Relax disp.spin lock offset+field - Revision history

Bugman: /* Literature comments */ Switched to labelled section transclusions for the citation.

2015-11-06T16:01:51Z

Literature comments: Switched to labelled section transclusions for the citation.

Bugman: /* spin lock field */ Fix for some incorrect information.

2015-11-03T14:06:26Z

spin lock field: Fix for some incorrect information.

Bugman: Fix for the symbols and maths - all $x$ usage has been replaced by parameter templates, $tags, or direct HTML conversion.$

2015-11-03T13:58:13Z

Fix for the symbols and maths - all $x$ usage has been replaced by parameter templates, <math> tags, or direct HTML conversion.

Bugman: Using the {{lowercase title}} template.

2015-10-19T16:25:49Z

Using the {{lowercase title}} template.

Bugman: Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.

2015-10-15T14:17:17Z

Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.

Bugman: Category link updates for the specific analyses.

2014-09-11T07:59:52Z

Category link updates for the specific analyses.

Bugman: Formatting of isotopes.

2014-09-09T09:14:00Z

Formatting of isotopes.

Tlinnet: /* spin lock offset */

2014-03-16T19:22:16Z

spin lock offset

Tlinnet: /* spin lock field */

2014-03-16T14:35:12Z

spin lock field

Tlinnet: /* spin lock field */

2014-03-16T14:34:52Z

spin lock field

@@ Line 21: / Line 21: @@
 == Literature comments ==
-See Figure 1 and 10 in the reference.
+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]
 [[File:Fig1 Palmer Massi 2006.png|thumb|center|upright=3|Try to reproduce Figure 1.]]

@@ Line 81: / Line 81: @@
 === spin lock field ===
-The spin lock field strength is noted {{:nu1}}, and relax requires these to be provided in unit of '''Hz'''.<br>
+The spin lock field strength is noted {{:nu1}}, and relax requires these to be provided in unit of '''rad/s'''.<br>
 The spin lock field strength is converted to rad/s, with the following function call.

@@ Line 30: / Line 30: @@
 === 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"''' : $\mathbf{\omega_{rf}}$.
+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 $\mathbf{\omega_{rf}}$ in ppm, and during calculations converts to the rad/s, with the following function call.
+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)
@@ Line 61: / Line 61: @@
 '''Offset in the literature'''<br>
-The offset is in the literature noted as $\Omega_S$, where $\Omega_S$ is the (Ex. $^{15}$N) resonance offset from the spin-lock carrier.
+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 $\Omega_S$ is dependent of the [[wikipedia:Chemical_shift | chemical shifts]] $\delta$ in ppm for the nuclei of interest.
+Note that Ω<sub>S</sub> is dependent of the [[wikipedia:Chemical_shift | chemical shifts]] δ in ppm for the nuclei of interest.
 <source lang="python">
 shifts[ei][si][mi] = frequency_to_rad_per_s(frq=shift, B0=frq, isotope=spin.isotope)
 </source>
-Then $\bar{\Omega}_S$ is calculated with: $\bar{\Omega}_{S,i} = \bar{\omega}_{S,i} - \omega_{rf}$, where $\bar{\omega}$ is the population averaged Larmor frequency of the spin and comes from the conversion of the [[wikipedia:Chemical_shift | Chemical Shifts]] $\delta_{S,i}$ to frequency $\bar{\omega}_{S,i}$.
+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]
@@ Line 77: / Line 81: @@
 === spin lock field ===
-The spin lock field strength is noted $\nu_1$, and relax requires these to be provided in unit of '''Hz'''.<br>
+The spin lock field strength is noted {{:nu1}}, and relax requires these to be provided in unit of '''Hz'''.<br>
 <source lang="python">
 omega1 = point * 2.0 * pi
 </source>
-Then the Rotating frame tilt angle $\theta$ is calculated.<br>
+Then the Rotating frame tilt angle θ is calculated.
-$\theta = \tan^{-1} \left( \frac{\omega_1}{\bar{\Omega}_{S,i}} \right)$
 <source lang="python">

← Older revision		Revision as of 16:25, 19 October 2015
Line 1:		Line 1:
		+	{{lowercase title}}
		+
	__TOC__		__TOC__

← Older revision		Revision as of 14:17, 15 October 2015
Line 1:		Line 1:
		+	__TOC__
		+
	== Setting up relax_disp.spin_lock_offset and relax_disp.spin_lock_field ==		== 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]		[http://www.nmr-relax.com/manual/Dispersion_model_summary.html Refer to the manual for parameter explanation]

@@ Line 130: / Line 130: @@
   deltadof2 = getval("deltadof2"),        /* offset for N15 spinlock */
 == See also ==
-[[Category:Relaxation_dispersion]]
+[[Category:Relaxation dispersion analysis]]

@@ Line 34: / Line 34: @@
 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
+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

@@ Line 54: / Line 54: @@
 The spin lock field strength is converted to rad/s, with the following function call.<br>
-$\omega_{S,1} = 2\pi \cdot \nu_1$
+$\omega_{S,1} = 2\pi \cdot \nu_{S,1}$
 <source lang="python">
 omega1 = point * 2.0 * pi

Relax disp.spin lock offset+field - Revision history

Bugman: /* Literature comments */ Switched to labelled section transclusions for the citation.

Bugman: /* spin lock field */ Fix for some incorrect information.

Bugman: Fix for the symbols and maths - all $x$ usage has been replaced by parameter templates, tags, or direct HTML conversion.

Bugman: Using the {{lowercase title}} template.

Bugman: Forced creation of a TOC - this will improve the formatting on the main page 'Did you know...' section.

Bugman: Category link updates for the specific analyses.

Bugman: Formatting of isotopes.

Tlinnet: /* spin lock offset */

Tlinnet: /* spin lock field */

Tlinnet: /* spin lock field */

Bugman: Fix for the symbols and maths - all $x$ usage has been replaced by parameter templates, $tags, or direct HTML conversion.$