Subsections


value.set

Image value

Synopsis

Set parameter values.

Defaults

value.set(val=None, param=None, index=0, spin_id=None, error=False, force=True)

Keyword arguments

val: The value(s).

param: The parameter(s).

index: The list index for when the parameter is a list of values. This is ignored in all other cases.

spin_id: The spin ID string to restrict value setting to.

error: A flag which if True will cause the error rather than parameter to be set.

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

Description

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

The value can be None, a single value, or an array of values while the parameter can be None, a string, or array of strings. The choice of which combination determines the behaviour of this function. The following table describes what occurs in each instance. In these columns, `None' corresponds to None, `1' corresponds to either a single value or single string, and `n' corresponds to either an array of values or an array of strings.

Please see Table 17.35 on page [*].


Table 17.35: The value and parameter combination options for the value.set user function.
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Spin ID string

For spin-specific parameters, the spin ID string can be used to restrict the value setting to a specific spin system or group of spins. It has no effect for global parameters such as in the N-state model and frame order analyses.

Relaxation curve fitting parameters

Please see Table 17.36 on page [*].


Table 17.36: Relaxation curve fitting parameter value setting.
Name Description Default
rx Either the R1 or R2 relaxation rate 8.0
i0 The initial intensity 10000.0
iinf The intensity at infinity 0.0

Model-free parameters

Please see Table 17.37 on page [*].


Table 17.37: Model-free parameter value setting.
Name Description Default
s2 S2, the model-free generalised order parameter (S2 = S2f.S2s) 0.8
s2f S2f, the faster motion model-free generalised order parameter 0.8
s2s S2s, the slower motion model-free generalised order parameter 0.8
local_tm The spin specific global correlation time (seconds) 1e-08
te Single motion effective internal correlation time (seconds) 1e-10
tf Faster motion effective internal correlation time (seconds) 1e-11
ts Slower motion effective internal correlation time (seconds) 1e-09
rex Chemical exchange relaxation (sigma_ex = Rex / omega**2) 0.0
csa Chemical shift anisotropy (unitless) -0.000172

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 17.38 on page [*].


Table 17.38: Reduced spectral density mapping parameter value setting.
Name Description Default
j0 Spectral density value at 0 MHz - J(0) None
jwx Spectral density value at the frequency of the heteronucleus - J(ωX) None
jwh Spectral density value at the frequency of the proton - J(ωH) None
csa Chemical shift anisotropy (unitless) -0.000172

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 17.39 on page [*].


Table 17.39: Consistency testing parameter value setting.
Name Description Default
j0 Spectral density value at 0 MHz (from Farrow et al. (1995) JBNMR, 6: 153-162) None
f_eta Eta-test (from Fushman et al. (1998) JACS, 120: 10947-10952) None
f_r2 R2-test (from Fushman et al. (1998) JACS, 120: 10947-10952) None
csa Chemical shift anisotropy (unitless) -0.000172
orientation Angle between the 15N-1H vector and the principal axis of the 15N chemical shift tensor 15.7
tc The single global correlation time estimate/approximation 1.3e-08

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 17.40 on page [*].


Table 17.40: N-state model parameter value setting.
Name Description Default Type
Axx The Axx component of the alignment tensor None float
Ayy The Ayy component of the alignment tensor None float
Axy The Axy component of the alignment tensor None float
Axz The Axz component of the alignment tensor None float
Ayz The Ayz component of the alignment tensor None float
probs The probabilities of each state 0.0 list
alpha The α Euler angles (for the rotation of each state) 0.0 list
beta The β Euler angles (for the rotation of each state) 0.0 list
gamma The γ Euler angles (for the rotation of each state) 0.0 list
paramagnetic_centre The paramagnetic centre None 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 17.41 on page [*].


Table 17.41: Relaxation dispersion parameter value setting.
Name Description Default Type
r2eff The effective transversal relaxation rate 10.0 dict
i0 The initial intensity 10000.0 dict
r1 The longitudinal relaxation rate 2.0 dict
r2 The transversal relaxation rate 10.0 dict
r2a The transversal relaxation rate for state A in the absence of exchange 10.0 dict
r2b The transversal relaxation rate for state B in the absence of exchange 10.0 dict
pA The population for state A 0.9 float
pB The population for state B 0.5 float
pC The population for state C 0.5 float
phi_ex The φ_ex = pA.pB.dw**2 value (ppmˆ2) 5.0 float
phi_ex_B The fast exchange factor between sites A and B (ppmˆ2) 5.0 float
phi_ex_C The fast exchange factor between sites A and C (ppmˆ2) 5.0 float
padw2 The pA.dw**2 value (ppmˆ2) 1.0 float
dw The chemical shift difference between states A and B (in ppm) 1.0 float
dw_AB The chemical shift difference between states A and B for 3-site exchange (in ppm) 1.0 float
dw_AC The chemical shift difference between states A and C for 3-site exchange (in ppm) 1.0 float
dw_BC The chemical shift difference between states B and C for 3-site exchange (in ppm) 1.0 float
dwH The proton chemical shift difference between states A and B (in ppm) 1.0 float
dwH_AB The proton chemical shift difference between states A and B for 3-site exchange (in ppm) 1.0 float
dwH_AC The proton chemical shift difference between states A and C for 3-site exchange (in ppm) 1.0 float
dwH_BC The proton chemical shift difference between states B and C for 3-site exchange (in ppm) 1.0 float
kex The exchange rate 1000.0 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) 1000.0 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) 1000.0 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) 1000.0 float
kB Approximate chemical exchange rate constant between sites A and B (rad.sˆ-1) 1000.0 float
kC Approximate chemical exchange rate constant between sites A and C (rad.sˆ-1) 1000.0 float
tex The time of exchange (tex = 1/kex) 0.001 float
k_AB The exchange rate from state A to state B 2.0 float
k_BA The exchange rate from state B to state A 1000.0 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 set the parameter values for the current data pipe to the default values, for all spins, type:

[numbers=none]
relax> value.set()

To set the parameter values of residue 10, which is in the current model-free data pipe `m4' and has the parameters {S2, τe, Rex}, the following can be used. Rex term is the value for the first given field strength.

[numbers=none]
relax> value.set([0.97, 2.048*1e-9, 0.149], spin_id=':10')

[numbers=none]
relax> value.set(val=[0.97, 2.048*1e-9, 0.149], spin_id=':10')

To set the CSA value of all spins to the default value, type:

[numbers=none]
relax> value.set(param='csa')

To set the CSA value of all spins to -172 ppm, type:

[numbers=none]
relax> value.set(-172 * 1e-6, 'csa')

[numbers=none]
relax> value.set(val=-172 * 1e-6, param='csa')

To set the NH bond length of all spins to 1.02 Å, type:

[numbers=none]
relax> value.set(1.02 * 1e-10, 'r')

[numbers=none]
relax> value.set(val=1.02 * 1e-10, param='r')

To set both the bond length and the CSA value to the default values, type:

[numbers=none]
relax> value.set(param=['r', 'csa'])

To set both τf and τs to 100 ps, type:

[numbers=none]
relax> value.set(100e-12, ['tf', 'ts'])

[numbers=none]
relax> value.set(val=100e-12, param=['tf', 'ts'])

To set the S2 and τe parameter values of residue 126, Ca spins to 0.56 and 13 ps, type:

[numbers=none]
relax> value.set([0.56, 13e-12], ['s2', 'te'], ':126@Ca')

[numbers=none]
relax> value.set(val=[0.56, 13e-12], param=['s2', 'te'], spin_id=':126@Ca')

[numbers=none]
relax> value.set(val=[0.56, 13e-12], param=['s2', 'te'], spin_id=':126@Ca')


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