I'll continue this at http://thread.gmane.org/gmane.science.nmr.relax.scm/22733/.
Regards, Edward On 18 August 2014 17:17, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > I will remove the nesting of IT99, since it also worried me. > > But do you really intent to stay on the argument that nesting should > always be from CR72? > > What if the model pipe for B14 is available. > Or from NS CPMG 2-site expanded ? > > Is this issue rather related how to sort the models first? > > Best > Troels > > > > 2014-08-18 16:41 GMT+02:00 Edward d'Auvergne <[email protected]>: >> Note that I used the CR72 model as a base for many other slow exchange >> models as it is a robust and quick solution which in most cases >> accurately approximates the parameters of other models, especially the >> numeric models. >> >> Regards, >> >> Edward >> >> >> On 18 August 2014 16:38, Edward d'Auvergne <[email protected]> wrote: >>> Hi, >>> >>> The model IT99 is extremely different to all other models, hence it is >>> not nested in the auto-analysis. No other model approximates it >>> parameters in any meaningful sense. See >>> test_suite/shared_data/dispersion/software_comparison for example. I >>> think that the model IT99 should have no corresponding nested model: >>> >>> MODEL_NESTING = { >>> ... >>> MODEL_IT99: None >>> ... >>> } >>> >>> To see this problem, just take any test data and optimise both CR72 >>> and IT99 and see if you can get any parameters to be close between the >>> two models. The new model nesting protocol is really starting to >>> worry me. Why did it change in the first place? >>> >>> Regards, >>> >>> Edward >>> >>> >>> >>> >>> On 12 August 2014 10:54, <[email protected]> wrote: >>>> Author: tlinnet >>>> Date: Tue Aug 12 10:54:49 2014 >>>> New Revision: 24988 >>>> >>>> URL: http://svn.gna.org/viewcvs/relax?rev=24988&view=rev >>>> Log: >>>> Fix for nesting kex, when model is CR72, and analysed models is IT99. >>>> >>>> sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation >>>> rate for the off-resonance R1rho relaxation dispersion models. >>>> >>>> Modified: >>>> branches/R1_fitting/specific_analyses/relax_disp/variables.py >>>> >>>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>>> >>>> Modified: branches/R1_fitting/specific_analyses/relax_disp/variables.py >>>> URL: >>>> http://svn.gna.org/viewcvs/relax/branches/R1_fitting/specific_analyses/relax_disp/variables.py?rev=24988&r1=24987&r2=24988&view=diff >>>> ============================================================================== >>>> --- branches/R1_fitting/specific_analyses/relax_disp/variables.py >>>> (original) >>>> +++ branches/R1_fitting/specific_analyses/relax_disp/variables.py >>>> Tue Aug 12 10:54:49 2014 >>>> @@ -911,6 +911,10 @@ >>>> elif param == 'phi_ex' and compa_model.model in >>>> MODEL_LIST_ANALYTIC_CPMG + MODEL_LIST_NUMERIC_CPMG and model in >>>> MODEL_LIST_ANALYTIC_CPMG + MODEL_LIST_NUMERIC_CPMG: >>>> continue >>>> >>>> + # Special situation, where 'kex'=1/tex can still be >>>> nested from IT99 model. >>>> + elif param == 'tex' and compa_model.model in >>>> MODEL_LIST_ANALYTIC_CPMG + MODEL_LIST_NUMERIC_CPMG and model in >>>> MODEL_LIST_ANALYTIC_CPMG + MODEL_LIST_NUMERIC_CPMG: >>>> + continue >>>> + >>>> # Else break out of the loop. >>>> else: >>>> # Break the for loop, if not found. >>>> @@ -953,6 +957,13 @@ >>>> if compa_model.model in MODEL_LIST_R1RHO_W_R1_ONLY + >>>> MODEL_LIST_R1RHO_FIT_R1_ONLY: >>>> return model_info, compa_model >>>> >>>> + # Special case for IT99. >>>> + elif model in [MODEL_IT99]: >>>> + # Loop over the models. >>>> + for compa_model in compa_models: >>>> + # If one of the comparable models is in list with R1rho >>>> R1, return this. >>>> + if compa_model.model in MODEL_LIST_ANALYTIC_CPMG + >>>> MODEL_LIST_NUMERIC_CPMG: >>>> + return model_info, compa_model >>>> >>>> # If there is no comparable models according to EXP_TYPE, check if >>>> some models can be nested anyway. >>>> else: >>>> >>>> Modified: >>>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>>> URL: >>>> http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py?rev=24988&r1=24987&r2=24988&view=diff >>>> ============================================================================== >>>> --- >>>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>>> (original) >>>> +++ >>>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>>> Tue Aug 12 10:54:49 2014 >>>> @@ -151,9 +151,27 @@ >>>> model = MODEL_CR72 >>>> >>>> # Test the return. >>>> - print nesting_model(self_models=self_models, model=model) >>>> self.assertEqual(nesting_model(self_models=self_models, >>>> model=model)[1].model, MODEL_LM63) >>>> >>>> + ## Test MODEL_IT99 model request, when models are CR72. >>>> + # Define all the models tested in the analysis. >>>> + self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_CR72, MODEL_IT99] >>>> + >>>> + # Define which current model is selected >>>> + model = MODEL_IT99 >>>> + >>>> + # Test the return. >>>> + self.assertEqual(nesting_model(self_models=self_models, >>>> model=model)[1].model, MODEL_CR72) >>>> + >>>> + ## Test MODEL_CR72 model request, when models are MODEL_IT99. >>>> + # Define all the models tested in the analysis. >>>> + self_models = [MODEL_R2EFF, MODEL_NOREX, MODEL_IT99, MODEL_CR72] >>>> + >>>> + # Define which current model is selected >>>> + model = MODEL_CR72 >>>> + >>>> + # Test the return. >>>> + self.assertEqual(nesting_model(self_models=self_models, >>>> model=model)[1].model, MODEL_IT99) >>>> >>>> >>>> def test_nesting_model_cpmg_mmq(self): >>>> >>>> >>>> _______________________________________________ >>>> relax (http://www.nmr-relax.com) >>>> >>>> This is the relax-commits mailing list >>>> [email protected] >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-commits >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
