Difference between revisions of "Hnca.m"
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{{DISPLAYTITLE:hnca.m}} __NOTOC__ | {{DISPLAYTITLE:hnca.m}} __NOTOC__ | ||
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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. | 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== | ==Syntax== | ||
| − | fid=hnca(spin_system,parameters,H,R,K) | + | fid=hnca(spin_system,parameters,H,R,K) |
==Arguments== | ==Arguments== | ||
| − | parameters.npoints - a vector of three integers giving the | + | parameters.npoints - a vector of three integers giving the |
number of points in the three temporal | number of points in the three temporal | ||
dimensions, ordered as [t1 t2 t3]. | dimensions, ordered as [t1 t2 t3]. | ||
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==Outputs== | ==Outputs== | ||
| − | fid - three-dimensional free induction decay | + | fid - three-dimensional free induction decay |
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==Examples== | ==Examples== | ||
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HNCA simulation (3D and three projections) of GB1 protein (examples/nmr_proteins/hnca_gb1.m): | HNCA simulation (3D and three projections) of GB1 protein (examples/nmr_proteins/hnca_gb1.m): | ||
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==Notes== | ==Notes== | ||
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# Dimensions: F1 is 1H, F2 is 13C, F3 is 15N. | # Dimensions: F1 is 1H, F2 is 13C, F3 is 15N. | ||
# Spin labels must be set to PDB atom IDs ('CA', 'HA', etc.) in sys.labels for this sequence to work properly. | # Spin labels must be set to PDB atom IDs ('CA', 'HA', etc.) in sys.labels for this sequence to work properly. | ||
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==See also== | ==See also== | ||
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[[Built-in experiments]], [[Protein NMR simulations]] | [[Built-in experiments]], [[Protein NMR simulations]] | ||
''Version 2.5, authors: [[Matt Walker]], [[Ilya Kuprov]]'' | ''Version 2.5, authors: [[Matt Walker]], [[Ilya Kuprov]]'' | ||
Revision as of 15:49, 5 April 2026
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):
Notes
- Dimensions: F1 is 1H, F2 is 13C, F3 is 15N.
- Spin labels must be set to PDB atom IDs ('CA', 'HA', etc.) in sys.labels for this sequence to work properly.
- 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
