Changes

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 ===[http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html Manual on relax_disp.spin_lock_offset]<br>The relax function relax_disp.spin_lock_offset() requires the values to be provided in ppm. relax_disp.spin_lock_offset(spectrum_id=None, offset=None) === spin lock field ===[http://www.nmr-relax.com/manual/relax_disp_spin_lock_field.html Manual on relax_disp.spin_lock_field]<br>The relax function relax_disp.spin_lock_field() requires the values to be provided in Hz.

== Literature comments ==See Figure 1 and 10 in the reference: * {{#lst:Citations|PalmerMassi06}} [[httpFile://wwwFig1 Palmer Massi 2006.png|thumb|center|upright=3|Try to reproduce Figure 1.]]Figure produced with script [[Relax_disp.spin_lock_offset%2Bfield_figure | found here.nmr]] == 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 relaxis noted as '''"Spin-lock offset, the frequency of of the rf field"''' : {{:omegarf}}.com Relax needs input for {{:omegarf}} in ppm, and during calculations converts to the rad/manual/relax_disp_spin_lock_offsets, with the following function call.html Manual on relax_disp<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 ¹⁵N (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 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=Nonesp_id, offset=NoneyCar_offset_ppm)</source>   '''Offset in the literature'''<br> The offset is in the literature noted as Ω_S, where Ω_S is the (Ex. ¹⁵N) resonance offset from the spin-lock carrier. Note that Ω_S 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. ¹⁵N and which have been loaded in with relax function [http://www.nmr-relax.com/manual/Dispersion_model_summarychemical_shift_read.html Refer 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 manual for parameter explanation]rad/s with the following function calls.

<source lang="python">shifts[ei][si][mi] = Literature comments frequency_to_rad_per_s(frq=shift, B0=See Figure 1 and 10 in the reference. Palmerfrq, A.G. & Massi, Fisotope=spin. (2006isotope). 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]source>

Then <span style="text-decoration: overline">Ω_S</span> is calculated with: <span style="text-decoration: overline">Ω_S,i</span> = <span style="text-decoration: overline">Ω_S,i</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 [[Filewikipedia:Fig1 Palmer Massi 2006.pngChemical_shift |thumb|Try Chemical Shifts]] δ_S,i to reproduce Figure 1frequency <span style="text-decoration: overline">Ω_S,i</span>.<source lang="python">Delta_omega = shifts[ei][si][mi] - offsets[ei][si][mi][oi]</source>

== Code reference calculations in relax ==The offset code which is called resides in the literature noted as $\Omega$, where Omega:

In the literature'''lib/nmr.py''' frequency_to_rad_per_s(frq=None, B0=None, the values are often stated as isotope=None):<source lang="offsetpython", >"carrier offset", "offset of Convert the spin-lock pulse" with values given in Hz, and have values frequency from 0-500 ppm to 10-20rad/s units.000 Hz"""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= spin lock offset ==None, fields=None):

Data structures<source lang== The trouble =="python">"""The trouble isdata structures consist of many different index types. These are:

Does - Ei: The index for each experiment type.- Si: The index for each spin of the Hz frequency refers to RF fields applied at 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 1H Larmor frequency or 15N frequency?spin-lock field strength."""</source>

At page 1708 is states that w_1S = w_1 and w_eS = w_e.And in pulse sequence it states that:Spectrometer notes ==

=== Varian / VnmrJ ===