Difference between revisions of "Hncaco.m"
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{{DISPLAYTITLE:hncaco.m}} __NOTOC__ | {{DISPLAYTITLE:hncaco.m}} __NOTOC__ | ||
| − | Protein-specific HN(CA)CO experiment (Figure 7.41 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). | + | |
| + | Protein-specific HN(CA)CO experiment (Figure 7.41 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). | ||
==Syntax== | ==Syntax== | ||
| − | + | fid=hncaco(spin_system,parameters,H,R,K) | |
==Arguments== | ==Arguments== | ||
| − | + | 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]. | ||
| − | + | ||
parameters.sweep - a vector of three real numbers giving | parameters.sweep - a vector of three real numbers giving | ||
the sweep widths in the three frequen- | the sweep widths in the three frequen- | ||
cy dimensions, ordered as [f1 f2 f3]. | cy dimensions, ordered as [f1 f2 f3]. | ||
| − | + | ||
| + | parameters.J_nh - 1H-15N J-coupling in Hz to be used for | ||
| + | magnetisation transfer. | ||
| + | |||
| + | parameters.T - evolution delay in the indirect 15N | ||
| + | dimension, in seconds. | ||
| + | |||
| + | parameters.delta2 - coherence transfer delay in seconds. | ||
| + | |||
H - Hamiltonian matrix, received from context function | H - Hamiltonian matrix, received from context function | ||
| − | + | ||
R - relaxation superoperator, received from context function | R - relaxation superoperator, received from context function | ||
| − | + | ||
K - kinetics superoperator, received from context function | K - kinetics superoperator, received from context function | ||
==Outputs== | ==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== | ==Examples== | ||
| + | |||
Below is the output (3D spectrum and three projections) of the HN(CA)CO pulse sequence for the GB1 protein (examples/nmr_proteins/hncano_gb1.m). | Below is the output (3D spectrum and three projections) of the HN(CA)CO pulse sequence for the GB1 protein (examples/nmr_proteins/hncano_gb1.m). | ||
| Line 32: | Line 51: | ||
==Notes== | ==Notes== | ||
| + | |||
# 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. | # 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. | ||
# Channels: F1 is 15N, F2 is 13C, F3 is 1H. | # Channels: F1 is 15N, F2 is 13C, F3 is 1H. | ||
| Line 37: | Line 57: | ||
==See also== | ==See also== | ||
| + | |||
[[Built-in_experiments#Protein_pulse_sequences|Protein pulse sequences]] | [[Built-in_experiments#Protein_pulse_sequences|Protein pulse sequences]] | ||
''Version 2.5, authors: [[Matt Walker]], [[Ilya Kuprov]]'' | ''Version 2.5, authors: [[Matt Walker]], [[Ilya Kuprov]]'' | ||
Revision as of 15:03, 5 April 2026
Protein-specific HN(CA)CO experiment (Figure 7.41 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).
Syntax
fid=hncaco(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.J_nh - 1H-15N J-coupling in Hz to be used for
magnetisation transfer.
parameters.T - evolution delay in the indirect 15N
dimension, in seconds.
parameters.delta2 - coherence transfer delay in seconds.
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
Below is the output (3D spectrum and three projections) of the HN(CA)CO pulse sequence for the GB1 protein (examples/nmr_proteins/hncano_gb1.m).
Notes
- 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.
- Channels: 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
See also
Version 2.5, authors: Matt Walker, Ilya Kuprov
