hcanh.m

Protein-specific H(CA)NH experiment (Figure 7.37 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=hcanh(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].

   parameters.spins       - isotopes affected by ideal broadband
                            pulses, specified as a cell array of
                            strings, e.g. {'1H'}.

   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

Note: spin labels must be set to PDB atom IDs ('CA', 'HA', etc.) in
      sys.labels for this sequence to work properly.

TODO: whoever understands how phase cycles and quadratures work in
      3D NMR is welcome to add a phase-sensitive version.

m.walker@soton.ac.uk
ilya.kuprov@weizmann.ac.il

Examples

An example (3D spectrum and three projections) of H(CA)NH spectrum of GB1 protein (examples/nmr_proteins/hcanh_gb1.m):

Notes

1. Channels: F1 is 1H, F2 is 15N, F3 is 1H.
2. Spin labels must be set to PDB atom IDs ('CA', 'HA', etc.) in sys.labels for this sequence to work properly.
3. 13C-1H and 15N-1H J-couplings have been hard-coded into the sequence text. Edit the file to change.

See also

Liquid state NMR experiments, Protein NMR simulations

Version 2.5, authors: Matt Walker, Ilya Kuprov