Module it99
source code
The Ishima and Torchia (1999) 2-site all time scale exchange (with pA
>> pB) IT99 model.
Description
This module is for the function, gradient and Hessian of the IT99 model.
References
The model is named after the reference:
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Ishima R. and Torchia D.A. (1999). Estimating the time scale of
chemical exchange of proteins from measurements of transverse
relaxation rates in solution. J. Biomol. NMR, 14,
369-372. (DOI: 10.1023/A:1008324025406).
Equations
The equation used is:
phi_ex * tex
Rex ~= ------------------- ,
1 + omega_a^2*tex^2
phi_ex = pA * pB * delta_omega^2 ,
omega_a^2 = sqrt(omega_1eff^4 + pA^2*delta_omega^4) ,
R2eff = R20 + Rex ,
where tex = 1/(2kex), kex is the chemical exchange rate constant, pA
and pB are the populations of states A and B, and delta_omega is the
chemical shift difference between the two states. The effective
rotating frame field for a CPMG-type experiment is given by:
omega_1eff = 4*sqrt(3) * nu_cpmg
and therefore:
omega_1eff^4 = 2304 * nu_cpmg^4
Links
More information on the IT99 model can be found in the:
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r2eff_IT99(r20=None,
pA=None,
dw=None,
dw_orig=None,
tex=None,
cpmg_frqs=None,
back_calc=None)
Calculate the R2eff values for the IT99 model. |
source code
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__package__ = ' lib.dispersion '
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Imports:
isfinite,
fabs,
sqrt,
sum,
fix_invalid,
masked_where
r2eff_IT99(r20=None,
pA=None,
dw=None,
dw_orig=None,
tex=None,
cpmg_frqs=None,
back_calc=None)
| source code
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Calculate the R2eff values for the IT99 model.
See the module docstring for details.
- Parameters:
r20 (numpy float array of rank [NE][NS][NM][NO][ND]) - The R20 parameter value (R2 with no exchange).
pA (float) - The population of state A.
dw (numpy float array of rank [NE][NS][NM][NO][ND]) - The chemical exchange difference between states A and B in rad/s.
dw_orig (numpy float array of rank-1) - The chemical exchange difference between states A and B in ppm.
This is only for faster checking of zero value, which result in
no exchange.
tex (float) - The tex parameter value (the time of exchange in s/rad).
cpmg_frqs (numpy float array of rank [NE][NS][NM][NO][ND]) - The CPMG nu1 frequencies.
back_calc (numpy float array of rank [NE][NS][NM][NO][ND]) - The array for holding the back calculated R2eff values. Each
element corresponds to one of the CPMG nu1 frequencies.
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