set(self,
run=None,
params=None,
time_scale=1.0,
d_scale=1.0,
angle_units='deg',
param_types=0,
axial_type=None,
fixed=1)
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Function for setting up the diffusion tensor.
Keyword Arguments
~~~~~~~~~~~~~~~~~
run: The name of the run to assign the data to.
params: The diffusion tensor data.
time_scale: The correlation time scaling value.
d_scale: The diffusion tensor eigenvalue scaling value.
angle_units: The units for the angle parameters.
param_types: A flag to select different parameter combinations.
axial_type: A string, which if supplied with axially symmetric parameters, will restrict
the tensor to either being 'oblate' or 'prolate'.
fixed: A flag specifying whether the diffusion tensor is fixed or can be optimised.
Description
~~~~~~~~~~~
Isotropic diffusion.
To select isotropic diffusion, the parameters argument should be a single floating point
number. The number is the value of the isotropic global correlation time in seconds. To
specify the time in nanoseconds, set the 'time_scale' argument to 1e-9. Alternative
parameters can be used by changing the 'param_types' flag to the following integers:
0 - tm (Default)
1 - Diso
where:
tm = 1 / 6Diso
Axially symmetric diffusion.
To select axially symmetric anisotropic diffusion, the parameters argument should be a tuple
of floating point numbers of length four. A tuple is a type of data structure enclosed in
round brackets, the elements of which are separated by commas. Alternative sets of
parameters, 'param_types', are:
0 - (tm, Da, theta, phi) (Default)
1 - (tm, Dratio, theta, phi)
2 - (Dpar, Dper, theta, phi)
3 - (Diso, Da, theta, phi)
4 - (Diso, Dratio, theta, phi)
where:
tm = 1 / 6Diso
Diso = 1/3 (Dpar + 2Dper)
Da = 1/3 (Dpar - Dper)
Dratio = Dpar / Dper
The diffusion tensor is defined by the vector Dpar. The angle alpha describes the bond
vector with respect to the diffusion frame while the spherical angles {theta, phi} describe
the diffusion tensor with respect to the PDB frame. Theta is the polar angle and phi is the
azimuthal angle defined between:
0 <= theta <= pi
0 <= phi <= 2pi
The angle alpha is defined between:
0 <= alpha <= 2pi
The 'axial_type' argument should be 'oblate', 'prolate', or None. The argument will be
ignored if the diffusion tensor is not axially symmetric. If 'oblate' is given, then the
constraint Dper >= Dpar is used. If 'prolate' is given, then the constraint Dper <= Dpar is
used. If nothing is supplied, then Dper and Dpar will be allowed to have any values. To
prevent minimisation of diffusion tensor parameters in a space with two minima, it is
recommended to specify which tensor to be minimised, thereby partitioning the two minima
into the two subspaces (the partition is where Da equals 0).
Anisotropic diffusion.
To select fully anisotropic diffusion, the parameters argument should be a tuple of length
six. A tuple is a type of data structure enclosed in round brackets, the elements of which
are separated by commas. Alternative sets of parameters, 'param_types', are:
0 - (tm, Da, Dr, alpha, beta, gamma) (Default)
1 - (Diso, Da, Dr, alpha, beta, gamma)
2 - (Dx, Dy, Dz, alpha, beta, gamma)
where:
tm = 1 / 6Diso
Diso = 1/3 (Dx + Dy + Dz)
Da = 1/3 (Dz - (Dx + Dy)/2)
Dr = (Dx - Dy)/2
The angles alpha, beta, and gamma are the Euler angles describing the diffusion tensor
within the PDB frame. These angles are defined using the z-y-z axis rotation notation where
alpha is the initial rotation angle around the z-axis, beta is the rotation angle around the
y-axis, and gamma is the final rotation around the z-axis again. The angles are defined
between:
0 <= alpha <= 2pi
0 <= beta <= pi
0 <= gamma <= 2pi
Within the PDB frame, the bond vector is described using the spherical angels theta and phi
where theta is the polar angle and phi is the azimuthal angle defined between:
0 <= theta <= pi
0 <= phi <= 2pi
Units.
The 'time_scale' argument should be a floating point number. Parameters affected by this
value are: tm.
The 'd_scale' argument should also be a floating point number. Parameters affected by this
value are: Diso; Dpar; Dper; Da; Dr; Dx; Dy; Dz.
The 'angle_units' argument should either be the string 'deg' or 'rad'. Parameters affected
are: theta; phi; alpha; beta; gamma.
Examples
~~~~~~~~
To set an isotropic diffusion tensor with a correlation time of 10ns, assigning it to the
run 'm1', type:
relax> diffusion_tensor('m1', 10e-9)
relax> diffusion_tensor(run='m1', params=10e-9)
relax> diffusion_tensor('m1', 10.0, 1e-9)
relax> diffusion_tensor(run='m1', params=10.0, time_scale=1e-9, fixed=1)
To select axially symmetric diffusion with a tm value of 8.5ns, Dratio of 1.1, theta value
of 20 degrees, and phi value of 20 degrees, and assign it to the run 'm8', type:
relax> diffusion_tensor('m8', (8.5e-9, 1.1, 20.0, 20.0), param_types=1)
To select an axially symmetric diffusion tensor with a Dpar value of 1.698e7, Dper value of
1.417e7, theta value of 67.174 degrees, and phi value of -83.718 degrees, and assign it to
the run 'axial', type one of:
relax> diffusion_tensor('axial', (1.698e7, 1.417e7, 67.174, -83.718), param_types=1)
relax> diffusion_tensor(run='axial', params=(1.698e7, 1.417e7, 67.174, -83.718),
param_types=1)
relax> diffusion_tensor('axial', (1.698e-1, 1.417e-1, 67.174, -83.718), param_types=1,
d_scale=1e8)
relax> diffusion_tensor(run='axial', params=(1.698e-1, 1.417e-1, 67.174, -83.718),
param_types=1, d_scale=1e8)
relax> diffusion_tensor('axial', (1.698e-1, 1.417e-1, 1.1724, -1.4612), param_types=1,
d_scale=1e8, angle_units='rad')
relax> diffusion_tensor(run='axial', params=(1.698e-1, 1.417e-1, 1.1724, -1.4612),
param_types=1, d_scale=1e8, angle_units='rad', fixed=1)
To select fully anisotropic diffusion, type:
relax> diffusion_tensor('m5', (1.340e7, 1.516e7, 1.691e7, -82.027, -80.573, 65.568),
param_types=2)
To select and minimise an isotropic diffusion tensor, type (followed by a minimisation
command):
relax> diffusion_tensor('diff', 10e-9, fixed=0)
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