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Function for copying model-free data from run1 to run2.
Keyword Arguments
~~~~~~~~~~~~~~~~~
run1: The name of the run to copy the sequence from.
run2: The name of the run to copy the sequence to.
sim: The simulation number.
Description
~~~~~~~~~~~
This function will copy all model-free data from 'run1' to 'run2'. Any model-free data in
'run2' will be overwritten. If the argument 'sim' is an integer, then only data from that
simulation will be copied.
Examples
~~~~~~~~
To copy all model-free data from the run 'm1' to the run 'm2', type:
relax> model_free.copy('m1', 'm2')
relax> model_free.copy(run1='m1', run2='m2')
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Function to create a model-free model.
Keyword Arguments
~~~~~~~~~~~~~~~~~
run: The run to assign the values to.
model: The name of the model-free model.
equation: The model-free equation.
params: The array of parameter names of the model.
res_num: The residue number.
Model-free equation
~~~~~~~~~~~~~~~~~~~
'mf_orig' selects the original model-free equations with parameters {S2, te}.
'mf_ext' selects the extended model-free equations with parameters {S2f, tf, S2, ts}.
'mf_ext2' selects the extended model-free equations with parameters {S2f, tf, S2s, ts}.
Model-free parameters
~~~~~~~~~~~~~~~~~~~~~
The following parameters are accepted for the original model-free equation:
'S2': The square of the generalised order parameter.
'te': The effective correlation time.
The following parameters are accepted for the extended model-free equation:
'S2f': The square of the generalised order parameter of the faster motion.
'tf': The effective correlation time of the faster motion.
'S2': The square of the generalised order parameter S2 = S2f * S2s.
'ts': The effective correlation time of the slower motion.
The following parameters are accepted for the extended 2 model-free equation:
'S2f': The square of the generalised order parameter of the faster motion.
'tf': The effective correlation time of the faster motion.
'S2s': The square of the generalised order parameter of the slower motion.
'ts': The effective correlation time of the slower motion.
The following parameters are accepted for all equations:
'Rex': The chemical exchange relaxation.
'r': The average bond length <r>.
'CSA': The chemical shift anisotropy.
Residue number
~~~~~~~~~~~~~~
If 'res_num' is supplied as an integer then the model will only be created for that residue,
otherwise the model will be created for all residues.
Examples
~~~~~~~~
The following commands will create the model-free model 'm1' which is based on the original
model-free equation and contains the single parameter 'S2'.
relax> model_free.create_model('m1', 'm1', 'mf_orig', ['S2'])
relax> model_free.create_model(run='m1', model='m1', params=['S2'], equation='mf_orig')
The following commands will create the model-free model 'large_model' which is based on the
extended model-free equation and contains the seven parameters 'S2f', 'tf', 'S2', 'ts',
'Rex', 'CSA', 'r'.
relax> model_free.create_model('test', 'large_model', 'mf_ext', ['S2f', 'tf', 'S2', 'ts',
'Rex', 'CSA', 'r'])
relax> model_free.create_model(run='test', model='large_model', params=['S2f', 'tf', 'S2',
'ts', 'Rex', 'CSA', 'r'], equation='mf_ext')
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Function for deleting all model-free data corresponding to the run.
Keyword Arguments
~~~~~~~~~~~~~~~~~
run: The name of the run.
Examples
~~~~~~~~
To delete all model-free data corresponding to the run 'm2', type:
relax> model_free.delete('m2')
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Function for removing the local tm parameter from a model.
Keyword Arguments
~~~~~~~~~~~~~~~~~
run: The run to assign the values to.
res_num: The residue number.
Description
~~~~~~~~~~~
This function will remove the local tm parameter from the model-free parameters of the given
run. Model-free parameters must already exist within the run yet, if there is no local tm,
nothing will happen.
If no residue number is given, then the function will apply to all residues.
Examples
~~~~~~~~
The following commands will remove the parameter 'tm' from the run 'local_tm':
relax> model_free.remove_tm('local_tm')
relax> model_free.remove_tm(run='local_tm')
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Function for the selection of a preset model-free model.
Keyword Arguments
~~~~~~~~~~~~~~~~~
run: The run to assign the values to.
model: The name of the preset model.
The preset models
~~~~~~~~~~~~~~~~~
The standard preset model-free models are
'm0': [],
'm1': [S2],
'm2': [S2, te],
'm3': [S2, Rex],
'm4': [S2, te, Rex],
'm5': [S2f, S2, ts],
'm6': [S2f, tf, S2, ts],
'm7': [S2f, S2, ts, Rex],
'm8': [S2f, tf, S2, ts, Rex],
'm9': [Rex].
The preset model-free models with optimisation of the CSA value are
'm10': [CSA],
'm11': [CSA, S2],
'm12': [CSA, S2, te],
'm13': [CSA, S2, Rex],
'm14': [CSA, S2, te, Rex],
'm15': [CSA, S2f, S2, ts],
'm16': [CSA, S2f, tf, S2, ts],
'm17': [CSA, S2f, S2, ts, Rex],
'm18': [CSA, S2f, tf, S2, ts, Rex],
'm19': [CSA, Rex].
The preset model-free models with optimisation of the bond length are
'm20': [r],
'm21': [r, S2],
'm22': [r, S2, te],
'm23': [r, S2, Rex],
'm24': [r, S2, te, Rex],
'm25': [r, S2f, S2, ts],
'm26': [r, S2f, tf, S2, ts],
'm27': [r, S2f, S2, ts, Rex],
'm28': [r, S2f, tf, S2, ts, Rex],
'm29': [r, CSA, Rex].
The preset model-free models with both optimisation of the bond length and CSA are
'm30': [r, CSA],
'm31': [r, CSA, S2],
'm32': [r, CSA, S2, te],
'm33': [r, CSA, S2, Rex],
'm34': [r, CSA, S2, te, Rex],
'm35': [r, CSA, S2f, S2, ts],
'm36': [r, CSA, S2f, tf, S2, ts],
'm37': [r, CSA, S2f, S2, ts, Rex],
'm38': [r, CSA, S2f, tf, S2, ts, Rex],
'm39': [r, CSA, Rex].
Warning: The models in the thirties range fail when using standard R1, R2, and NOE
relaxation data. This is due to the extreme flexibly of these models where a change in the
parameter 'r' is compensated by a corresponding change in the parameter 'CSA' and
vice versa.
Additional preset model-free models, which are simply extensions of the above models with
the addition of a local tm parameter are:
'tm0': [tm],
'tm1': [tm, S2],
'tm2': [tm, S2, te],
'tm3': [tm, S2, Rex],
'tm4': [tm, S2, te, Rex],
'tm5': [tm, S2f, S2, ts],
'tm6': [tm, S2f, tf, S2, ts],
'tm7': [tm, S2f, S2, ts, Rex],
'tm8': [tm, S2f, tf, S2, ts, Rex],
'tm9': [tm, Rex].
The preset model-free models with optimisation of the CSA value are
'tm10': [tm, CSA],
'tm11': [tm, CSA, S2],
'tm12': [tm, CSA, S2, te],
'tm13': [tm, CSA, S2, Rex],
'tm14': [tm, CSA, S2, te, Rex],
'tm15': [tm, CSA, S2f, S2, ts],
'tm16': [tm, CSA, S2f, tf, S2, ts],
'tm17': [tm, CSA, S2f, S2, ts, Rex],
'tm18': [tm, CSA, S2f, tf, S2, ts, Rex],
'tm19': [tm, CSA, Rex].
The preset model-free models with optimisation of the bond length are
'tm20': [tm, r],
'tm21': [tm, r, S2],
'tm22': [tm, r, S2, te],
'tm23': [tm, r, S2, Rex],
'tm24': [tm, r, S2, te, Rex],
'tm25': [tm, r, S2f, S2, ts],
'tm26': [tm, r, S2f, tf, S2, ts],
'tm27': [tm, r, S2f, S2, ts, Rex],
'tm28': [tm, r, S2f, tf, S2, ts, Rex],
'tm29': [tm, r, CSA, Rex].
The preset model-free models with both optimisation of the bond length and CSA are
'tm30': [tm, r, CSA],
'tm31': [tm, r, CSA, S2],
'tm32': [tm, r, CSA, S2, te],
'tm33': [tm, r, CSA, S2, Rex],
'tm34': [tm, r, CSA, S2, te, Rex],
'tm35': [tm, r, CSA, S2f, S2, ts],
'tm36': [tm, r, CSA, S2f, tf, S2, ts],
'tm37': [tm, r, CSA, S2f, S2, ts, Rex],
'tm38': [tm, r, CSA, S2f, tf, S2, ts, Rex],
'tm39': [tm, r, CSA, Rex].
Residue number
~~~~~~~~~~~~~~
If 'res_num' is supplied as an integer then the model will only be selected for that
residue, otherwise the model will be selected for all residues.
Examples
~~~~~~~~
To pick model 'm1' for all selected residues and assign it to the run 'mixed', type:
relax> model_free.select_model('mixed', 'm1')
relax> model_free.select_model(run='mixed', model='m1')
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