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) |
| − | == | + | ==Parameters== |
| − | 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 - | + | fid - a structure with four fields: fid.pos_pos, fid.pos_neg, |
| − | + | fid.neg_pos, fid.neg_neg that are used in the subsequ- | |
| − | + | ent States quadrature processing | |
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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== | ||
| − | + | # Dimensions: F1 is 15N, F2 is 13C, F3 is 1H. | |
| − | # Dimensions: F1 is | ||
# 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. | ||
# 15N-1H J-coupling is hard-coded to 92 Hz. Edit the code to change. | # 15N-1H J-coupling is hard-coded to 92 Hz. Edit the code to change. | ||
==See also== | ==See also== | ||
| − | + | [[hcanh.m]], [[hcch_cosy.m]], [[hncaco.m]], [[hnco.m]], [[hncoca.m]], [[noesyhsqc.m]], [[Built-in experiments]], [[Protein NMR simulations]] | |
| − | [[Built-in experiments]], [[Protein NMR simulations]] | ||
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''Version 2.5, authors: [[Matt Walker]], [[Ilya Kuprov]]'' | ''Version 2.5, authors: [[Matt Walker]], [[Ilya Kuprov]]'' | ||
Latest revision as of 10:11, 30 August 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)
Parameters
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 - a structure with four fields: fid.pos_pos, fid.pos_neg,
fid.neg_pos, fid.neg_neg that are used in the subsequ-
ent States quadrature processing
Examples
HNCA simulation (3D and three projections) of GB1 protein (examples/nmr_proteins/hnca_gb1.m):
Notes
- Dimensions: F1 is 15N, F2 is 13C, F3 is 1H.
- 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
hcanh.m, hcch_cosy.m, hncaco.m, hnco.m, hncoca.m, noesyhsqc.m, Built-in experiments, Protein NMR simulations
Version 2.5, authors: Matt Walker, Ilya Kuprov
