value.set

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.

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)	-0.00017199999999999998

Setting a parameter value may have no effect depending on which model-free model is chosen. For example if S²_f values and S²_s 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 R_ex 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)	-0.00017199999999999998

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)	-0.00017199999999999998
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 (ppm^2)	5.0	float
phi_ex_B	The fast exchange factor between sites A and B (ppm^2)	5.0	float
phi_ex_C	The fast exchange factor between sites A and C (ppm^2)	5.0	float
padw2	The pA.dw**2 value (ppm^2)	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.s^-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.s^-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.s^-1)	1000.0	float
kB	Approximate chemical exchange rate constant between sites A and B (rad.s^-1)	1000.0	float
kC	Approximate chemical exchange rate constant between sites A and C (rad.s^-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, τ_e, R_ex}, the following can be used. R_ex 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 τ_f and τ_s 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 τ_e 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')