dx.map

params: The parameters to be mapped. This should be an array of strings, the meanings of which are described below.

map_type: The type of map to create. For example the default, a 3D isosurface, the type is `Iso3D'. See below for more details.

inc: The number of increments to map in each dimension. This value controls the resolution of the map.

lower: The lower bounds of the space. If you wish to change the lower bounds of the map then supply an array of length equal to the number of parameters in the model. A lower bound for each parameter must be supplied. If nothing is supplied then the defaults will be used.

upper: The upper bounds of the space. If you wish to change the upper bounds of the map then supply an array of length equal to the number of parameters in the model. A upper bound for each parameter must be supplied. If nothing is supplied then the defaults will be used.

axis_incs: The number of increments or ticks displaying parameter values along the axes of the OpenDX plot.

file_prefix: The file name. All the output files are prefixed with this name. The main file containing the data points will be called the value of `file'. The OpenDX program will be called `file.net' and the OpenDX import file will be called `file.general'.

dir: The directory to output files to. Set this to `None' if you do not want the files to be placed in subdirectory. If the directory does not exist, it will be created.

point: This argument allows specific points in the optimisation space to be displayed as coloured spheres. This can be used to highlight a minimum or other any other feature of the space. Either a single point or a list of points can be supplied. Each point is a list of floating point numbers in the form [x, y, z]

chi_surface: A list of 4 numbers, setting the level for the 4 isosurfaces. Useful in scripting if you create a set of OpenDX maps with all the same contour levels. Ideal for comparisons.

create_par_file: A flag specifying whether to create a file with parameters and associated chi2 value. The default of False causes the file not to be created.

Description

This will map the space corresponding to the spin identifier and create the OpenDX files. The map type can be changed to one of the following supported map types:

**Table 17.2:** OpenDx mapping types.
Surface type	Name
3D isosurface	'Iso3D'

Model-free parameters

**Table 17.3:** Model-free parameters.
Name	Description
tm	Global correlation time
Diso	Isotropic component of the diffusion tensor
Dx	Eigenvalue associated with the x-axis of the diffusion tensor
Dy	Eigenvalue associated with the y-axis of the diffusion tensor
Dz	Eigenvalue associated with the z-axis of the diffusion tensor
Dpar	Diffusion coefficient parallel to the major axis of the spheroid diffusion tensor
Dper	Diffusion coefficient perpendicular to the major axis of the spheroid diffusion tensor
Da	Anisotropic component of the diffusion tensor
Dr	Rhombic component of the diffusion tensor
Dratio	Ratio of the parallel and perpendicular components of the spheroid diffusion tensor
alpha	The first Euler angle of the ellipsoid diffusion tensor
beta	The second Euler angle of the ellipsoid diffusion tensor
gamma	The third Euler angle of the ellipsoid diffusion tensor
theta	The polar angle defining the major axis of the spheroid diffusion tensor
phi	The azimuthal angle defining the major axis of the spheroid diffusion tensor
s2	S², the model-free generalised order parameter (S² = S²_f.S2s)
s2f	S²_f, the faster motion model-free generalised order parameter
s2s	S²_s, 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 = R_ex / omega**2)
csa	Chemical shift anisotropy (unitless)

N-state model parameters

**Table 17.4:** 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

Relaxation dispersion parameters

**Table 17.5:** 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 (ppm^2)	float
phi_ex_B	The fast exchange factor between sites A and B (ppm^2)	float
phi_ex_C	The fast exchange factor between sites A and C (ppm^2)	float
padw2	The pA.dw**2 value (ppm^2)	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.s^-1)	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)	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)	float
kB	Approximate chemical exchange rate constant between sites A and B (rad.s^-1)	float
kC	Approximate chemical exchange rate constant between sites A and C (rad.s^-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

Frame order parameters

**Table 17.6:** Frame order parameters.
Name	Description
pivot_x	The pivot point position x coordinate
pivot_y	The pivot point position y coordinate
pivot_z	The pivot point position z coordinate
pivot_disp	The 2 ^nd pivot point displacement - the minimum distance between the two rotor axes
ave_pos_x	The average position x translation
ave_pos_y	The average position y translation
ave_pos_z	The average position z translation
ave_pos_alpha	The average position α Euler angle
ave_pos_beta	The average position β Euler angle
ave_pos_gamma	The average position γ Euler angle
eigen_alpha	The Eigenframe α Euler angle
eigen_beta	The Eigenframe β Euler angle
eigen_gamma	The Eigenframe γ Euler angle
axis_theta	The cone axis polar angle (for the isotropic cone model)
axis_phi	The cone axis azimuthal angle (for the isotropic cone model)
axis_alpha	The rotor axis α angle (the rotation angle out of the xy plane)
cone_theta_x	The pseudo-ellipse cone opening half-angle for the x-axis
cone_theta_y	The pseudo-ellipse cone opening half-angle for the y-axis
cone_theta	The isotropic cone opening half-angle
cone_sigma_max	The torsion angle
cone_sigma_max_2	The torsion angle of the 2 ^nd motional mode

Prompt examples

The following commands will generate a map of the extended model-free space for model `m5' consisting of the parameters {S², S²_f, τ_s}. Files will be output into the directory `dx' and will be prefixed by `map'. In this case, the system is a protein and residue number 6 will be mapped.

To map the model-free space `m4' for residue 2, spin N6 defined by the parameters {S², τ_e, R_ex}, name the results `test', and to place the files in the current directory, use one of the following commands: