Subsections


value.copy

Image value Image list-add

Synopsis

Copy parameters from one data pipe to another.

Defaults

value.copy(pipe_from=None, pipe_to=None, param=None, force=False)

Keyword arguments

pipe_from: The name of the pipe to copy from.

pipe_to: The name of the pipe to copy to.

param: The parameter to copy. Only one parameter may be selected.

force: A flag which, if set to True, will cause the destination parameter to be overwritten.

Description

If this is used to change values of previously minimised parameters, then the minimisation statistics (chi-squared value, iteration count, function count, gradient count, and Hessian count) will be reset.

Relaxation curve fitting parameters

Please see Table 17.27 on page [*].


Table 17.27: Relaxation curve fitting parameters.
Name Description
rx Either the R1 or R2 relaxation rate
i0 The initial intensity
iinf The intensity at infinity

Model-free parameters

Please see Table 17.28 on page [*].


Table 17.28: Model-free parameters.
Name Description
s2 S2, the model-free generalised order parameter (S2 = S2f.S2s)
s2f S2f, the faster motion model-free generalised order parameter
s2s S2s, the slower motion model-free generalised order parameter
local_tm The spin specific global correlation time (seconds)
te Single motion effective internal correlation time (seconds)
tf Faster motion effective internal correlation time (seconds)
ts Slower motion effective internal correlation time (seconds)
rex Chemical exchange relaxation (sigma_ex = Rex / omega**2)
csa Chemical shift anisotropy (unitless)

Setting a parameter value may have no effect depending on which model-free model is chosen. For example if S2f values and S2s values are set but the data pipe corresponds to the model-free model `m4' then because these data values are not parameters of the model they will have no effect.

Note that the Rex values are scaled quadratically with field strength and should be supplied as a field strength independent value. Use the following formula to obtain the correct value:

    value = rex / (2.0 * pi * frequency) ** 2

where:

rex is the chemical exchange value for the current frequency.
frequency is the proton frequency corresponding to the data.

Reduced spectral density mapping parameters

Please see Table 17.29 on page [*].


Table 17.29: Reduced spectral density mapping parameters.
Name Description
j0 Spectral density value at 0 MHz - J(0)
jwx Spectral density value at the frequency of the heteronucleus - J(ωX)
jwh Spectral density value at the frequency of the proton - J(ωH)
csa Chemical shift anisotropy (unitless)

In reduced spectral density mapping, the CSA value must be set prior to the calculation of spectral density values.

Consistency testing parameters

Please see Table 17.30 on page [*].


Table 17.30: Consistency testing parameters.
Name Description
j0 Spectral density value at 0 MHz (from Farrow et al. (1995) JBNMR, 6: 153-162)
f_eta Eta-test (from Fushman et al. (1998) JACS, 120: 10947-10952)
f_r2 R2-test (from Fushman et al. (1998) JACS, 120: 10947-10952)
csa Chemical shift anisotropy (unitless)
orientation Angle between the 15N-1H vector and the principal axis of the 15N chemical shift tensor
tc The single global correlation time estimate/approximation

In consistency testing, the CSA value, angle Theta (`orientation') and global correlation time must be set prior to the calculation of consistency functions.

N-state model parameters

Please see Table 17.31 on page [*].


Table 17.31: N-state model parameters.
Name Description Type
Axx The Axx component of the alignment tensor float
Ayy The Ayy component of the alignment tensor float
Axy The Axy component of the alignment tensor float
Axz The Axz component of the alignment tensor float
Ayz The Ayz component of the alignment tensor float
probs The probabilities of each state list
alpha The α Euler angles (for the rotation of each state) list
beta The β Euler angles (for the rotation of each state) list
gamma The γ Euler angles (for the rotation of each state) list
paramagnetic_centre The paramagnetic centre list

Setting parameters for the N-state model is a little different from the other type of analyses as each state has a set of parameters with the same names as the other states. To set the parameters for a specific state c (ranging from 0 for the first to N-1 for the last, the number c should be given as the index argument. So the Euler angle γ of the third state is specified using the parameter name `gamma' and index of 2.

Relaxation dispersion parameters

Please see Table 17.32 on page [*].


Table 17.32: Relaxation dispersion parameters.
Name Description Type
r2eff The effective transversal relaxation rate dict
i0 The initial intensity dict
r1 The longitudinal relaxation rate dict
r2 The transversal relaxation rate dict
r2a The transversal relaxation rate for state A in the absence of exchange dict
r2b The transversal relaxation rate for state B in the absence of exchange dict
pA The population for state A float
pB The population for state B float
pC The population for state C float
phi_ex The φ_ex = pA.pB.dw**2 value (ppmˆ2) float
phi_ex_B The fast exchange factor between sites A and B (ppmˆ2) float
phi_ex_C The fast exchange factor between sites A and C (ppmˆ2) float
padw2 The pA.dw**2 value (ppmˆ2) float
dw The chemical shift difference between states A and B (in ppm) float
dw_AB The chemical shift difference between states A and B for 3-site exchange (in ppm) float
dw_AC The chemical shift difference between states A and C for 3-site exchange (in ppm) float
dw_BC The chemical shift difference between states B and C for 3-site exchange (in ppm) float
dwH The proton chemical shift difference between states A and B (in ppm) float
dwH_AB The proton chemical shift difference between states A and B for 3-site exchange (in ppm) float
dwH_AC The proton chemical shift difference between states A and C for 3-site exchange (in ppm) float
dwH_BC The proton chemical shift difference between states B and C for 3-site exchange (in ppm) float
kex The exchange rate float
kex_AB The exchange rate between sites A and B for 3-site exchange with kex_AB = k_AB + k_BA (rad.sˆ-1) float
kex_AC The exchange rate between sites A and C for 3-site exchange with kex_AC = k_AC + k_CA (rad.sˆ-1) float
kex_BC The exchange rate between sites B and C for 3-site exchange with kex_BC = k_BC + k_CB (rad.sˆ-1) float
kB Approximate chemical exchange rate constant between sites A and B (rad.sˆ-1) float
kC Approximate chemical exchange rate constant between sites A and C (rad.sˆ-1) float
tex The time of exchange (tex = 1/kex) float
k_AB The exchange rate from state A to state B float
k_BA The exchange rate from state B to state A float

Any of the relaxation dispersion parameters which are of the `float' type can be set. Note that setting values for parameters which are not part of the model will have no effect.

Frame order parameters

Please see Table 17.6 on page [*].

Prompt examples

To copy the CSA values from the data pipe `m1' to `m2', type:

[numbers=none]
relax> value.copy('m1', 'm2', 'csa')


The relax user manual (PDF), created 2016-10-28.