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<section start=references/>* [*Carver and Richards 1972] Carver, J. P. and Richards, R. E. (1972). General 2-site solution for chemical exchange produced dependence of T2 upon Carr-Purcell pulse separation. ''J. Magn. Reson.'', '''6'''(1), 89-105. (DOI [http{{#lst://dx.doi.org/10.1016/0022-2364(72)90090-X 10.1016/0022-2364(72)90090-X]).Citations|CarverRichards72}}* [*d'Auvergne and Gooley 2006] {{#lst:Citations|dAuvergneGooley06}}* [*d'Auvergne, E. J. and Gooley, P. R. (2006). Model-free model elimination2007] {{#lst: A new step in the model-free dynamic analysis of NMR relaxation data. ''J. Biomol. NMR'Citations|dAuvergneGooley07}}* [*d'Auvergne and Gooley, '''35'''(2), 117-135. (DOI [http2008b] {{#lst://dx.doi.org/10.1007/s10858-006-9007-z 10.1007/s10858-006-9007-z]).Citations|dAuvergneGooley08b}}* [*Davis et al., 1994] Davis, D. G., Perlman, M. E., and London, R. E. (1994). Direct measurements of the dissociation-rate constant for inhibitor-enzyme complexes via the T1rho and T2 (CPMG) methods. ''J. Magn. Reson.'', '''104'''(3), 266-275. (DOI [http{{#lst://dx.doi.org/10.1006/jmrb.1994.1084 10.1006/jmrb.1994.1084]).Citations|Davis94}}* [*Ishima and Torchia 1999] Ishima, R{{#lst:Citations|IshimaTorchia99}}* [*Korzhnev et al. and Torchia, D. A. (2005). Error estimation and global fitting in transverse-relaxation dispersion experiments to determine chemical-exchange parameters. ''J. Biomol. NMR'', '''32'''(1), 41-54. (DOI [http2005a] {{#lst://dx.doi.org/10.1007/s10858-005-3593-z 10.1007/s10858-005-3593-z]).Citations|Korzhnev05a}}* [*Luz and Meiboom 1963] Luz, Z. and Meiboom, S. (1963). Nuclear magnetic resonance study of protolysis of trimethylammonium ion in aqueous solution - order of reaction with respect to solvent. ''J. Chem. Phys.'', '''39'''(2), 366-370. (DOI [http{{#lst://dx.doi.org/10.1063/1.1734254 10.1063/1.1734254]).Citations|LuzMeiboom63}}* [*Meiboom 1961] Meiboom, S. (1961). Nuclear magnetic resonance study of proton transfer in water. ''J. Chem. Phys.'', '''34'''(2), 375-388. (DOI [http{{#lst://dx.doi.org/10.1063/1.1700960 10.1063/1.1700960]).Citations|Meiboom61}}* [*Miloushev and Palmer 2005] Miloushev, V. Z. and Palmer, 3rd, A. G. (2005). R(1rho) relaxation for two-site chemical exchange: general approximations and some exact solutions. ''J. Magn. Reson.'', '''177'''(2), 221-227. (DOI [http{{#lst://dx.doi.org/10.1016/j.jmr.2005.07.023 10.1016/j.jmr.2005.07.023]).Citations|MiloushevPalmer05}}* [*Morin et al., 2014] Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger, M., Teilum, K., Gagne, S., Marion, D., Griesinger, C., Blackledge, M., and d'Auvergne, E. J. (2014). relax{{#lst: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. ''Bioinformatics'', '''30'''(15), 2219-2220. (DOI [http://dx.doi.org/10.1093/bioinformatics/btu166 10.1093/bioinformatics/btu166]).Citations|Morin14}}* [*Tollinger et al., 2001] Tollinger, M., Skrynnikov, N. R., Mulder, F. A. A., Forman-Kay, J. D., and Kay, L. E. (2001). Slow dynamics in folded and unfolded states of an sh3 domain. ''J. Am. Chem. Soc.'', '''123'''(46), 11341-11352. (DOI [http{{#lst://dx.doi.org/10.1021/ja011300z 10.1021/ja011300z]).Citations|Tollinger01}}* [*Trott and Palmer 2002] Trott, O. and Palmer, 3rd, A. G. (2002). R1rho relaxation outside of the fast-exchange limit. ''J. Magn. Reson.'', '''154'''(1), 157-160. (DOI [http{{#lst://dx.doi.org/10.1006/jmre.2001.2466 10.1006/jmre.2001.2466]).Citations|TrottPalmer02}}* [*Trott et al., 2003] Trott, O., Abergel, D., and Palmer, A. (2003). An average-magnetization analysis of R-1 rho relaxation outside of the fast exchange. ''Mol. Phys.'', '''101'''(6), 753-763. (DOI [http{{#lst://dx.doi.org/10.1080/0026897021000054826 10.1080/0026897021000054826]).<section end=references/>Citations|Trott03}}
Convert to internal links for Tutorial for adding relaxation dispersion models to relax.
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{{infobox relax release| version = 3.1.0| prev = 3.0.2| next = 3.1.1| keywords = Initial relaxation dispersion| type = Major feature| date = 28 November 2013| manual = yes}} == Description ==
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== Download ==
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== CHANGES file ==
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=== Features ===
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=== Changes ===
<section begin=changes/>
* Started to implement relaxation dispersion system tests.
* Created the user_functions.relax_disp module by copying user_functions.relax_fit. This file now needs to be modified to suit the needs of relaxation dispersion.
* Manually created the relax_disp user functions. This is equivalent to {{relax developer link|username=semor|text=Seb's }} commit for the prompt.relax_disp module. The equivalent changes to the user_functions.relax_disp were hand edited. Added functions to select the experiment type and mathematical model used. These functions allow the user to select the experiment type (cpmg or r1rho) as well as the mathematical model to fit the data (fast or slow).
* Copied the 'relax_fit.py' script to 'relax_disp.py'. This file, obviously, will need to be modified to suit the needs of the relaxation dispersion code.
* Modified the script so it will test for fast-exchange curve fitting from CPMG data. Data and functions to treat it are still missing.
* The cpmg_frq argument of the [http://www.nmr-relax.com/manual/relax_disp_cpmg_frq.html relax_disp.cpmg_frq user function] can now be an integer as well as a float.
* Updates for the relaxation dispersion system test scripts for the newer design of relax. A number of changes were required as the code was quite old.
* Created the lib.dispersion.equations module. This is a translation of {{relax developer link|username=semor|text=Sebastien Morin's }} C code in the old relax_disp branch.* Created a very basic initial target function class for relaxation dispersion. This code is a translation of {{relax developer link|username=semor|text=Sebastien Morin's }} C code in the old relax_disp branch.
* The relaxation dispersion specific analysis code now uses the Python target function rather than the C.
* Fix for the Relax_disp.test_curve_fitting_cpmg_fast system test variable names.
* The scaling flag is now initialised in the relaxation dispersion target function class.
* Created the lib.curve_fit package and associated unit tests. This will be used for holding modules such as for exponential curve-fitting required for the relaxation dispersion analysis.
* Created the new lib.curve_fit.exponential module for exponential curve-fitting. This contains the single exponential_2param_neg() function which will be used for the relaxation dispersion target functions. This is based on {{relax developer link|username=semor|text=Sebastien Morin's }} function exp_2param_neg in maths_fns.exponential.c in his dormant inversion-recovery branch.
* Typo fix for the new lib.curve_fit.exponential.exponential_2param_neg() function.
* The relaxation dispersion func_exp_fit() target function now uses exponential_2param_neg(). This is from the lib.curve_fit.exponential module.
* Fixes for the dispersion specific _back_calc() method. This method still has a long way to go before it is of any use.
* Created a custom base_data_loop() method for the relaxation dispersion analysis. This defines the base data as the peak intensities of a single exponential curve and yields the spin container and exponential curve key identifying the individual curves.
* Activated Monte Carlo simulations for the relaxation dispersion analysis. This required a bit of work. The key parts were renaming _block_loop() to the API method model_loop() as that is exactly what the model_loop() method is supposed to do, converting a bunch of API common spin-based methods to handle dispersion clustering, and to modify existing methods from {{relax developer link|username=semor|text=Seb's }} original branch to handle the base_data_loop() method. The following methods have been added or modified. _back_calc(): This method has been modified to handle clustering and the returning of peak intensities from only one exponential curve. _exp_curve_index_from_key(): This new method is used to convert exponential curve key into the corresponding index. _intensity_key(): This new method is for converting an exponential curve key and relaxation time into the corresponding intensity key. create_mc_data(): This method is now functional and handles the data from the base_data_loop() method. return_error(): This method now handles the data from the base_data_loop() method. set_selected_sim(): This new method has been modified from the common _set_selected_sim_spin() method but modified for the model_loop() method. sim_pack_data(): This method now handles the data from the base_data_loop() method. sim_return_param(): This new method has been modified from the common _sim_return_param_spin() method to suit the model_loop(). sim_return_selected(): This new method has been modified from the common _sim_return_selected_spin() method again to suit the model_loop().
* Modified the Relax_disp.test_exp_fit system test to be faster and not create plots which it cannot.
* The Relax_disp.test_exp_fit system test now checks some of the final results.
* Renamed the relaxation dispersion test suite data directory to 'dispersion'.
* Changed the [http://www.nmr-relax.com/manual/relax_disp_cpmg_frq.html relax_disp.cpmg_frq user function] id argument to spectrum_id. All the relax_disp user functions now operate with the spectrum IDs instead of experiment IDs.
* The [http://www.nmr-relax.com/manual/relax_disp_cpmg_delayT.html relax_disp.cpmg_delayT user function] backend now uses the spectrum ID rather than experiment ID.
* Expanded the [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] to include the fixed period CPMG experiments.
* The [http://www.nmr-relax.com/manual/relax_disp_cpmg_delayT.html relax_disp.cpmg_delayT] backend can now handle the 'cpmg fixed' experiment type.
* Missing import in the gui.analyses.auto_relax_disp module.
* Added support for all the relaxation dispersion user functions in the Peak_intensity_wizard object.
* Modified how the fixed time period is specified in the Flemming Hansen data system test. Instead of using [http://www.nmr-relax.com/manual/relax_disp_cpmg_delayT.html relax_disp.cpmg_delayT user function], the [http://www.nmr-relax.com/manual/relax_disp_relax_time.html relax_disp.relax_time user function] will be used. The functionality is duplicated and relax_disp.cpmg_delayT is not needed.
* Modified the Spectra_list GUI element to handle relaxation dispersion data.
* The relaxation dispersion GUI analysis now uses the dispersion parts of the peak intensity elements. This includes activating the dispersion parts of the Spectra_list GUI element for displaying the spectrum ID with associated metadata and the dispersion parts of the Peak_intensity_wizard for loading the data.
* Fixed for the error_analysis() method of the relaxation dispersion auto-analysis. The method can now handle missing spectrometer field strength data.
* More fixed for the peak intensity error analysis method of the relaxation dispersion auto-analysis. The fixed relaxation time period type experiments can now be handled.
* Elimination of the [http://www.nmr-relax.com/manual/relax_disp_cpmg_delayT.html relax_disp.cpmg_delayT user function]. This user function is not necessary as the [http://www.nmr-relax.com/manual/relax_disp_relax_time.html relax_disp.relax_time user function] serves the same purpose. The use of relax_disp.relax_time instead allows for code sharing between the fixed and variable time period relaxation dispersion experiment types.* Elimination of the [http://www.nmr-relax.com/manual/relax_disp_calc_r2eff.html relax_disp.calc_r2eff user function]. This user function, which is non-functional anyway, is not needed. The calculation of the R<sub>2eff</sub> values will occur with the optimisation of the [[R2eff]] model (with a call to the [http://www.nmr-relax.com/manual/calc.html calc user function] for the fixed time period experiment types) so direct calculation through a specific user function is not needed.
* Improvements to the GUI text subscripting in the relaxation dispersion analysis frame.
* Removed the temporary relaxation dispersion SVG graphic for the GUI analysis.
* Fix for the calculation part of the relaxation dispersion auto-analysis. This is for the fixed relaxation period data types.
* The 2D Grace plots of the exponential curves are now skipped for the fixed relaxation period data types. This is in the relaxation dispersion auto-analysis.
* Started to implement the relaxation dispersion analysis specific calculate() method. This will be used to calculate the R<sub>2eff</sub>/R<sub>1ρ</sub> values for the fixed relaxation time period data types and is equivalent to {{relax developer link|username=semor|text=Sebastien Morin's }} relax_disp.calc_r2eff user function which was deleted (see http://thread.gmane.org/gmane.science.nmr.relax.scm/17336).
* Converted the specific_analyses.relax_disp module into its own package. This is to allow the code to be broken up into separate modules to simplify the analysis.
* Shifted out all of the variables and dispersion data specific code into separate modules. The dispersion data private methods have been converted into functions of the specific_analyses.relax_disp.disp_data module. The package variables have also been shifted into the specific_analyses.relax_disp.variables module to avoid circular imports.
* Fixes for the backend of the [http://www.nmr-relax.com/manual/relax_disp_plot_exp_curves.html relax_disp.plot_exp_curves user function]. This code needed to be updated for the major changes in the relax_disp branch.
* Fixes for the checks in the Relax_disp.test_exp_fit system test. The r2eff and i0 spin data structure keys are now strings.
* Two class variables have been added to the dispersion auto-analysis for fast optimisation. This includes variables for the function tolerance and maximum number of iterations, and matches those of the model-free auto-analysis of the dauvergne_protocol module[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]. These will be used to speed up the test suite.
* Speed up of the system tests using Flemming Hansen's CPMG data. The grid search increments, function tolerance and maximum number of iterations have all been made looser.
* Added parameter checks to the Relax_disp.test_hansen_cpmg_data_LM63 system test.
* Fix for the [http://www.nmr-relax.com/manual/relax_disp_cpmgfit_input.html relax_disp.cpmgfit_input user function] for when no directory is given. This was causing tracebacks.
* Fix for the [[LM63]] model for the [http://www.nmr-relax.com/manual/relax_disp_cpmgfit_input.html relax_disp.cpmgfit_input user function]. The grid search was incorrectly set up - the parameter is Tau, not t<sub>ex</sub>.
* Fixes for the [[IT99]] model for the [http://www.nmr-relax.com/manual/relax_disp.cpmgfit_inputrelax_disp_cpmgfit_input.html relax_disp.cpmgfit_input user function].
* Changed the CPMGFit grid search options for the [[IT99]] model in the [http://www.nmr-relax.com/manual/relax_disp_cpmgfit_input.html relax_disp.cpmgfit_input user function].
* Fix for the setup of the relaxation dispersion target functions for the [[IT99]] model.
* Fixes for the [http://www.nmr-relax.com/manual/relax_disp_cpmgfit_input.html relax_disp.cpmgfit_input user function] for the [[IT99]] model grid search options.
* Updated the CPMGFit results for the [[IT99]] grid search fixes of the last commit.
* Basic fix for the checks of the [http://www.nmr-relax.com/manual/Relax_disp_test_hansen_cpmgfit_input.html Relax_disp.test_hansen_cpmgfit_input user function]. The 't<sub>ex</sub>' parameter is now set as 'Tau'.
* Disabled the Relax_disp.test_r1rho_on_res_fixed_time_m61b system test as the [[M61b]] model is rubbish. The model cannot be properly optimised as the parameters are not independent of each other.
* Fixes for the dispersion specific code. The Grace graph code of lib.software.grace no longer accepts the axis min and max arguments.
* Expanded the modelling of dispersion data section of the relax user manual.
* Expansion of the modelling of dispersion data section of the relax user manual.
* The relaxation dispersion auto-analysis now outputs text and Grace files for all parameters. This is in response to [https://gna.org/bugs/?20917 bug #20917] submitted by [https://gna.org/users/{{relax developer link|username=tlinnet |text=Troels Linnet]}}.
* The Monte Carlo simulations now generate parameter errors for the relaxation dispersion analysis. The simulation index was being ignored, hence the input data was never the randomised data and all errors were zero.
* Removed many decimal points from the MHz value in the Grace plots from relax_disp.plot_disp_curves.
* Fix for the dispersion auto-analysis - p<sub>A</sub> and p<sub>B</sub> parameters are no longer output for the [[IT99]] model. These are not parameters of this model.
* Updated the relax results for Flemming Hansen's truncated CPMG data for all the recent changes.
* Fix for [https://gna.org/bugs/?20916 bug #2091 - Suggestion for Python script for PNG/EPS/SVG conversion of grace files]. {{relax developer link|username=tlinnet|text=Troels Linnet }} provided this patch, and was discovered during work on a Windows 7 system. This patch will provide a grace2images.py file in each folder where a call to specific_analyses/relax_disp/disp_data.py is called. It is called in plot_disp_curves(dir=None, force=None) and call the function lib.software.grace.script_grace2images(). The conversion script can be executed in Linux and Windows, if the PATH to xmgrace has been specified. It will look in a folder for grace files of ending *.agr and by default convert to PNG. One can also convert to EPS and SVG. Probably more options could be added, as PDF. The conversion depends on xmgrace compilation, and so PNG conversion is for fast inspection of graphs in folder, and EPS for further external conversion to PDF etc. The patch, the output file, and small script to test is attached. I miss to make the file executable in relax, so the script can be executed directly in Linux.
* Mac OS X bug fix for the new analysis GUI wizard. The blank button is now using the blank_150x150.png file instead of no image, preventing nasty wxPython bugs from appearing on that system.
* Fix for [https://gna.org/bugs/?20917 bug #20917]. The problem is that the Grace files for each spin system are not created by the [http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html relax_disp.plot_disp_curves user function] as the ':' character cannot be placed in a file name in MS Windows. All of the file name from the ':' onwards is lost. The solution is to replace each of the characters '#:@' in the spin ID string with '_'.
* Another update of the relax results for Flemming Hansen's truncated CPMG data. This includes the grace2images.py script creation contributed by {{relax developer link|username=tlinnet|text=Troels Linnet (https://gna.org/users/tlinnet) }} and the change of the file name of the per-spin dispersion curves.
* The value checks in the Relax_disp.test_hansen_cpmg_data_auto_analysis system test are now less precise. This is to allow the tests to pass on certain MS Windows systems.
* Fix for the setting of the execute permissions on the grace2images.py scripts. The problem was identified in the post at http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. This is within the [http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html relax_disp.plot_disp_curves user function] after the grace2images.py script has been created. The commit matches the changes from trunk for the [[Modelfree4 ]] batch script.
* Shifted from argparse to optparse in the grace2images.py scripts from relax_disp.plot_disp_curves. This is associated with [https://gna.org/bugs/?20916 bug #20916] and the change suggested in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. The argparse module is only available from for Python 2.7.3 (the version with many Python 3 features backported) and Python ≥ 3.2. The module has been replaced with the similar optparse module as used by relax, and which available in all Python version supported by relax.
* Updated the grace2images.py scripts created by the [http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html relax_disp.plot_disp_curves user function]. This was discussed in [https://gna.org/bugs/?20916 bug #20916] and the change suggested in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000. Improved that both small and big letters for image types can be used on the command line.
* Loosened a parameter check in the Relax_disp.test_hansen_cpmg_data_IT99 system test to pass on certain Linux systems.
* Small edit of the legend of the relaxation dispersion figure showing the Ishima & Torchia 2005 being wrong.
* Added [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda's] }} code for the numerical solution to the Bloch-McConnell equations for 2-sites. This is specifically code which uses complex conjugate matrices. The code was submitted at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132.
* Made the lib.dispersion.ns_2site_star module importable in the absence of Scipy.
* Polished the lib.dispersion.ns_2site_star module docstring.
* Added the [[NS CPMG 2-site star|NS 2-site star]] model to the specific_analyses.relax_disp.variables module. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Added the lib.dispersion.ns_2site_star module name to the package __all__ list.
* Updated the lib.dispersion.ns_2site_star module with additional information from [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}. The details come from http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4135. The exchange-free R<sub>2</sub> value parameter names have been changed to match the convention of the other lib.dispersion modules.
* Added the [[NS CPMG 2-site star|NS 2-site star]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] frontend. This is the model of the numerical solution for the 2-site Bloch-McConnell equations using complex conjugate matrices. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Fix for the non-ASCII character '\xe2' in the lib.dispersion.ns_2site_star module.
* Better support for the R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> relaxation rate parameters in the relaxation dispersion analysis. This includes a number of fixes to allow these two parameters to be handled correctly.
* Added parameter conversions to go from p<sub>A</sub> and k<sub>ex</sub> to k<sub>ge</sub> and k<sub>eg</sub>. This is for the [[NS CPMG 2-site star|NS 2-site star]] numerical model. The conversions have been added to the start of the target function to minimise mathematical operations to speed up the code.
* Added the missing mpower() function as lib.linear_algebra.matrix_power.square_matrix_power(). This is needed by the lib.dispersion.ns_2site_star module. The function comes from the '[https://gna.org/support/download.php?file_id=18263 fitting_main_kex.py]' file attached to [https://{{gna.org/task/?link|7712#comment3 |comment=3|text=comment 3 of task #7712]}}. The mpower() function was copied and modified to suite relax's coding conventions.
* Added a module docstring to lib.linear_algebra.matrix_power.
* Created the lib.dispersion.ns_matrices module. This module contains a collection of functions for generating the relaxation matrices for the numerical solutions to the Bloch-McConnell equations for relaxation dispersion. The code comes from the '[https://gna.org/support/download.php?file_id=18263 fitting_main_kex.py]' file attached to https://{{gna.org/task/?url|7712#comment3|comment=3}}.
* Docstring fix for the lib.dispersion.ns_matrices.rcpmg_2d() function.
* Added the functions for creating the X-axis pi-pulse rotation matrices in lib.dispersion.ns_matrices. The code comes from the '[https://gna.org/support/download.php?file_id=18263 fitting_main_kex.py]' file attached to https://{{gna.org/task/?url|7712#comment3|comment=3}}.* Huge amounts of documentation added to the lib.dispersion.ns_2site_star module. This comes from [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda's] }} post at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4152
* Spacing fixes for the lib.dispersion.ns_2site_star module as determined by the 2to3 program. This is the Python 2 to 3 conversion program.
* Docstring fix for the lib.dispersion.ns_2site_star.r2eff_ns_2site_star() function.
* Improvements for the write_results() method of the dispersion auto-analysis. The parameter value and Grace files are now correctly created for all the recent models.
* Fix for the Relax_disp.test_hansen_cpmg_data_auto_analysis system test for model name change. This is for the change from the [[CR72]] model to [[CR72|CR72 red]] model.
* Added the [[NS CPMG 2-site 3D|NS 2-site]] model to the specific_analyses.relax_disp.variables module. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the [[NS CPMG 2-site 3D|NS 2-site]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] frontend. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the [[NS CPMG 2-site 3D|NS 2-site]] R<sub>2eff</sub> calculating function to the relax library. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Updates and fixes for the lib.dispersion.ns_2site module. The function has been renamed, and the R<sub>1</sub> arguments default to 0.0. The flip angle for the from the pulse.
* Created the [[NS CPMG 2-site 3D|NS 2-site]] model target function. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Converted the [[NS CPMG 2-site 3D|NS 2-site]] model to [[NS CPMG 2-site 3D|NS 2-site 3D]] to be more specific. This might change again in the future.
* Added support for the [[NS CPMG 2-site 3D|NS 2-site 3D]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] back end. This is the model of the numerical solution for the 2-site Bloch-McConnell equations. It originates as optimization function number 1 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Lots of fixes for the relaxation dispersion target function module for the [[NS CPMG 2-site 3D|NS 2-site 3D]] model.
* Improvements to the nesting() method of the relaxation dispersion auto-analysis. The use of the parameters of the simpler model in a nested pair now only works if the simpler model is in the model list.
* Converted the pi-pulse propagator matrices to numpy array format. This is to enable the use of the much faster numpy.dot() function for performing the dot products.
* Speed ups for the [[NS CPMG 2-site 3D|NS 2-site 3D]] model. The pi-pulse propagator is created only once upon target function initialisation rather than for each function call, each spin cluster, each magnetic field strength, each dispersion point, and each CPMG block.
* Modified the df, fA, and fB parameters to match the relax omega conventions of δω, wA, and wB. This follows from [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda's] }} confirmation at http://thread.gmane.org/gmane.science.nmr.relax.devel/4132/focus=4159.
* Speed up for the lib.dispersion.ns_matrices.rcpmg_3d() function. The p<sub>A</sub> and p<sub>B</sub> parameters are now sent into the function rather than being recreated by the function.
* More changes to the numerical solution dispersion code to match relax's conventions. This includes the changes of df->δω, fA->wA, fB->wB, and Mgx->Mx.
* Added the [[NS CPMG 2-site expanded|NS 2-site expanded]] model to the specific_analyses.relax_disp.variables module. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Added the [[NS CPMG 2-site expanded|NS 2-site expanded]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] frontend. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Added the [[NS CPMG 2-site expanded|NS 2-site expanded]] R<sub>2eff</sub> calculating function to the relax library. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Fix for the lib.dispersion.ns_2site_expanded.r2eff_ns_2site_expanded() function. The pg variable should have been p<sub>A</sub> and it needs to be sent into the function.
* Created the [[NS CPMG 2-site expanded|NS 2-site expanded]] model target function. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the [[NS CPMG 2-site expanded|NS 2-site expanded]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] back end. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, {{relax developer link|username=pasa|text=Paul Schanda][https://gna.org/users/pasa }}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Fix for the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] for the [[NS CPMG 2-site expanded|NS 2-site expanded]] model. There is only one R<sub>2</sub><sup>0</sup> parameter as R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> in this model.
* Added the [[NS CPMG 2-site expanded|NS 2-site expanded]] model to the relax user manual. This is the numerical model for the 2-site Bloch-McConnell equations expanded using Maple by Nikolai Skrynnikov. It originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda]}}, and Dominique Marion (see http://thread.gmane.org/gmane.science.nmr.relax.devel/4138, https://{{gna.org/task/?url|7712#comment2 |comment=2}} and https://gna.org/support/download.php?file_id=18262). This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Large renaming of the relaxation dispersion models. This includes both the analytic and numerical models. All of the models with separate R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> parameters now have ' full' added to the end of the model name. And all of the corresponding reduced models whereby R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> = R<sub>2</sub><sup>0</sup> have had the trailing ' red' removed. All descriptions and variable names have been updated to match.
* Updated the dispersion auto-analysis write_results() method for the recent model changes.
* Updated the numeric model results for the software_comparison file.
* Updated the relax results for Flemming Hansen's truncated CPMG data. This includes the [[CR72 full]] model and all the numeric models (excluding the *full models).
* Added Dominique Marion to the copyright notices of all the lib/dispersion/ns_*.py files. This is in response to [https://gna.org/users/{{relax developer link|username=pasa |text=Paul Schanda's] }} message at http://thread.gmane.org/gmane.science.nmr.relax.devel/4225/focus=4226.
* Small fix for the relax_disp.cluster documentation.
* Added the new pre_run_dir argument to the relaxation dispersion auto-analysis. This is to enable clustered optimisation. This specifies a directory containing a completed analysis. The parameters from this previous run will be used as the starting point for optimisation of the clustered analysis.
* Started to create the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test.
* A fix for older numpy versions, as the numpy.add() function argument 'out' is relatively new.
* Added the new [[TSMFK01]] model to the specific_analyses\relax_disp\variables.py module. This is the Tollinger/Kay model for the 2-site very-slow exchange model for CPMG-type experiments, which cover the range of microsecond to second time scale. Paper by M. Tollinger, N.R. Skrynnikov, F.A.A. Mulder, J.D.F. Kay and L.E. Kay (2001). Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* lib/dispersion/lm63.py is copied to tsmfk01.py as part of the implementation of the [[TSMFK01]] model equation. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added the [[TSMFK01]] model to the user_functions/relax_disp.py select_model user function frontend. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Created the [[TSMFK01]] model target function for 2-site very-slow exchange model, range of microsecond to second time scale. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added the [[TSMFK01]] model equations to the relax library lib/dispersion/tsmfk01.py. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* The chemical shift of each spin is now taken into account for the synthetic data for the [[TP02]] dispersion model. The data now properly reflects the spin lock offset.
* Updated all of the dispersion system tests for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function] changes. The arguments heteronuc and proton have been replaced with 'dim'.
* Updated the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test script for the new file names.
* Added a new user function to the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. This is the [http://www.nmr-relax.com/manual/chemical_shift_read.html chemical_shift.read user function] which currently does not exist. Chemical shifts are needed to interpret off-resonance R<sub>1ρ</sub> data.
* Copyright of {{relax developer link|username=semor|text=Sebastien Morin }} and {{relax developer link|username=bugman|text=Edward d'Auvergne }} re-inserted, since tsmfk01 is an alteration of lm63.py and m61.py in same directory. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fix for converting δω from ppm to rad/s. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added support for the [[TSMFK01]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] back end. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Fix for the reading of chemical shifts in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test.
* Added the Trott and Palmer, 2002 bibtex reference for the user manual.
* Implemented the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html relax_disp.spin_lock_offset user function]. This includes both the front end and the back end specific_analyses.relax_disp.disp_data.spin_lock_offset() function.
* The offset is now set for all spectra in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. Previously only the reference was set.
* Fixed a typo in the dispersion chapter of the user manual. This was identified by {{relax developer link|username=tlinnet|text=Troels Linnet }} at http://thread.gmane.org/gmane.science.nmr.relax.devel/4410.
* Fix for the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html relax_disp.spin_lock_offset user function]. The cdp.dispersion_points structure was being updated when it should not be touched - a remnant of the relax_disp.spin_lock_field backend which this code was copied from.
* Added some more arguments to the dispersion target function class for off-resonance R<sub>1ρ</sub> models. This is the structure for the spin-lock offsets and the tilt angles for each spin.
* Turned off clustering in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test. This speeds the test up by more than half.
* Fix for the [[TP02]] dispersion model. The rotating frame tilt angle for this model is calculated from the population averaged chemical shift and not the equal weighted average.
* Attempt at fixing [https://gna.org/bugs/?21080 bug #21080]. This was reported by {{relax developer link|username=tlinnet|text=Troels Linnet}}. The problem is a standard GUI problem. The text from a wxPython GUI is a Unicode string. But relax requires standard strings. Therefore the gui.string_conv.gui_to_str() function needs to be used on the return value of the GUI element GetValue() method, but this call was forgotten.
* Fix for the synthetic data for the [[TP02]] dispersion model. The chemical shift is being set to that of state A, the major species, rather than the non-weighted chemical shift average. This could also have been set to the population weighted average.
* The [[TP02]] dispersion model now assumes the chemical shift is that of the major population A. Previously the linear chemical shift average was assumed.
* Added the [[NS R1rho 2-site]] model to the specific_analyses.relax_disp.variables module. This is the numerical model for the 2-site Bloch-McConnell equations for R<sub>1ρ</sub> data. This commit follows step 1 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Added the [[NS R1rho 2-site]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] frontend. This is the numerical model for the 2-site Bloch-McConnell equations for R<sub>1ρ</sub> data. This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Added the [[NS R1rho 2-site]] R<sub>1ρ</sub> calculating function to the relax library. This is the numerical model for the 2-site Bloch-McConnell equations for R<sub>1ρ</sub> data. This code originates from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://{{gna.org/task/?url|7712#comment5|comment=5}}). Specifically the funNumrho.m file. This commit follows step 3 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Fix for the function name in the lib.dispersion.ns_r1rho_2site module and removed misplaced copyrights.
* Created the [[NS R1rho 2-site]] model target function. This is the numerical model for the 2-site Bloch-McConnell equations for R<sub>1ρ</sub> data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://{{gna.org/task/?url|7712#comment5|comment=5}}). This commit follows step 4 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added support for the [[NS R1rho 2-site]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] back end. This is the numerical model for the 2-site Bloch-McConnell equations for R<sub>1ρ</sub> data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://{{gna.org/task/?url|7712#comment5|comment=5}}). This commit follows step 6 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].* Added the [[NS R1rho 2-site]] model to the relax user manual. This is the numerical model for the 2-site Bloch-McConnell equations for R<sub>1ρ</sub> data. The code originates from the funNumrho.m file from the Skrynikov & Tollinger code (the sim_all.tar file https://gna.org/support/download.php?file_id=18404 attached to https://{{gna.org/task/?url|7712#comment5|comment=5}}). This commit follows step 2 of the [http://thread.gmane.org/gmane.science.nmr.relax.devel/3907 relaxation dispersion model addition tutorial].
* Rearrangement of the model sections in the dispersion chapter of the user manual. These are now better separated into different categories.
* Created a save file for the r1rho_off_res_tp02 dispersion data optimised to the [[R2eff]] model. This will be used for faster system tests.
* Fix for the Relax_disp.test_hansen_cpmgfit_input system test. The '#:@' characters are no longer used in the file names.
* Updates to the Relax_disp system tests for the lower precision of MS Windows. These fixes allow the tests to pass on MS Windows.
* Renamed ka parameter to kA, to be consistent with naming conventions. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fix for r20 should be called r20a. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fix for unpacking the parameters correctly. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Added the k<sub>AB</sub> and k<sub>BA</sub> parameters to the table of all dispersion parameters.
* Proper ordering of all the dispersion models. See the thread at http://thread.gmane.org/gmane.science.nmr.relax.devel/4498 for details.
* Added the [[NS R1rho 2-site]] model to the dispersion auto-analysis.
* Added the [[TP02]] model to the dispersion auto-analysis.
* The tutorial for adding dispersion models in the user manual has been simplified. Most of the text from the dispersion model addition tutorial in the dispersion chapter of the manual has been removed. Instead a link to the tutorial on the wiki is given as this is a much better place for such information (http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]]).* Moved the ordering of the model TSMF. Ordering conventions mentioned in this post http://article.gmane.org/gmane.science.nmr.relax.devel/4500. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Added the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html relax_disp.spin_lock_offset user function] to the peak intensity wizard of the GUI. This is only for R<sub>1ρ</sub>-type data and allows off-resonance data to be analysed in the GUI.
* Data provided for the implementation of the slow-exchange analytic model of the Tollinger/Kay (2001). This model were used for fitting in the paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458987.
* Unicode strings in the dispersion GUI elements is now set up with the compat.u() function.
* Fix for the y-axis in the per spin dispersion curve plots. This fix follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/4512. The test for CPMG-type data was incorrect and should use the CPMG_EXP variable.
* Added setup function for the system test of KTeilum_FMPoulsen_MAkke_2006 data. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Fixed a spelling mistake in a number of file names. This is for the test suite data located at test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006.
* Fixes for the units in the dispersion parameter table in the user manual. The units for δω are rad.s<sup>-1</sup> when used in the equations, but it is stored internally as ppm.
* Truncated the dataset to only one residue L61. The truncated dataset will be expanded later. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Modified the script file for saving of a truncated base_pipe state file. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added script files for generating a saved state file with R<sub>2eff</sub> values. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added the first system test for model [[CR72]] for the kteilum_fmpoulsen_makke_cpmg_data. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fix trailing spaces. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fix epydoc HTML markup code. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Added some MQ dispersion data taken from the GUARDD program.
* Modified the Relax_disp.test_dpl94_data_to_dpl94 system test for a relax_disp.exp_type change. This is so that the [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] associates the experiment types with a spectrum ID. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530.
* Bug fix for the spectrum list GUI element popup menu relax_disp.spin_lock_field entry. This was calling the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_field.html relax_disp.spin_lock_field user function] incorrectly. The bug was identified by the Relax_disp.test_tp02_data_to_tp02 system test.
* Fix for the Mf.test_auto_analysis GUI test due to the spectrum list GUI element changes. The Fake_right_click() class now needs a GetPosition() method.
* Moved the experiment type setting into per spectra settings. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fixed typo. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added the truncated test data for system test: relax -s Relax_disp.test_kteilum_fmpoulsen_makke_cpmg_data_to_cr72. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Created a relax save file with just R<sub>2eff</sub> values for the r1rho_on_res_m61 dispersion system tests data.
* Created 3 new dispersion system tests. These are for checking a new function that doesn't exist yet. The get_curve_type() function will be used to determine if the experiment corresponding to the given ID consists of exponential curves or of fixed time data.
* Fixed values for system test: relax -s Relax_disp.test_kteilum_fmpoulsen_makke_cpmg_data_to_cr72. The test now passes. The values are compared to a relax run with 500 Monte Carlo simulations. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added "[[CR72 full]]" test suite for kteilum_fmpoulsen_makke_cpmg_data. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added file which setup a truncated spin system. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Changed the initialization script to use the truncated spin system. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Changed the saved states to the truncated spin system. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fix for the residue index in the test suite when using the truncated spin system. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* The R<sub>2eff</sub> result save file for the r1rho_on_res_m61 dispersion data now contains the full data set. The previous file did not contain the full exponential curves.
* The get_curve_type() function now works with the spectrum ID. This specific_analyses.relax_disp.disp_data.get_curve_type() function already existed but it operated on all the loaded data. Now it can handle a single spectrum ID. The count_relax_times() function has been added to aid get_curve_type().
* Modified the Relax_disp.test_dpl94_data_to_dpl94 system test. This is in preparation for another relax_disp.exp_type change - the fixed and exponential parts will be dropped as this can be determined automatically by relax.
* Changed the [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] front end. The supported types will now be 'CPMG' and 'R1rho', as the fixed time verses full exponential curve can be automatically determined by relax from what the user inputs.
* Started a system test for model [[TSMFK01]]. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Modified the script for the full analysis of all models of CPMG type. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Simplified the dispersion experiment type classes. The supported types will now be 'CPMG' and 'R1rho', as the fixed time verses full exponential curve can be automatically determined by relax from what the user inputs. The EXP_TYPE_* dispersion variables have all changed and many have now been lost. To support the changes, the new specific_analyses.relax_disp.disp_data.loop_spectrum_ids() function has been created. This is a loop over all spectrum IDs whereby the experiment type, magnetic field strength, dispersion point, or relaxation time can be specified to isolate ID subsets. Many of the specific_analyses.relax_disp.checks.check_*() has also been modified as their logic no longer works. The auxiliary get_times() function has been added to create a per-experiment dictionary of relaxation times so that the checks can be independent of the other dispersion modules.
* Updated much of the dispersion test data. The experiment type has been changed in all the scripts and the relax save files updated.
* Fixed expydoc formatting. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Created some more specific_analyses.relax_disp.checks.check_*() functions. This is for better checking of the dispersion data. The check_spectra_id_setup() is useful for checking that all of the spectrum information is set up.
* The checks prior to minimisation of the dispersion models is now more comprehensive.
* Fixes for some of the R<sub>1ρ</sub> dispersion system test scripts. The relaxation time must be set for the reference spectrum.
* Fixes for the Relax_disp.test_exp_fit system test - the spectrometer frequency is now set. This information is now compulsory.
* Converted references of ka and kA to k<sub>AB</sub>. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Updated the CPMG dispersion analysis sample script for the [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] changes.
* Updated the user manual for the [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] changes. The script in the prompt/script UI section of the dispersion chapter needed to be updated.
* Referencing fixes for the dispersion chapter of the user manual.
* Updated the scripts and save files for the KTeilum_FMPoulsen_MAkke_2006 dispersion data. This is for the recent [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] changes and this allows the tests to pass. Information on how to run the scripts and tee the output to logs has been added, and the logs added to the repository.
* Added k<sub>AB</sub> to parameters. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* More fixes for the [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] changes.
* The relaxation dispersion GUI elements now use the lib.text.gui module for Unicode strings.
* Increased the size of the dispersion model list GUI window so that all models fit without scrolling.
* Refinement of the dispersion model list in the GUI. Descriptions have been added and the fixed window size adjusted to the best fit.
* Modified system test after inclusion of 1M GuHCl dataset. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Moved files into folder which is specific for the experiment. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Changed scripts after moving data. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Re-run of data after movement of scripts. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added dataset experiment in 1.01 M GuHCl (guanidine hydrochloride). Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added to the README file for the 1.01 M GuHCL experiment. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Modified doc string for the script analysing all models for residue L61. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added the output from relax after analysis of all models. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Removed the size variable from the dispersion model list GUI window as it is no longer used.
* Added the k<sub>AB</sub> and k<sub>BA</sub> conversion equations to the dispersion parameter table in the user manual.
* Changed reference to Tollinger et al. instead of Tollinger/Kay. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Fixes for the dispersion GUI tests for the changes to the model list GUI element.
* Added the button for the [http://www.nmr-relax.com/manual/interatom_define.html interatom.define user function] in preparation for the MQ dispersion data. This is in the dispersion tab of the GUI.
* Speed ups for the optimisation of all of the R<sub>1ρ</sub> dispersion models. The spin-lock field strength data structure is now converted from Hz to rad.s<sup>-1</sup> in the dispersion target function initialisation. Previously the conversion was happening multiple times per target function call. This has a noticeable effect on the test suite timings.
* Some small speed ups for the [[TP02]] R<sub>1ρ</sub> dispersion model optimisation. Some unneeded calculations and aliases were removed.
* Added the write-out of 'δω' and 'k<sub>AB</sub>' for model [[TSMFK01]], when performing auto-analysis. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added to calculate the tau_cpmg times when model is [[TSMFK01]]. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Optimized the target function for model TSMFK. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added the conversion to k<sub>AB</sub> from k<sub>ex</sub> and p<sub>A</sub>. k<sub>AB</sub> = k<sub>ex</sub> * (1.0 - p<sub>A</sub>). Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Some more speed ups for the R<sub>1ρ</sub> dispersion models. For many models, the square of the spin-lock field strength is a part of the equations. Therefore this is now pre-calculated when the target function is initialised.
* Added the relaxation dispersion documentation to all of the value user function documentation.
* Added a sample script for an off-resonance R<sub>1ρ</sub> dispersion analysis.
* Created the empty specific_analyses.relax_disp.optimisation module. This will contain functions and other objects relating to the optimisation of the dispersion models.
* Fixed bug, where k<sub>ex</sub> to k<sub>AB</sub> where not possible if the model does not contain parameter p<sub>A</sub>. The conversion is now skipped. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added the conversion to k<sub>BA</sub> from k<sub>ex</sub> and p<sub>A</sub>. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added system test for testing conversion to k<sub>BA</sub> from k<sub>ex</sub> and p<sub>A</sub>. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fix for passing system test on Windows with Python 32. Precision lowered by 2 decimals. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added system tests for conversion of k<sub>ex</sub> to k<sub>AB</sub>/k<sub>BA</sub> for models where k<sub>ex</sub> and p<sub>A</sub> is present. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Modified headers for scripts producing analysis for data which is full or truncated. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Created the dispersion default_value_doc object. This table is needed for the [http://www.nmr-relax.com/manual/value_set.html value.set user function].
* Huge speed win for the relaxation dispersion analysis - optimisation now uses the multi-processor. The relaxation dispersion optimisation has been parallelised at the level of the spin clustering. It uses {{relax developer link|username=varioustoxins|text=Gary Thompson's }} multi-processor framework. This allows the code to run on multi-core, multi-processor systems, clusters, grids, and anywhere the OpenMPI protocol is available. Because the parallelisation is at the cluster level there are some situations, whereby instead of optimisation being faster when running on multiple slaves, the optimisation will be slower. This is the case when all spins being studied in clustered into a small number of clusters. It is also likely to be slower for the [http://www.nmr-relax.com/manual/minimise.html minimise user function] when no clustering is defined, due to the overhead costs of data transfer (but for the numeric models, in this case there will be a clear win). The two situations where there will be a huge performance win is the [http://www.nmr-relax.com/manual/grid_search.html grid_search user function] when no clustering is defined and the Monte Carlo simulations for error analysis.
* Decreased the number of grid increments in the dispersion sample scripts from 21 to 11. This is a much easier optimisation problem than the other analyses in relax, so 21 increments is an overkill. It also takes far too long for some of the models due to the high number of parameters.
* Removed a tonne of unused imports from the modules of the specific_analyses.relax_disp package.
* Deselected most of the default dispersion models from the dispersion GUI model list. Now only one analytic and numeric model is selected per experiment type. This is to hint to the user that maybe they shouldn't just use all models.
* Added desc. item for model [[TSMFK01]]. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added [[TSMFK01]] to model overview table. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added subsection with [[TSMFK01]] model. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fix for adding [[TSMFK01]] to sample scripts. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Updated the relax_disp_trunc.py script for Flemming Hansen's CMPG test data.
* Started to create the [http://www.nmr-relax.com/manual/relax_disp_catia_input.html relax_disp.catia_input user function]. The frontend has been written and a stub of a function for the backend. The new specific_analyses.relax_disp.catia module has been created for this.
* Rearranged the numeric CPMG models in the dispersion model list in the GUI.
* The main CATIA input file requires the chemical shifts and R<sub>1</sub> values to be fixed, even when missing. This is for the [http://www.nmr-relax.com/manual/relax_disp_catia_input.html relax_disp.catia_input user function].
* Added Tollinger reference. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Added Tollinger model [[TSMFK01]] to sample scripts. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].* Fixed several typo errors of "Is it selected"->"It is selected". A copy-paste error which has spread. Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)]. Following the guide at: http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax]].
* Spacing fixes for the Tollinger01 Bibtex entry for the author initials.
* Removed some strange characters from the Tollinger01 Bibtex abstract.
* Enabled the parallelisation of Monte Carlo simulations for the relaxation dispersion analysis.
* Created a set of scripts for testing out the multi-processor abilities of the dispersion analysis.
* Added Remco Sprangers' truncated ClpP data to test_suite/shared_data/dispersion/Spranger_ClpP. This is the data attached to https://{{gna.org/task/?url|7712#comment6|comment=6}}, and it will be used for testing the implementation of the [[NS MMQ 2-site|MQ NS 2-site]] model, when added to relax.
* Concatenated the peak intensity files.
* Created a relax script for analysing Remco Sprangers' ClpP data with the [[NS MMQ 2-site|MQ NS 2-site]] model. This currently does not work, as the model is absent.
* Created the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. This checks the [[NS MMQ 2-site|MQ NS 2-site]] model against Remco Sprangers' MQ CPMG data using the auto-analysis.
* Fixes for the checks of the new Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. The [[NS MMQ 2-site|MQ NS 2-site]] model checks were still set up to those of the Relax_disp.test_hansen_cpmg_data_auto_analysis system test.
* Added the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model to the dispersion variables. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list ]] The new dispersion variable MODEL_MQ_NS_CPMG_2SITE has been added. As this is a new data type, multi-quantum CPMG, the new MODEL_LIST_MQ_CPMG and MODEL_LIST_MQ_CPMG_FULL lists have been created.
* Rearranged the documentation for the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] to simplify the text.
* Created the lib.text.gui.dwH Unicode string for use with the [[NS MMQ 2-site|MQ NS 2-site]] dispersion model.
* Added the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] frontend. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_dispThe relax disp.select_model_user_function_front_end select model user function front end]] Two new sections were added to the user function docstring for the MQ CPMG and MQ R<sub>1ρ</sub> experiment types.* Added support for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] back end. This is the numeric solution for 2-site exchange for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_dispThe relax disp.select_model_user_function_back_endselect model user function back end]].* Added support for the new 'δω<sub>H</sub>' dispersion parameter. This is needed for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model support. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_support_for_the_parametersAdding support for the parameters]].
* Improved the RelaxError from the [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] when an invalid experiment type is set.
* Added the multi-quantum CPMG and R<sub>1ρ</sub> experiment types to the dispersion variables. This is needed for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr- [[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_typeCreating a new experiment type]].
* Added relaxation dispersion model lists for the MQ R<sub>1ρ</sub> models. These are stubs as no MQ R<sub>1ρ</sub> models are yet supported by relax.
* Added support for the MQ dispersion data type to the specific_analyses.relax_disp.disp_data module. This is needed for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_typeCreating a new experiment type]].* Added support for the MQ dispersion data types to the rest of relax. This is needed for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model, and the changes affect the dispersion data checks and the dispersion target functions. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_typeCreating a new experiment type]].
* Updated the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test for 'MQ CPMG' data. This also affects the script in the shared_data test suite directory. The [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] exp_type argument has been changed from 'CPMG' to 'MQ CPMG'.
* Updated the [http://www.nmr-relax.com/manual/relax_disp_exp_type.html relax_disp.exp_type user function] for the new 'MQ CPMG' and 'MQ R1rho' experiment types. This is needed for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_typeCreating a new experiment type]].* Created the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model target function. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_functionThe target function]].* Added the [[NS MMQ 2-site|MQ NS CPMG 2-site]] R<sub>1ρ</sub> calculating function to the relax library. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_libraryThe relax library]].
* Updated the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model target function to match the function in the relax library.
* Decreased the grid increments in the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test. This is to speed up this test.
* Some small changes for the script for optimising Sprangers' ClpP MQ CPMG data.
* Added the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model to the dispersion auto-analysis. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_autoThe auto-analysis]].* Added the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model to the GUI model list. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUIThe GUI]].
* Rearranged the 'Implemented models' subsection of the dispersion chapter of the manual.
* Fixed the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model description in the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function]. The magnitisation vector is 2D, not 3D.
* Added a latex definition for the δω<sub>H</sub> dispersion parameter and added the 'MQ' abbreviation.
* Added the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model to the relax user manual. This is the 2-site numeric solution for multi-quantum CPMG-type data. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manualThe relax manual]].
* Simplified the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model code in lib.dispersion.
* Fixes for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model equations in the user manual.
* Artificially increased the errors in Sprangers ClpP data to match the publication. The R<sub>2eff</sub> errors are simply multiplied by 5, as the errors from the paper cannot be replicated.
* Converted the Relax_disp.test_sprangers_cpmg_data_auto_analysis system test to not use the auto-analysis. The test has been renamed to Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site. The optimisation is now for the cluster and has been severely cut back. The [[NS MMQ 2-site|MQ NS CPMG 2-site]] model appears to be rubbish anyway - it looks to be indeterminate with multiple solutions, and possibly infinite lines of solutions. The test now passes, and quickly.
* Created the Relax_disp.test_sprangers_data_to_mq_cr72 system test. This was copied from the Relax_disp.test_sprangers_data_to_mq_ns_cpmg_2site system test and the model changed to [[MQ CR72]]. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suiteThe test suite]].* Added the [[MQ CR72]] model to the dispersion variables. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_listAdding the model to the list]].* Added the [[MQ CR72]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] frontend. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_dispThe relax disp.select_model_user_function_front_endselect model user function front end]].* Added support for the [[MQ CR72]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] back end. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_dispThe relax disp.select_model_user_function_back_endselect model user function back end]].* Created the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model target function. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr- [[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_functionThe target function]].* Added the [[MQ CR72]] R<sub>2eff</sub> calculating function to the relax library. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_libraryThe relax library]]. The corresponding target function was updated to input the correct arguments.* Added the [[MQ CR72]] model to the dispersion auto-analysis. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_autoThe auto-analysis]].* Added the [[MQ CR72]] model to the GUI model list. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUIThe GUI]].
* A number of fixes for the lib.dispersion.mq_cr72 module.
* The lib.dispersion.mq_cr72 module now more closely resembles the cr72 module in syntax.
* Added the Tollinger et al., 2001 reference for the [[NS CPMG 2-site expanded]] model. This reference was communicated in a private email.
* Improvements for the LaTeX maths commands used in the dispersion chapter of the user manual.
* Added Skrynnikov and Tollinger to the copyright notice in lib/dispersion/ns_cpmg_2site_star.py. I can now see that the code derives from the funNumcpmg.m of the sim_all.tar file (https://gna.org/support/download.php?file_id=18404) attached to https://{{gna.org/task/?url|7712#comment5|comment=5}}. This sim_all.tar file is the original code of Nikolai and Martin.
* Modified the relaxation dispersion auto-analysis to take nesting of MQ models. This is specifically the nesting of the analytic [[MQ CR72]] model and the [[NS MMQ 2-site|MQ NS CPMG 2-site]] models. The analytic solution is now used as the optimisation starting point for the numeric model.
* Used the \imath LaTeX symbol for complex numbers in the dispersion chapter of the manual.
* Added scripts and results for optimising Sprangers' ClpP MQ CPMG data to the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model. This includes two scripts for non-clustered followed by clustered analysis using the [[MQ CR72]] model in the auto-analysis so its parameters will be used as the optimisation starting point for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model. The results files for both scripts have been added to the repository.
* Added the [[MQ CR72]] model to the relax user manual. This is the Carver and Richards (1972) 2-site model expanded for MQ CPMG data by Korzhnev et al., 2004. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manualThe relax manual]].
* Modified the δω<sub>H</sub> symbol in the relax user manual.
* Created a 'TODO' section in the dispersion chapter of the relax user manual. This lists all of the features and models currently missing from the dispersion analysis in relax.
* Added the original Maple script to the lib.dispersionns_cpmg_2site_expanded module docstring for reference. This was sent by Nikolai in a private communication.
* More expansion of the lib.dispersionns_cpmg_2site_expanded module docstring for reference. The link https://{{gna.org/task/?url|7712#comment8 |comment=8}} to the p3.analytical script in the Gna! tasks has been added and the contents of the sim_all.tar file funNikolai.m has been copied into the docstring as well.
* Epydoc docstring fixes to allow the API documentation to be properly compiled.
* Python 3 fix for the lib.dispersion.mq_ns_cpmg_2site module. The numpy.linalg.matrix_power requires an integer power, but Python 3 was creating a floating point number for the 'fact' variable.
* Fix for the [[NS CPMG 2-site expanded]] model equations in the manual.
* Better section spacing in the dispersion chapter of the manual. Each model section is now on a new page.
* Fix for the display of the spin-lock ν<sub>1</sub> values in the dispersion GUI tab. This was reported by {{relax developer link|username=tlinnet|text=Troels }} at http://thread.gmane.org/gmane.science.nmr.relax.devel/4708. The GUI spectrum element at gui.components.spectrum was at fault, the add_disp_point() method was buggy.
* Fix for the right click pop up menu entry "Set the spin-lock field" in the dispersion GUI tab. This is for the spectra list [http://www.nmr-relax.com/manual/relax_disp_spin_lock_field.html relax_disp.spin_lock_field user function] call. The reference spectra are now detected and the field value set to None. This fix has been propagated to the [http://www.nmr-relax.com/manual/relax_disp_cpmg_frq.html relax_disp.cpmg_frq user function] menu entry as well.
* Correcting the R<sub>1ρ</sub> settings script for the right calculation of the spin-lock offset, omega_rf, in ppm when offset values are provided in Hz.
* Started the conversion of the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model to [[MMQ 2-site]]. This follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734.
* Renamed all of the [[NS MMQ 2-site|MQ NS CPMG 2-site]] modules and functions for the change to [[MMQ 2-site]]. This follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734.
* Added the ZQ and DQ CPMG experiment types to the dispersion variables. This is needed for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model change to [[MMQ 2-site]] and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_typeCreating a new experiment type]].
* Created two new dispersion variables - EXP_TYPE_LIST_CPMG and EXP_TYPE_LIST_R1RHO. This will be used to simplify identifying CPMG vs. R<sub>1ρ</sub> data types.
* Added support for the ZQ and DQ CPMG data type to the specific_analyses.relax_disp.disp_data module. This is needed for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model change to [[MMQ 2-site]] and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_typeCreating a new experiment type]].* Completed the support for ZQ and DQ CPMG experiment types in relax. This is needed for the [[NS MMQ 2-site|MQ NS CPMG 2-site]] model change to [[MMQ 2-site]] and follows from the post at http://article.gmane.org/gmane.science.nmr.relax.devel/4734. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Creating_a_new_experiment_typeCreating a new experiment type]].
* The [[MMQ 2-site]] model target function can now handle multiple CPMG data types.
* Added dispersion curve plotting to the relax script for Korzhnev et al., 2005 [[:Category:MMQ CPMG data|MMQ data]].
* Updated some ShereKhan language details in the dispersion software comparison table of the manual.
* The dispersion GUI analysis now uses graphics.fetch_icon() for all icons. The gui.paths module no longer exists.
* Created the Relax_disp.test_tp02_data_to_mp05 system test. This was copied from the Relax_disp.test_tp02_data_to_tp02 system test. The r1rho_off_res_tp02.py system test script was modified to handle both tests by allowing the list of models to optimise to be set via the ds.models variable. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suiteThe test suite].* Added the [[MP05]] model to the dispersion variables. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_listAdding the model to the list]].* Added the [[MP05]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] frontend. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_dispThe relax disp.select_model_user_function_front_endselect model user function front end]].* Added support for the [[MP05]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] back end. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_dispThe relax disp.select_model_user_function_back_endselect model user function back end]].* Created the [[MP05]] model target function. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr- [[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_functionThe target function]].* Added the [[MP05]] R<sub>2eff</sub> calculating function to the relax library. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_libraryThe relax library]]. Just in case git-svn does not preserve the file copying history, the lib/dispersion/mp05.py file was copied from the tp02.py file.* Debugging of the [[MP05]] dispersion model - optimisation is now setup correctly. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.html#Debugging]].* Fixes and improvements to the Relax_disp.test_tp02_data_to_mp05 system test. The [[MP05]] model values, which are almost the same as the [[TP02]] model parameters, are now being checked. The optimised parameters are now being printed out to aid in debugging. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.html#Debugging]].
* Speed ups of the Relax_disp.test_tp02_data_to_tp02 and Relax_disp.test_tp02_data_to_mp05 system tests. The optimisation precision and number of Monte Carlo simulations have both been dropped.
* Added the [[MP05]] model to the GUI model list. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUIThe GUI]].* Added the [[MP05]] model to the dispersion auto-analysis. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_autoThe auto-analysis]].* Added the [[MP05]] model to the relax user manual. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manualThe relax manual]]. The [[MP05]] model was already partly in the manual, however it was listed as unimplemented. All of the tables and the dispersion chapter text has been updated for the model.* Modified the R1rho_analysis.py sample script to use the [[MP05]] model. This is the Miloushev and Palmer 2005 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_sample_scriptsThe sample scripts]].
* The limitations of the 'TP03' dispersion model are now listed in the user manual.
* The [[MP05]] and [[NS R1rho 2-site]] are now nested in the dispersion auto-analysis. As the [[MP05]] model is valid across all times scales and does not require skewed populations, its optimised parameters can be used as the starting point of optimisation of the [[NS R1rho 2-site]] numeric model. This results in huge speed ups of the numeric model as previously a grid search was being performed.
* Removed all remnants of the MQ R<sub>1ρ</sub> data type. This data type does not exist and was mostly removed, but some small bits remained.
* Created the Relax_disp.test_tp02_data_to_tap03 system test. This is the Trott et al, 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite The test suite] This was copied from the Relax_disp.test_tp02_data_to_mp05 system test.* Added the [[TAP03]] model to the dispersion variables. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_listAdding the model to the list]].* Added the [[TAP03]] model to the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] frontend. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_dispThe relax disp.select_model_user_function_front_endselect model user function front end]].* Added support for the [[TAP03]] model to the r[http://www.nmr-relax.com/manual/elax_disp_select_model.html elax_disp.select_model user function] back end. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_dispThe relax disp.select_model_user_function_back_endselect model user function back end]].* Created the [[TAP03]] model target function. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr- [[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_functionThe target function]].* Added the [[TAP03]] R<sub>2eff</sub> calculating function to the relax library. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_libraryThe relax library]].* Debugging of the [[TAP03]] dispersion model - optimisation is now setup correctly. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.html#Debugging]].* Debugging of the [[TAP03]] dispersion model. Removed a Unicode character from the lib.dispersion.tap03 module docstring to allow it to be used in Python 2. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.html#Debugging]].
* The lib.dispersion.tap03 module can now handle negative γ values. This avoids fatal errors during optimisation.
* Many fixes for the lib.dispersion.tap03 module to match the original equations. The [[TAP03]] model solution is now similar to those of [[TP02]] and [[MP05]].
* Updated the Relax_disp.test_tp02_data_to_tap03 system test numbers to match the optimised values. These were so close to the [[MP05]] model values that the test was passing anyway.
* Added the [[TAP03]] model to the GUI model list. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUIThe GUI]].* Added the [[TAP03]] model to the dispersion auto-analysis. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_autoThe auto-analysis]].* Added the [[TAP03]] model to the relax user manual. This is the Trott, Abergel and Palmer 2003 R<sub>1ρ</sub> analytic model for 2-site off-resonance exchange. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-[[Tutorial for adding relaxation dispersion models to relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manualThe relax manual]]. The [[TAP03]] model was already partly in the manual, however it was listed as unimplemented. All of the tables and the dispersion chapter text has been updated for the model.
* Added the [[TAP03]] and [[MP05]] models to the abbreviations in the user manual.
* Improvements to all of the R<sub>1ρ</sub> model descriptions in the dispersion chapter of the manual.
* Added support for <sup>1</sup>H SQ CPMG data for the [[:Category:MMQ CPMG data|MMQ-type]] dispersion models. The key is to skip the protons in the spin cluster loops and to instead find the proton spin containers attached to the heteronuclei of the spins of the cluster. The EXP_TYPE_PROTON_SQ_CPMG and EXP_TYPE_PROTON_MQ_CPMG experiment type variables have been created to aid this. The MODEL_LIST_MMQ list variable has also been created to more consistently identify the [[:Category:MMQ CPMG data|MMQ-type]] dispersion models. The has_disp_data() function has been created to simplify the finding of dispersion data for a given cluster, experiment type, spectrometer frequency and dispersion point. The has_proton_sq_cpmg() and has_proton_mq_cpmg() are used to determine if there is proton dispersion data for the given heteronucleus. The loop_exp() function has been modified to yield the proton SQ and MQ data if present. Similarly the num_exp_types() and return_index_from_exp_type() functions exhibit different behaviour if this data is present. The return_r2eff_arrays() function now assembles all of the proton data on top of the heteronuclear data by fetching the protons attached to the heteronuclei and aliasing the correct spin for the given experiment type.
* Updated the relaxation dispersion target functions. The input data structures have changed type.
* Implemented the [[MMQ 2-site]] CPMG model equations from the [Korzhnev et al., 2005 reference. The paper reference is "Dmitry M. Korzhnev, Philipp Neudecker, Anthony Mittermaier, Vladislav Yu. Orekhov, and Lewis E. Kay (2005). Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: An application to the folding of a Fyn SH3 domain mutant. J. Am. Chem. Soc., 127, 15602-15611. (doi: http://dx.doi.org/10.1021/ja054550e)"2005a]. The original code from Mathilde Lescanne and Dominique Marion has only slightly been modified for this change as the MQ data treatment in the Korzhnev et al., 2004 reference is the same as in the 2005 reference, but using a different notation. This has been renamed to r2eff_mmq_2site_mq(). The new r2eff_mmq_2site_sq_dq_zq() function has been added to the lib.dispersion.mmq_2site module to allows the SQ, DQ, and ZQ R<sub>2eff</sub> data to be calculated. This function follows the notation of the 2005 paper. The populate_matrix() function has been modified to only accept one combined chemical shift difference value. It can now also accept different values for R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup>, though the mmq_2site module defaults to R<sub>2A</sub><sup>0</sup>=R<sub>2B</sub><sup>0</sup>.
* The r2eff_mmq_*() functions of lib.dispersion.mmq_2site now accept different R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> arguments. These are set to the same thing within the dispersion target function.
* Converted the spin specific 'r2', 'r2a', and 'r2b' dispersion parameters from lists to dictionaries. The new parameter keys are based on the experiment type and the spectrometer frequency. These keys are supported by the generate_r20_key() and decompose_r20_key() pair of functions in the specific_analyses.relax_disp.disp_data module. This enables support for different R<sub>2</sub><sup>0</sup> parameters for each experiment type - a key piece of infrastructure for the [[:Category:MMQ CPMG data|MMQ]] models. The [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] backend was modified so the parameter list only contains one instance for each of the 'r2', 'r2a', or 'r2b' strings. The specific_analyses.relax_disp.parameters.loop_parameters() function was modified so that the R<sub>2</sub><sup>0</sup>key rather than frequency index is returned for the R<sub>2</sub><sup>0</sup> parameters. Many other code changes were required.
* Created a Grace plot of the <sup>15</sup>N MQ CPMG data fitting from cpmg_fit.
* Bug fix for the multiple quantum relaxation dispersion models. These require both the heteronuclear and proton chemical shift differences. But the proton difference was being scaled by the heteronuclear Larmor frequency and not the proton frequency.
* The relaxation dispersion [http://www.nmr-relax.com/manual/calculatecalc.html calculate user function] now stores the back calculated R<sub>2eff</sub> values. A number of changes were required for this. The code from the end of the Disp_result_command.run() method was converted to the function specific_analyses.relax_disp.disp_data.pack_back_calc_r2eff(). This allows the back calculation R<sub>2eff</sub> unpacking code to be shared. The new has_proton_mmq_cpmg() function has also been created to simplify the code.* Bug fix for the dispersion [http://www.nmr-relax.com/manual/calculatecalc.html calculate user function].
* Created a script to compare the cpmg_fit and relax solutions for the [[MMQ 2-site]] dispersion model.
* Clean ups and speed ups of the <sup>1</sup>H MMQ flag calls.
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>
<section end=bugfixes/>
== Links ==
<section begin=links/>
For reference, the following links are also part of the announcement for this release:
* [http://wiki.nmr-relax.com/Relax_3.1.0 Official release notes]
* [https://{{gna link|url=gna.org/forum/forum.php?forum_id=2421 |text=Gna! news item]}}
* [http://article.gmane.org/gmane.science.nmr.relax.announce/46 Gmane]
* [https://mail.gna.org/public/relax-announce/2013-11/msg00001.html Local archives]
<section end=links/>
== Announcements ==
{{:relax release announcements}}
== References ==
<HarvardReferences />
== See also ==
* [http://www.nmr-relax.com/api/3.1/ The relax 3.1 API documentation]
{{:relax release see also}}
[[Category:MMQ CPMG data]]
[[Category:Relaxation dispersion analysis]]
