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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]
This page is a little help to understand how to use the functions:
#relax_disp.spin_lock_offset()
#relax_disp.spin_lock_field()
=== spin lock offset ===
== 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* {{#lst://dx.doi.org/10.1021/cr04042875 DOI]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 frequencysfrq = 799.7773991 # MHz# Carrier positionyCAR = 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 10.000yCar_offset_Hz = yCAR_Hz + float(deltadof2)# The code 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 Ω<sub>S</sub>, where Ω<sub>S</sub> is the (Ex. <sup>15</sup>N) resonance offset from the spin-lock carrier. Note that Ω<sub>S</sub> is dependent of the [[wikipedia:Chemical_shift | chemical shifts]] δ in ppm for the nuclei of interest. The [[wikipedia:Chemical_shift | Chemical Shifts]] δ in ppm for nuclei of interest (ex. <sup>15</sup>N and which is called resides have been loaded inwith relax function [http://www.nmr-relax.com/manual/chemical_shift_read.html chemical_shift_read] from a [http://www.nmr-relax.com/manual/spectrum_read_intensities.html peak list formatted file]) is first converted to to the rad/s with the following function calls.
Then <span style="text-decoration: overline">Ω<sub>S</sub></span> is calculated with: <span style="text-decoration: overline">Ω<sub>S,i</sub></span> = <span style="text-decoration: overline">Ω<sub>S,i</sub></span> - {{:omegarf}}, where <span style="text-decoration: overline">Ω</span> is the population averaged Larmor frequency of the spin and comes from the conversion of the [[wikipedia:Chemical_shift | Chemical Shifts]] δ<sub>S,i</sub> to frequency <span style="text-decoration: overline">Ω<sub>S,i</sub></span>.
<source lang="python">
Delta_omega = shifts[ei][si][mi] - offsets[ei][si][mi][oi]
</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>Relax needs input in ppm, and converts The spin lock field strength is converted to the rad/s, with the following function callscall. <math>\omega_{S,1} = 2\pi \cdot \nu_{S,1}</math> <source lang="python">omega1 = point * 2.0 * pi</source> Then the Rotating frame tilt angle θ is calculated.
<math>\theta === spin lock offset ===\tan^{-1} \left( \frac{\omega_1}{\bar{\Omega}_{S,i}} \right)</math>
<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= The trouble None, fields=None): Data structures<source lang="python">"""The trouble isdata structures consist of many different index types. These are:
=== Varian / VnmrJ ===
In some pulse sequences, the following is seen:
'trim' is a basic timeunit and the total spinlock time is calculated as '''2.0*ncyc*trim'''
b1 = getval("b1"), /* spin-lock field, Hz! */
deltadof2 = getval("deltadof2"), /* offset for N15 spinlock */
== See also ==
[[Category:Relaxation dispersion analysis]]