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relaxation Module

The relaxation module provides utilities for calculating NMR relaxation rates and order parameters.

Overview

NMR relaxation is a primary source of information about protein dynamics. This module provides tools to calculate these rates from synthetic structures, leveraging the synth-nmr engine.

Main Functions

calculate_relaxation_rates = _nmr.calculate_relaxation_rates module-attribute

predict_order_parameters = _nmr.predict_order_parameters module-attribute

spectral_density = _rel.spectral_density module-attribute

Usage Examples

Predicting Order Parameters

from synth_pdb.relaxation import predict_order_parameters

# structure: biotite.structure.AtomArray
s2 = predict_order_parameters(structure)

# s2: List[float] (per-residue S2 values)

Calculating Relaxation Rates

Calculate R1, R2, and NOE from structural coordinates and magnetic field strength.

from synth_pdb.relaxation import calculate_relaxation_rates

rates = calculate_relaxation_rates(
    structure,
    field_mhz=600.0,
    correlation_time_ns=10.0
)

# rates: Dict[str, np.ndarray] (r1, r2, noe)

References

  • Lipari-Szabo Model-Free: Lipari, G., & Szabo, A. (1982). "Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules." Journal of the American Chemical Society. DOI: 10.1021/ja00381a009
  • NMR Dynamics: Palmer, A. G. (2004). "NMR characterization of the dynamics of macromolecules." Chemical Reviews. DOI: 10.1021/cr030413t

See Also