Difference between revisions of "NS R1rho 2-site"
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For this model, the equations from Korzhnev05 have been used. | For this model, the equations from Korzhnev05 have been used. | ||
The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as | The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as | ||
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\begin{equation} | \begin{equation} | ||
\mathrm{R}_{1\rho} = - \frac{1}{T_\textrm{relax}} \cdot \ln \left( M_0^T \cdot e^{R \cdot T_\textrm{relax}} \cdot M_0 \right), | \mathrm{R}_{1\rho} = - \frac{1}{T_\textrm{relax}} \cdot \ln \left( M_0^T \cdot e^{R \cdot T_\textrm{relax}} \cdot M_0 \right), | ||
\end{equation} | \end{equation} | ||
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where | where | ||
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\begin{align} | \begin{align} | ||
M_0 &= \begin{pmatrix} \sin{\theta} \\ 0 \\ \cos{\theta} \\ 0 \\ 0 \\ 0 \end{pmatrix}, \\ | M_0 &= \begin{pmatrix} \sin{\theta} \\ 0 \\ \cos{\theta} \\ 0 \\ 0 \\ 0 \end{pmatrix}, \\ | ||
\theta &= \arctan \left( \frac{\omega_1}{\Omega_\textrm{A}} \right). | \theta &= \arctan \left( \frac{\omega_1}{\Omega_\textrm{A}} \right). | ||
\end{align} | \end{align} | ||
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The relaxation evolution matrix is defined as | The relaxation evolution matrix is defined as | ||
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\begin{equation} | \begin{equation} | ||
R = \begin{pmatrix} | R = \begin{pmatrix} | ||
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\end{pmatrix}, | \end{pmatrix}, | ||
\end{equation} | \end{equation} | ||
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=== Essentials === | === Essentials === | ||
Revision as of 11:52, 3 November 2015
The relaxation dispersion model for the numeric solution (NS) to the Bloch-McConnell equations for 2-site exchange for R1rho-type data. This model is labelled as NS R1rho 2-site in relax.
Equation
This is the numerical model for 2-site exchange using 3D magnetisation vectors. It is selected by setting the model to NS R1rho 2-site. The simple constraint $\textrm{p}_\textrm{A} > \textrm{p}_\textrm{B}$ is used to halve the optimisation space, as both sides of the limit are mirror image spaces.
For this model, the equations from Korzhnev05 have been used. The $\mathrm{R}_{1\rho}$ value for state A magnetisation is defined as
[math] \begin{equation} \mathrm{R}_{1\rho} = - \frac{1}{T_\textrm{relax}} \cdot \ln \left( M_0^T \cdot e^{R \cdot T_\textrm{relax}} \cdot M_0 \right), \end{equation} [/math]
where
[math] \begin{align} M_0 &= \begin{pmatrix} \sin{\theta} \\ 0 \\ \cos{\theta} \\ 0 \\ 0 \\ 0 \end{pmatrix}, \\ \theta &= \arctan \left( \frac{\omega_1}{\Omega_\textrm{A}} \right). \end{align} [/math]
The relaxation evolution matrix is defined as
[math] \begin{equation} R = \begin{pmatrix} -\mathrm{R}_{1\rho}{´}-\textrm{k}_\textrm{AB} & -\delta_A & 0 & \textrm{k}_\textrm{BA} & 0 & 0 \\ \delta_A & -\mathrm{R}_{1\rho}{´}-\textrm{k}_\textrm{AB} & -\omega_1 & 0 & \textrm{k}_\textrm{BA} & 0 \\ 0 & \omega_1 & -\mathrm{R}_1-\textrm{k}_\textrm{AB} & 0 & 0 & \textrm{k}_\textrm{BA} \\ \textrm{k}_\textrm{AB} & 0 & 0 & -\mathrm{R}_{1\rho}{´}-\textrm{k}_\textrm{BA} & -\delta_B & 0 \\ 0 & \textrm{k}_\textrm{AB} & 0 & \delta_B & -\mathrm{R}_{1\rho}{´}-\textrm{k}_\textrm{BA} & -\omega_1 \\ 0 & 0 & \textrm{k}_\textrm{AB} & 0 & \omega_1 & -\mathrm{R}_1-\textrm{k}_\textrm{BA} \\ \end{pmatrix}, \end{equation} [/math]
Essentials
It is essential to read in $R_{1}$ values before starting a calculation:
relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_values.txt', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
Where the data could be stored like
# mol_name res_num res_name spin_num spin_name value error
None 13 L None N 1.323940 0.146870
None 15 R None N 1.344280 0.140560
None 16 T None N 1.715140 0.136510
Parameters
The NS R1rho 2-site model has the parameters {$R_{1\rho}'$, $...$, $p_A$, $\Delta\omega$, $k_{ex}$}.
Reference
The reference for the NS R1rho 2-site model is:
- Korzhnev, D. M., Orekhov, V. Y., and Kay, L. E. (2005). Off-resonance R(1rho) NMR studies of exchange dynamics in proteins with low spin-lock fields: an application to a Fyn SH3 domain. J. Am. Chem. Soc., 127(2), 713-721. (10.1021/ja0446855).
Links
The implementation of the NS R1rho 2-site model in relax can be seen in the:
