This was the relax commands for the analysis:
-----------------------------
== cpmg fixed ==
=== Initial ===
<pre>
# Create the 'rx' data pipe.
pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx')
# The type of experiment
relax_disp.exp_type(exp_type='cpmg fixed')
# Read the sequence from file
sequence.read(file='table_ser_files_model.txt',
dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)
#### Repeat for all peak intensity files
# Read the intensities from columns
spectrum.read_intensities(file='table_ser_files_model.txt',
dir=None, spectrum_id='0_2', heteronuc='N', proton='HN', int_method='point
sum', int_col=(6), spin_id_col=None, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
spin_id=None, ncproc=None)
relax_disp.cpmg_frq(spectrum_id='0_2', cpmg_frq=40.0)
relax_disp.relax_time(spectrum_id='0_2', time=0.05)
spectrometer.frequency(id='0_2', frq=750.0614444, units='MHz')
#Define replicated:
relax> spectrum.replicated(spectrum_ids=['0_2', '7_2', '14_2'])
relax> spectrum.replicated(spectrum_ids=['15_14', '16_14', '20_14'])
relax> spectrum.replicated(spectrum_ids=['3_30', '8_30', '17_30'])
relax> spectrum.replicated(spectrum_ids=['9_46', '19_46', '22_46'])
# Define isotope
relax> spin.isotope(isotope='15N', spin_id='@N*', force=True)
# Make error analysis
spectrum.error_analysis(subset=['0_2', '1_0', '2_8', '3_30', '4_4', '5_42',
'6_6', '7_2', '8_30', '9_46', '10_10', '11_18', '12_26', '13_38', '14_2',
'15_14', '16_14', '17_30', '18_22', '19_46', '20_14', '21_34', '22_46'])
</pre>
=== - The 'R2eff' model - ===
<pre>
pipe.copy(pipe_from='origin rx', pipe_to='R2eff', bundle_to='rx')
pipe.switch(pipe_name='R2eff')
relax_disp.select_model(model='R2eff')
calc(verbosity=1)
results.write(file='results', dir='R2eff', compress_type=1, force=True)
relax_disp.plot_disp_curves(dir='R2eff', force=True)
value.write(param='r2eff', file='r2eff.out', dir='R2eff', scaling=1.0,
comment=None, bc=False, force=True)
grace.write(x_data_type='res_num', y_data_type='r2eff', spin_id=None,
plot_data='value', file='r2eff.agr', dir='R2eff', force=True, norm=False)
</pre>
=== - The 'No Rex' model - ===
<pre>
pipe.copy(pipe_from='origin rx', pipe_to='No Rex', bundle_to='rx')
pipe.switch(pipe_name='No Rex')
relax_disp.select_model(model='No Rex')
value.copy(pipe_from='R2eff', pipe_to='No Rex', param='r2eff')
grid_search(lower=None, upper=None, inc=21, constraints=True, verbosity=1)
minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000,
constraints=True, scaling=True, verbosity=1)
monte_carlo.setup(number=500)
monte_carlo.create_data(method='back_calc')
monte_carlo.initial_values()
minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000,
constraints=True, scaling=True, verbosity=1)
monte_carlo.error_analysis()
results.write(file='results', dir='No Rex', compress_type=1, force=True)
relax_disp.plot_disp_curves(dir='No Rex', force=True)
#Value write?
grace.write(x_data_type='res_num', y_data_type='chi2', spin_id=None,
plot_data='value', file='chi2.agr', dir='No Rex', force=True, norm=False)
</pre>
=== - The 'LM63' model - ===
<pre>
pipe.copy(pipe_from='origin rx', pipe_to='LM63', bundle_to='rx')
pipe.switch(pipe_name='LM63')
relax_disp.select_model(model='LM63')
value.copy(pipe_from='R2eff', pipe_to='LM63', param='r2eff')
grid_search(lower=None, upper=None, inc=21, constraints=True, verbosity=1)
minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000,
constraints=True, scaling=True, verbosity=1)
monte_carlo.setup(number=500)
monte_carlo.create_data(method='back_calc')
monte_carlo.initial_values()
minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000,
constraints=True, scaling=True, verbosity=1)
monte_carlo.error_analysis()
results.write(file='results', dir='LM63', compress_type=1, force=True)
relax_disp.plot_disp_curves(dir='LM63', force=True)
value.write(param='phi_ex', file='phi_ex.out', dir='LM63', scaling=1.0,
comment=None, bc=False, force=True)
grace.write(x_data_type='res_num', y_data_type='phi_ex', spin_id=None,
plot_data='value', file='phi_ex.agr', dir='LM63', force=True, norm=False)
grace.write(x_data_type='res_num', y_data_type='chi2', spin_id=None,
plot_data='value', file='chi2.agr', dir='LM63', force=True, norm=False)
</pre>
=== - The 'CR72' model - ===
<pre>
pipe.copy(pipe_from='origin rx', pipe_to='CR72', bundle_to='rx')
pipe.switch(pipe_name='CR72')
relax_disp.select_model(model='CR72')
value.copy(pipe_from='R2eff', pipe_to='CR72', param='r2eff')
grid_search(lower=None, upper=None, inc=21, constraints=True, verbosity=1)
minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000,
constraints=True, scaling=True, verbosity=1)
monte_carlo.setup(number=500)
monte_carlo.create_data(method='back_calc')
monte_carlo.initial_values()
minimise(min_algor='simplex', line_search=None, hessian_mod=None,
hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000,
constraints=True, scaling=True, verbosity=1)
monte_carlo.error_analysis()
results.write(file='results', dir='CR72', compress_type=1, force=True)
relax_disp.plot_disp_curves(dir='CR72', force=True)
#Value write?
grace.write(x_data_type='res_num', y_data_type='chi2', spin_id=None,
plot_data='value', file='chi2.agr', dir='CR72', force=True, norm=False)
</pre>
=== Model selection ===
<pre>
model_selection(method='AIC', modsel_pipe='final', bundle=None, pipes=['No
Rex', 'LM63', 'CR72'])
results.write(file='results', dir='final', compress_type=1, force=True)
relax_disp.plot_disp_curves(dir='final', force=True)
value.write(param='phi_ex', file='phi_ex.out', dir='final', scaling=1.0,
comment=None, bc=False, force=True)
grace.write(x_data_type='res_num', y_data_type='phi_ex', spin_id=None,
plot_data='value', file='phi_ex.agr', dir='final', force=True, norm=False)
grace.write(x_data_type='res_num', y_data_type='chi2', spin_id=None,
plot_data='value', file='chi2.agr', dir='final', force=True, norm=False)
</pre>
Troels Emtekær Linnet
2013/6/11 Troels Emtekær Linnet <tlinnet@xxxxxxxxx>
Hi!
I performed 'cpmg fixed' a relaxation dispersion analysis, for dataset
with 68 residues.
Having 22 intensity files, with 4 triple replications.
I took from 17 pm to 13 pm following day, app 20 hours.
The analysed models were: R2eff', 'No Rex','LM63','CR72'
Is 20 hours for an analysis expected?
, or should I look for some errors somewhere?
Relax made a model selection.
model_selection(method='AIC', modsel_pipe='final', bundle=None, pipes=['No
Rex', 'LM63', 'CR72'])
How can I inspect which model is then chosen?
Then I would like to make a global fit / cluster analysis.
Is this implemented yet?
And should I use the:
User functions (n-z) -> relax_disp -> cluster ?
By the way.
The sherekhan input function is super great!
Thanks a lot :-)
This is super great
Troels Emtekær Linnet
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Re: Time of running, Model selection and global/cluster analysis for relaxation dispersion analysis