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== Setting up relax_disp.spin_lock_offset and relax_disp.spin_lock_field ==
[http://www.nmr-relax.com/manual/Dispersion_model_summary.html Refer to the manual for parameter explanation]
== Literature comments ==
See Figure 1 and 10 in the reference. Palmer, A.G. & Massi, F. (2006). Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700-1719 [http://dx.doi.org/10.1021/cr04042875 DOI]
* {{#lst:Citations|PalmerMassi06}} [[File:Fig1 Palmer Massi 2006.png|thumb|center|upright=43|Try to reproduce Figure 1.]]
Figure produced with script [[Relax_disp.spin_lock_offset%2Bfield_figure | found here. ]]
== Calculations in relax ==
=== spin lock offset ===
In the literature, the values are often stated as "offset", "carrier offset", "offset of the spin-lock pulse" with values given in Hz, and can have values from 0-500 to 10-20.000 Hz.<br>
These values reflects offset frequencies to the carrier frequency, and in relax is noted as '''"Spin-lock offset, the frequency of of the rf field"''' : {{:omegarf}}.
Relax needs input for {{:omegarf}} in ppm, and during calculations converts to the rad/s, with the following function call.
<source lang="python">
offsets[ei][si][mi][oi] = frequency_to_rad_per_s(frq=cdp.spin_lock_offset[id], B0=frq, isotope=spin.isotope)
</source>
If you need to convert to ppm from Hz values, consider during this in your relax script. <br>
If for example you have recorded at a 800 MHz spectrometer, you could find the Carrier position for <sup>15</sup>N (Value of yCar in NMRPipe scripts). If yCAR = 118.078 ppm, then
<source lang="python">
from lib.nmr import frequency_to_Hz, frequency_to_ppm
# Spectrometer frequency
sfrq = 799.7773991 # MHz
# Carrier position
yCAR = 118.078 # ppm
# We take the absolute value, since the gyromagnetic ratio of N15 is negative.
yCAR_Hz = abs(frequency_to_Hz(frq=yCAR, B0=sfrq*1E6, isotope='15N'))
# We add the offset (deltadof2 in varian pulse sequences) in Hz, and from 0 to 10.000
yCar_offset_Hz = yCAR_Hz + float(deltadof2)
# The convert back from Hz to ppm. Again absolute value, because of the gyromagnetic ratio of N15 is negative.
yCar_offset_ppm = abs(frequency_to_ppm(frq=yCar_offset_Hz, B0=sfrq*1E6, isotope='15N'))
relax_disp.spin_lock_offset(spectrum_id=sp_id, offset=yCar_offset_ppm)
</source>
'''Offset in the literature'''<br>
The offset is in the literature noted as $\Omega$Ω<sub>S</sub>, where $\Omega$ Ω<sub>S</sub> is the $^{(Ex. <sup>15}$</sup>N ) resonance offset from the spin-lock carrier.
<source lang="python">
</source>
=== spin lock field ===
The spin lock field strength is noted {{:nu1}}, and relax requires these to be provided in unit of '''$\nu_1$rad/s'''.<br> The [http:/spin lock field strength is converted to rad/en.wikipedias, with the following function call.org/wiki/Chemical_shift Chemical Shifts] $\delta$
<math>\omega_{S,1} === The trouble ===2\pi \cdot \nu_{S,1}The trouble is.</math>
== Code reference calculations in relax ==
'''lib/nmr.py'''
frequency_to_rad_per_s(frq=None, B0=None, isotope=None):
<source lang="python">
"""Convert the given frequency from ppm to rad/s units."""
return frq * 2.0 * pi * B0 / g1H * return_gyromagnetic_ratio(isotope) * 1e-6
</source>
'''specific_analyses/relax_disp/disp_data.py'''
return_offset_data(spins=None, spin_ids=None, field_count=None, fields=None):
Data structures
<source lang="python">
"""
The data structures consist of many different index types. These are:
- Ei: The index for each experiment type.
- Si: The index for each spin of the spin cluster.
- Mi: The index for each magnetic field strength.
- Oi: The index for each spin-lock offset.
- Di: The index for each dispersion point, the spin-lock field strength.
"""
</source>
== Spectrometer notes ==
deltadof2 = getval("deltadof2"), /* offset for N15 spinlock */
== See also ==
[[Category:Relaxation_dispersionRelaxation dispersion analysis]]