hnca.m

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Protein-specific HNCA experiment (Figure 7.31a of "Protein NMR Spectroscopy", 2nd edition) using pre-set values of J-couplings used in the magnetisation transfer stages. The simulation uses the bidirectional propagation method described in (http://dx.doi.org/10.1016/j.jmr.2014.04.002). The sequence is hard-wired to work on 1H,13C,15N proteins and uses PDB labels to select spins that will be affected by otherwise ideal pulses.

Syntax

    fid=hnca(spin_system,parameters,H,R,K)

Arguments

   parameters.npoints     - a vector of three integers giving the
                            number of points in the three temporal
                            dimensions, ordered as [t1 t2 t3].

   parameters.sweep       - a vector of three real numbers giving
                            the sweep widths in the three frequen-
                            cy dimensions, ordered as [f1 f2 f3].

   H   - Hamiltonian matrix, received from context function

   R   - relaxation superoperator, received from context function

   K   - kinetics superoperator, received from context function

Outputs

    fid - three-dimensional free induction decay

Examples

HNCA simulation (3D and three projections) of GB1 protein (examples/nmr_proteins/hnca_gb1.m):

Hnca gb1.png

Notes

  1. Dimensions: F1 is 1H, F2 is 13C, F3 is 15N.
  2. Spin labels must be set to PDB atom IDs ('CA', 'HA', etc.) in sys.labels for this sequence to work properly.
  3. 15N-1H J-coupling is hard-coded to 92 Hz. Edit the code to change.

See also

Built-in experiments, Protein NMR simulations


Version 2.5, authors: Matt Walker, Ilya Kuprov