemical_shifts — Chemical Shift Prediction
Re-exports predict_chemical_shifts and predict_empirical_shifts from
synth-nmr.
predict_chemical_shifts(structure, use_shiftx2=True)
Predicts backbone and CB chemical shifts. Selects the predictor backend via
use_shiftx2:
use_shiftx2 |
Backend | Notes |
|---|---|---|
True (default) |
SHIFTX2 (Han et al., 2011) | Requires the external binary; falls back to empirical if missing |
False |
SPARTA+-style empirical | Always available; no external dependencies |
synth_pdb.coupling — J-Couplings
Re-exports calculate_hn_ha_coupling and predict_couplings_from_structure
(Karplus equation for \({}^3J(\text{HN,HA})\) couplings).