Subsections
grace.write
Create a grace `.agr' file to visualise the 2D data.
grace.write(x_data_type=`res_num', y_data_type=None, spin_id=None, plot_data=`value', norm_type=`first', file=None, dir=`grace', force=False, norm=False)
x_data_type: The data type for the X-axis (no regular expression is allowed).
y_data_type: The data type for the Y-axis (no regular expression is allowed).
spin_id: The spin ID string.
plot_data: The data to use for the plot.
norm_type: How the graph should be normalised, if the norm flag is set.
file: The name of the file.
dir: The directory name.
force: A flag which, if set to True, will cause the file to be overwritten.
norm: A flag which, if set to True, will cause all graphs to be normalised to 1. This is for the normalisation of series type data. The point for normalisation is set with the norm_type argument.
This is designed to be as flexible as possible so that any combination of data can be plotted. The output is in the format of a Grace plot (also known as ACE/gr, Xmgr, and xmgrace) which only supports two dimensional plots. Three types of information can be used to create various types of plot. These include the x-axis and y-axis data types, the spin ID string, and the type of data plot.
The x-axis and y-axis data types should be plain strings, regular expression is not allowed. The two axes of the Grace plot can be any of the data types listed in the tables below. The only limitation is that the data must belong to the same data pipe.
If the x-axis data type is not given, the plot will default to having the residue numbering along the x-axis.Two special data types for the axes are:
- `res_num' -
- The axis will consist of the residue numbering.
- `spin_num' -
- The axis will consist of the spin numbering.
The spin ID string can be used to limit which spins are used in the plot. The default is that all spins will be used, however, the ID string can be used to select a subset of all spins, or a single spin for plots of Monte Carlo simulations, etc.
The property which is actually plotted can be controlled by the plot data setting. This can be one of the following:
- `value' -
- Plot values (with errors if they exist).
- `error' -
- Plot errors.
- `sims' -
- Plot the simulation values.
Normalisation is only allowed for series type data, for example the R2 exponential curves, and will be ignored for all other data types. If the norm flag is set to True then the y-value of the first point of the series will be set to 1. This normalisation is useful for highlighting errors in the data sets.
Please see Table 17.8 on page .
Table 17.8:
Relaxation curve fitting parameters and minimisation statistics.
Name |
Description |
rx |
Either the R1 or R2 relaxation rate |
i0 |
The initial intensity |
iinf |
The intensity at infinity |
chi2 |
Chi-squared value |
iter |
Optimisation iterations |
f_count |
Number of function calls |
g_count |
Number of gradient calls |
h_count |
Number of Hessian calls |
warning |
Optimisation warning |
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Please see Table 17.9 on page .
Table 17.9:
Steady-state NOE parameters.
Name |
Description |
noe |
The steady-state NOE value |
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Please see Table 17.10 on page .
Table 17.10:
Model-free parameters and minimisation statistics.
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) |
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Please see Table 17.11 on page .
Table 17.11:
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) |
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Please see Table 17.12 on page .
Table 17.12:
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 |
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Please see Table 17.13 on page .
Table 17.13:
Relaxation dispersion parameters and minimisation statistics.
Name |
Description |
r2eff |
The effective transversal relaxation rate |
i0 |
The initial intensity |
r1 |
The longitudinal relaxation rate |
r2 |
The transversal relaxation rate |
r2a |
The transversal relaxation rate for state A in the absence of exchange |
r2b |
The transversal relaxation rate for state B in the absence of exchange |
pA |
The population for state A |
pB |
The population for state B |
pC |
The population for state C |
phi_ex |
The φ_ex = pA.pB.dw**2 value (ppm^2) |
phi_ex_B |
The fast exchange factor between sites A and B (ppm^2) |
phi_ex_C |
The fast exchange factor between sites A and C (ppm^2) |
padw2 |
The pA.dw**2 value (ppm^2) |
dw |
The chemical shift difference between states A and B (in ppm) |
dw_AB |
The chemical shift difference between states A and B for 3-site exchange (in ppm) |
dw_AC |
The chemical shift difference between states A and C for 3-site exchange (in ppm) |
dw_BC |
The chemical shift difference between states B and C for 3-site exchange (in ppm) |
dwH |
The proton chemical shift difference between states A and B (in ppm) |
dwH_AB |
The proton chemical shift difference between states A and B for 3-site exchange (in ppm) |
dwH_AC |
The proton chemical shift difference between states A and C for 3-site exchange (in ppm) |
dwH_BC |
The proton chemical shift difference between states B and C for 3-site exchange (in ppm) |
kex |
The exchange rate |
kex_AB |
The exchange rate between sites A and B for 3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1) |
kex_AC |
The exchange rate between sites A and C for 3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1) |
kex_BC |
The exchange rate between sites B and C for 3-site exchange with kex_BC = k_BC + k_CB (rad.s^-1) |
kB |
Approximate chemical exchange rate constant between sites A and B (rad.s^-1) |
kC |
Approximate chemical exchange rate constant between sites A and C (rad.s^-1) |
tex |
The time of exchange (tex = 1/kex) |
k_AB |
The exchange rate from state A to state B |
k_BA |
The exchange rate from state B to state A |
chi2 |
Chi-squared value |
iter |
Optimisation iterations |
f_count |
Number of function calls |
g_count |
Number of gradient calls |
h_count |
Number of Hessian calls |
warning |
Optimisation warning |
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To write the NOE values for all spins to the Grace file `noe.agr', type one of:
[numbers=none]
relax> grace.write('res_num', 'noe', file='noe.agr')
[numbers=none]
relax> grace.write(y_data_type='noe', file='noe.agr')
[numbers=none]
relax> grace.write(x_data_type='res_num', y_data_type='noe', file='noe.agr')
[numbers=none]
relax> grace.write(y_data_type='noe', file='noe.agr', force=True)
To create a Grace file of `s2' vs. `te' for all spins, type one of:
[numbers=none]
relax> grace.write('s2', 'te', file='s2_te.agr')
[numbers=none]
relax> grace.write(x_data_type='s2', y_data_type='te', file='s2_te.agr')
[numbers=none]
relax> grace.write(x_data_type='s2', y_data_type='te', file='s2_te.agr', force=True)
To create a Grace file of the Monte Carlo simulation values of `rex' vs. `te' for residue 123, type one of:
[numbers=none]
relax> grace.write('rex', 'te', spin_id=':123', plot_data='sims', file='s2_te.agr')
[numbers=none]
relax> grace.write(x_data_type='rex', y_data_type='te', spin_id=':123', plot_data='sims', file='s2_te.agr')
By plotting the peak intensities, the integrity of exponential relaxation curves can be checked and anomalies searched for prior to model-free analysis or reduced spectral density mapping. For example the normalised average peak intensities can be plotted verses the relaxation time periods for the relaxation curves of all residues of a protein. The normalisation, whereby the initial peak intensity of each residue I(0) is set to 1, emphasises any problems. To produce this Grace file, type:
[numbers=none]
relax> grace.write(x_data_type='relax_times', y_data_type='ave_int', file='intensities_norm.agr', force=True, norm=True)
The relax user manual (PDF), created 2020-08-26.