Difference between revisions of "Relax 3.2.0"

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{{lowercase title}}
 
{{lowercase title}}
  
= Description =
+
{{infobox relax release
 +
| version  = 3.2.0
 +
| prev    = 3.1.7
 +
| next    = 3.2.1
 +
| keywords = Manual, relaxation dispersion
 +
| type    = Major feature
 +
| date    = 20 May 2014
 +
| manual  = yes
 +
}}
 +
 
 +
== Description ==
  
 
<section begin=description/>
 
<section begin=description/>
This is a major feature release.  It includes the addition of the new [[B14]] and [[B14 full]] [[:Category:relaxation dispersion|relaxation dispersion]] models [Baldwin 2014], a complete rearrangement of the module layout of the specific analyses packages, a number of new [http://www.nmr-relax.com/manual/list_functions.html user functions], documentation improvements including the addition of a [http://www.nmr-relax.com/manual/N_state_model_or_ensemble_analysis.html new chapter to the manual for the N-state model or ensemble analysis], and numerous of other features.  This is also a major bugfix release, so all users are recommended to upgrade.  This is essential if you are using the new relaxation dispersion analysis in relax as a severe bug in the error calculation has been corrected.  See below for a comprehensive list of new features, the rather large number of changes, and the long list of all bugs fixed.
+
This is a major feature release.  It includes the addition of the new [[B14]] and [[B14 full]] [[:Category:relaxation dispersion analysis|relaxation dispersion]] models [Baldwin 2014], a complete rearrangement of the module layout of the specific analyses packages, a number of new [http://www.nmr-relax.com/manual/The_list_of_functions.html user functions], documentation improvements including the addition of a [http://www.nmr-relax.com/manual/The_N_state_model_or_ensemble_analysis.html new chapter to the manual for the N-state model or ensemble analysis], and numerous of other features.  This is also a major bugfix release, so all users are recommended to upgrade.  This is essential if you are using the new relaxation dispersion analysis in relax as a severe bug in the error calculation has been corrected.  See below for a comprehensive list of new features, the rather large number of changes, and the long list of all bugs fixed.
 
<section end=description/>
 
<section end=description/>
  
= Download =
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== Download ==
  
 
<section begin=download/>
 
<section begin=download/>
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<section end=download/>
 
<section end=download/>
  
= CHANGES file =
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== CHANGES file ==
  
 
<section begin=metadata/>
 
<section begin=metadata/>
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<section end=metadata/>
 
<section end=metadata/>
  
== Features ==
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=== Features ===
  
 
<section begin=features/>
 
<section begin=features/>
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*  Expansion of the [http://www.nmr-relax.com/manual/value_set.html value.set user function] to handle parameters which consist of lists of values.  The index argument has been added to allow the index of the list to be specified, and this is then propagated into the specific analysis API.
 
*  Expansion of the [http://www.nmr-relax.com/manual/value_set.html value.set user function] to handle parameters which consist of lists of values.  The index argument has been added to allow the index of the list to be specified, and this is then propagated into the specific analysis API.
 
*  Improvements for the parameter definitions in all analysis types.  This allows for better output in 2D plots and text files.
 
*  Improvements for the parameter definitions in all analysis types.  This allows for better output in 2D plots and text files.
*  Implemented linear constraints for the frame order analysis.  This uses the log-barrier constraint algorithm in the [https://gna.org/projects/minfx/ minfx library] to provide constraints without requiring gradients.
+
*  Implemented linear constraints for the frame order analysis.  This uses the log-barrier constraint algorithm in the [{{minfx homepage}} minfx library] to provide constraints without requiring gradients.
 
*  Improved and expanded the relax command line options for debugging.
 
*  Improved and expanded the relax command line options for debugging.
 
*  Full independence of the relax library so that it can be used outside of relax.
 
*  Full independence of the relax library so that it can be used outside of relax.
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*  Support for multiple point creation for the [http://www.nmr-relax.com/manual/dx_map.html OpenDX chi-squared space mapping user function].
 
*  Support for multiple point creation for the [http://www.nmr-relax.com/manual/dx_map.html OpenDX chi-squared space mapping user function].
 
*  Automatic determination of reasonable initial contour levels for the [http://www.nmr-relax.com/manual/dx_map.html OpenDX mapping user function].
 
*  Automatic determination of reasonable initial contour levels for the [http://www.nmr-relax.com/manual/dx_map.html OpenDX mapping user function].
*  Addition of a [http://www.nmr-relax.com/manual/N_state_model_or_ensemble_analysis.html new chapter to the manual for the N-state model or ensemble analysis].
+
*  Addition of a [http://www.nmr-relax.com/manual/The_N_state_model_or_ensemble_analysis.html new chapter to the manual for the N-state model or ensemble analysis].
 
*  Creation of the new [http://www.nmr-relax.com/manual/pymol_frame_order.html pymol.frame_order user function] for visualising results.
 
*  Creation of the new [http://www.nmr-relax.com/manual/pymol_frame_order.html pymol.frame_order user function] for visualising results.
 
*  Expansion of the Grace 2D data plotting capabilities.
 
*  Expansion of the Grace 2D data plotting capabilities.
 
<section end=features/>
 
<section end=features/>
  
== Changes ==
+
=== Changes ===
  
 
<section begin=changes/>
 
<section begin=changes/>
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*  The J(w) mapping parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
 
*  The J(w) mapping parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
 
*  The consistency testing parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
 
*  The consistency testing parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
*  The relaxation dispersion parameter setting documentation has been shifted into the parameter list object.  The documentation has also been rewritten as it originates from Sebastien Morin back in 2009 and is now very much out of date.
+
*  The relaxation dispersion parameter setting documentation has been shifted into the parameter list object.  The documentation has also been rewritten as it originates from {{relax developer link|username=semor|text=Sebastien Morin}} back in 2009 and is now very much out of date.
 
*  Deleted the relaxation curve-fitting parameter setting documentation.  This really didn't say anything.
 
*  Deleted the relaxation curve-fitting parameter setting documentation.  This really didn't say anything.
 
*  The N-state model parameter setting documentation has been shifted into the parameter list object.
 
*  The N-state model parameter setting documentation has been shifted into the parameter list object.
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*  Created the new '-r' or '--traceback' relax command line option.  If supplied, stack tracebacks will be shown for all RelaxWarnings and RelaxErrors.  This allows for finer debugging control.
 
*  Created the new '-r' or '--traceback' relax command line option.  If supplied, stack tracebacks will be shown for all RelaxWarnings and RelaxErrors.  This allows for finer debugging control.
 
*  Clean up of the debugging command line options.  The debug flag now will cause stack tracebacks to be printed on all RelaxWarnings.
 
*  Clean up of the debugging command line options.  The debug flag now will cause stack tracebacks to be printed on all RelaxWarnings.
*  Created the '--error-state' command line option for saving a pickled state when a RelaxError is raised.  This gives greater control of a powerful feature added to relax by [http://gna.org/users/macraild Chris MacRaild].  The pickled state can then be attached to bug reports or can be used to quickly load the state prior to failure when in the scripting UI mode.
+
*  Created the '--error-state' command line option for saving a pickled state when a RelaxError is raised.  This gives greater control of a powerful feature added to relax by {{relax developer link|username=macraild|text=Chris MacRaild}}.  The pickled state can then be attached to bug reports or can be used to quickly load the state prior to failure when in the scripting UI mode.
 
*  Reordered the debugging command line options and removed the '-r' shortcut.
 
*  Reordered the debugging command line options and removed the '-r' shortcut.
 
*  The lib.errors module is now really independent of relax - the compat module is no longer used.  Instead, the Python 2 and 3 versions of the pickle module are imported using try statements.
 
*  The lib.errors module is now really independent of relax - the compat module is no longer used.  Instead, the Python 2 and 3 versions of the pickle module are imported using try statements.
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*  Shifted all of the dispersion model descriptions and parameter lists to the variables module.  The descriptions and parameter lists which were part of the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] backend have been shifted into the specific_analyses.relax_disp.variables module as MODEL_DESC_* and MODEL_PARAMS_* variables.  The descriptions have also all been standardised.  The MODEL_DESC and MODEL_PARAMS dictionaries have also been created to hold all of the descriptions and parameters in one place.
 
*  Shifted all of the dispersion model descriptions and parameter lists to the variables module.  The descriptions and parameter lists which were part of the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] backend have been shifted into the specific_analyses.relax_disp.variables module as MODEL_DESC_* and MODEL_PARAMS_* variables.  The descriptions have also all been standardised.  The MODEL_DESC and MODEL_PARAMS dictionaries have also been created to hold all of the descriptions and parameters in one place.
 
*  The General.test_bug_21720_pipe_switching_with_tab_closure GUI test now works without compiled C modules.
 
*  The General.test_bug_21720_pipe_switching_with_tab_closure GUI test now works without compiled C modules.
*  Updated the release checklist for the new minfx version 1.0.6 release.  See https://gna.org/forum/forum.php?forum_id=2456 and https://freecode.com/projects/minfx.
+
*  Updated the release checklist for the new minfx version 1.0.6 release.  See {{gna url|1=gna.org/forum/forum.php?forum_id=2456}} and https://freecode.com/projects/minfx.
 
*  Fixes for the specific API _set_param_values_spin() method for lists and dictionaries.  This is for the [http://www.nmr-relax.com/manual/value_set.html value.set user function] to allow it to handle parameters of different types.  For example the R<sub>2</sub> parameter in the relaxation dispersion analysis.  This API common method now sets all dictionary elements, list elements, or the variable to the given value.
 
*  Fixes for the specific API _set_param_values_spin() method for lists and dictionaries.  This is for the [http://www.nmr-relax.com/manual/value_set.html value.set user function] to allow it to handle parameters of different types.  For example the R<sub>2</sub> parameter in the relaxation dispersion analysis.  This API common method now sets all dictionary elements, list elements, or the variable to the given value.
 
*  Created the new specific_analyses.relax_disp.variables.PARAMS_R20 list.  This variable is a list of all R<sub>2</sub><sup>0</sup> parameters of the dispersion models.  It has been shifted out of the parameters module.
 
*  Created the new specific_analyses.relax_disp.variables.PARAMS_R20 list.  This variable is a list of all R<sub>2</sub><sup>0</sup> parameters of the dispersion models.  It has been shifted out of the parameters module.
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*  Fix for script for the visualising the spin dynamics point which generated the data.  This is to the script, which can visualize the synthetic CPMG data.  [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].  This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
 
*  Fix for script for the visualising the spin dynamics point which generated the data.  This is to the script, which can visualize the synthetic CPMG data.  [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].  This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
 
*  Fix for the file name writing of the point file.  [https://gna.org/bugs/?22023 Bug #22023: relax dx.map produce .net files which makes error].
 
*  Fix for the file name writing of the point file.  [https://gna.org/bugs/?22023 Bug #22023: relax dx.map produce .net files which makes error].
*  Made system test Relax_disp.test_cpmg_synthetic_dx_map_points to start testing.  Modified also sample CPMG script to allow for this.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Made system test Relax_disp.test_cpmg_synthetic_dx_map_points to start testing.  Modified also sample CPMG script to allow for this.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
*  Modified [http://www.nmr-relax.com/manual/dx_map.html user function dx.map] to accept list of lists with values.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Modified [http://www.nmr-relax.com/manual/dx_map.html user function dx.map] to accept list of lists with values.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
*  Added is_list_val_or_list_of_list_val to lib/arg_check.py.  This function is not yet done.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Added is_list_val_or_list_of_list_val to lib/arg_check.py.  This function is not yet done.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
*  Added list_of_lists to user_functions/objects.py.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Added list_of_lists to user_functions/objects.py.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
*  Added list_of_lists to uf_objects.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Added list_of_lists to uf_objects.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
*  Made multiple writing of point files.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Made multiple writing of point files.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
 
*  Added [[B14]] to the dispersion software comparison table in the manual (docs/latex/dispersion_software.tex).  [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].  This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
 
*  Added [[B14]] to the dispersion software comparison table in the manual (docs/latex/dispersion_software.tex).  [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].  This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
 
*  Added [[B14]] to the dispersion auto-analysis.  The B14 models will not create output files until this is done.  [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].  This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI
 
*  Added [[B14]] to the dispersion auto-analysis.  The B14 models will not create output files until this is done.  [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].  This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI
*  Completely removed the list_of_lists argument.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Completely removed the list_of_lists argument.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
*  Modified the description of making x,y,z points in the &chi;<sup>2</sup> space for the [http://www.nmr-relax.com/manual/dx_map.html user function dx.map].  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Modified the description of making x,y,z points in the &chi;<sup>2</sup> space for the [http://www.nmr-relax.com/manual/dx_map.html user function dx.map].  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
 
*  Made solutions for math domain error.  Prevented to take log of negative values, and division by zero.  This though slows the implementation down.  System test Relax_disp.test_baldwin_synthetic_full went from 6.x seconds to 8-9.x seconds.  [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].  This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
 
*  Made solutions for math domain error.  Prevented to take log of negative values, and division by zero.  This though slows the implementation down.  System test Relax_disp.test_baldwin_synthetic_full went from 6.x seconds to 8-9.x seconds.  [https://gna.org/support/?3154 Sr #3154, implementation of Baldwin (2014) B14 model - 2-site exact solution model for all time scales].  This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
 
*  Changed an 'align' environment to 'equation' as there was only one equation.
 
*  Changed an 'align' environment to 'equation' as there was only one equation.
 
*  Removed invisible equations from the [[B14]] dispersion model section of the relax manual.  The trailing "\\" were causing equation numbers to be produced on empty lines after the block of equations.
 
*  Removed invisible equations from the [[B14]] dispersion model section of the relax manual.  The trailing "\\" were causing equation numbers to be produced on empty lines after the block of equations.
 
*  The f00 equation in the [[B14]] dispersion model section of the manual is a single equation.  The 'subequations' and 'align' environments are therefore superfluous.
 
*  The f00 equation in the [[B14]] dispersion model section of the manual is a single equation.  The 'subequations' and 'align' environments are therefore superfluous.
*  Modified dx.map to accept more than one point.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Modified dx.map to accept more than one point.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
*  Added system test for the production of dx map.  Relax_disp.test_cpmg_synthetic_dx_map_points.  [https://gna.org/task/?7791 Task #7791, the dx.map should accept a list of list with values for points].
+
*  Added system test for the production of dx map.  Relax_disp.test_cpmg_synthetic_dx_map_points.  {{gna task link|7791|text=Task #7791, the dx.map should accept a list of list with values for points}}.
 
*  Added proper punctuation to the [[B14]] dispersion model equations in the manual.  Equations should be readable as English sentences and they follow standard punctuation rules.  All of the equations in the [[B14]] model section of the dispersion chapter have been updated to follow this.
 
*  Added proper punctuation to the [[B14]] dispersion model equations in the manual.  Equations should be readable as English sentences and they follow standard punctuation rules.  All of the equations in the [[B14]] model section of the dispersion chapter have been updated to follow this.
 
*  Fixes for quotation marks in the [[B14]] dispersion model section of the manual.  LaTeX requires `' for single quotes rather than ''.
 
*  Fixes for quotation marks in the [[B14]] dispersion model section of the manual.  LaTeX requires `' for single quotes rather than ''.
Line 562: Line 572:
 
*  Shifted the model-free model equations for the HTML manual to the subequations environment.  This is for the relax manual at http://www.nmr-relax.com/manual/index.html  This is to preserve the equation numbering so that the HTML and PDF equation numbers match as closely as possible.
 
*  Shifted the model-free model equations for the HTML manual to the subequations environment.  This is for the relax manual at http://www.nmr-relax.com/manual/index.html  This is to preserve the equation numbering so that the HTML and PDF equation numbers match as closely as possible.
 
*  Fixes for the equation number in the HTML version of the manual.  This is for the relax manual at http://www.nmr-relax.com/manual/index.html.
 
*  Fixes for the equation number in the HTML version of the manual.  This is for the relax manual at http://www.nmr-relax.com/manual/index.html.
*  Made collecting of min, max and median value of &chi;<sup>2</sup>, when creating the &chi;<sup>2</sup> map.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Made collecting of min, max and median value of &chi;<sup>2</sup>, when creating the &chi;<sup>2</sup> map.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Made the parsing of the min, max and median &chi;<sup>2</sup> value to be used to define the &chi;<sup>2</sup> hypersurfaces when writing the dx .net program.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Made the parsing of the min, max and median &chi;<sup>2</sup> value to be used to define the &chi;<sup>2</sup> hypersurfaces when writing the dx .net program.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
 
*  Updated the latex2html HTML version to 4.1.  This is for the relax manual at http://www.nmr-relax.com/manual/index.html.
 
*  Updated the latex2html HTML version to 4.1.  This is for the relax manual at http://www.nmr-relax.com/manual/index.html.
*  Removed the "remap" keyword in the dx.map function, since this is not in use.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Removed the "remap" keyword in the dx.map function, since this is not in use.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Removed the keywords for "remap" in backend function, since this was not used.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Removed the keywords for "remap" in backend function, since this was not used.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Added the keyword "chi_surface" to the front-end dx.map function.  To set the &chi;<sup>2</sup> surface level for the innermost, inner, middle and outer isosurface.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Added the keyword "chi_surface" to the front-end dx.map function.  To set the &chi;<sup>2</sup> surface level for the innermost, inner, middle and outer isosurface.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Added the chi_surface=None to the backend function.  When None, it will try to find reasonable &chi;<sup>2</sup> values.  These will define surface levels for the innermost, inner, middle and outer isosurface.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Added the chi_surface=None to the backend function.  When None, it will try to find reasonable &chi;<sup>2</sup> values.  These will define surface levels for the innermost, inner, middle and outer isosurface.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Now saves all &chi;<sup>2</sup> values, to better find reasonable chi level for the innermost, inner, middle and outer isosurface.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Now saves all &chi;<sup>2</sup> values, to better find reasonable chi level for the innermost, inner, middle and outer isosurface.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Made the standard values of &chi;<sup>2</sup> surface be 10, 20, 50 and 90 percentile of all &chi;<sup>2</sup> values.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Made the standard values of &chi;<sup>2</sup> surface be 10, 20, 50 and 90 percentile of all &chi;<sup>2</sup> values.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
 
*  Increased the precision of many of the Frame_order.test_rigid_data_to_*_model system tests.  This is to fix a test which was failing due to the recent re-parameterisation of the rotor frame order model to eliminate one parameter.  The precision of the numeric Sobol' sequence integration has been increased by shifting the fixed parameter values even closer to zero.  As a consequence, the chi-squared value of five of these tests is now lower.
 
*  Increased the precision of many of the Frame_order.test_rigid_data_to_*_model system tests.  This is to fix a test which was failing due to the recent re-parameterisation of the rotor frame order model to eliminate one parameter.  The precision of the numeric Sobol' sequence integration has been increased by shifting the fixed parameter values even closer to zero.  As a consequence, the chi-squared value of five of these tests is now lower.
*  Fix for system test Relax_dips.test_cpmg_synthetic_dx_map_points.  Removing keyword "remap", since this is not in use anymore.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Fix for system test Relax_dips.test_cpmg_synthetic_dx_map_points.  Removing keyword "remap", since this is not in use anymore.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Changed the import of percentile from lib.mathematics to lib.numpy_future.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Changed the import of percentile from lib.mathematics to lib.numpy_future.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Changed the percentage which is different in percentile from numpy_future.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Changed the percentage which is different in percentile from numpy_future.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Added lib/numpy_future.py.  This module is for implementing numpy function code from higher versions of numpy.  The relax dependencies listed at the download page of relax: http://www.nmr-relax.com/download.html#Source_code_release currently only requires numpy >= 1.0.4.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Added lib/numpy_future.py.  This module is for implementing numpy function code from higher versions of numpy.  The relax dependencies listed at the download page of relax: http://www.nmr-relax.com/download.html#Source_code_release currently only requires numpy >= 1.0.4.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Added "numpy_future" to the __init__.py file in lib directory.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Added "numpy_future" to the __init__.py file in lib directory.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
*  Moved numpy_future from lib to extern.  Extern is special package for external software or code that is bundled with relax.  [https://gna.org/task/?7792 Task #7792, make the dx.map write suggest chi surface values].
+
*  Moved numpy_future from lib to extern.  Extern is special package for external software or code that is bundled with relax.  {{gna task link|7792|text=Task #7792, make the dx.map write suggest chi surface values}}.
 
*  Updated synthetic CPMG data script.  This is to analyse complex dispersion data.  Related to [https://gna.org/bugs/?22021 bug #22021 model B14 shows bad fitting to data].  [https://gna.org/bugs/?22024 Bug #22024 minimisation space for CR72 is catastrophic]. The &chi;<sup>2</sup> surface over &Delta;&omega; and p<sub>A</sub> is bounded.
 
*  Updated synthetic CPMG data script.  This is to analyse complex dispersion data.  Related to [https://gna.org/bugs/?22021 bug #22021 model B14 shows bad fitting to data].  [https://gna.org/bugs/?22024 Bug #22024 minimisation space for CR72 is catastrophic]. The &chi;<sup>2</sup> surface over &Delta;&omega; and p<sub>A</sub> is bounded.
 
*  Added 4 unit tests for the lib.geometry.lines.closest_point_ax() function.  This relax library function was previously not being checked in the test suite.
 
*  Added 4 unit tests for the lib.geometry.lines.closest_point_ax() function.  This relax library function was previously not being checked in the test suite.
Line 616: Line 626:
 
<section end=changes/>
 
<section end=changes/>
  
== Bugfixes ==
+
=== Bugfixes ===
  
 
<section begin=bugfixes/>
 
<section begin=bugfixes/>
Line 655: Line 665:
 
*  Fixed the rotor axis direction in the lib.frame_order.rotor_axis module.  The normalisation code has also been simplified.
 
*  Fixed the rotor axis direction in the lib.frame_order.rotor_axis module.  The normalisation code has also been simplified.
 
*  Fix for tabular space and forgotten "\n" when writing dx.maps config files.  [https://gna.org/bugs/?22023 Bug #22023: relax dx.map produce .net files which makes error].
 
*  Fix for tabular space and forgotten "\n" when writing dx.maps config files.  [https://gna.org/bugs/?22023 Bug #22023: relax dx.map produce .net files which makes error].
*  Added another sentence telling the user that multiple field relaxation data is essential.  This is for the model-free dauvergne_protocol auto-analysis section of the relax manual and relates to [https://gna.org/bugs/?21799 bug #21799].
+
*  Added another sentence telling the user that multiple field relaxation data is essential.  This is for the model-free dauvergne_protocol auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] section of the relax manual and relates to [https://gna.org/bugs/?21799 bug #21799].
 
*  Another sentence about multiple field relaxation data added to the manual.  This is for the model-free dauvergne_protocol GUI section of the relax manual and relates to [https://gna.org/bugs/?21799 bug #21799].
 
*  Another sentence about multiple field relaxation data added to the manual.  This is for the model-free dauvergne_protocol GUI section of the relax manual and relates to [https://gna.org/bugs/?21799 bug #21799].
 
*  Documentation fix for [[IT99]].  Changed k<sub>ex</sub> to t<sub>ex</sub>.  Still needs to be changed at homepage: http://www.nmr-relax.com/analyses/relaxation_dispersion.html#IT99.  [https://gna.org/bugs/?22019 Bug #22019: the IT99 model is listed with parameter k<sub>ex</sub> instead of t<sub>ex</sub>].
 
*  Documentation fix for [[IT99]].  Changed k<sub>ex</sub> to t<sub>ex</sub>.  Still needs to be changed at homepage: http://www.nmr-relax.com/analyses/relaxation_dispersion.html#IT99.  [https://gna.org/bugs/?22019 Bug #22019: the IT99 model is listed with parameter k<sub>ex</sub> instead of t<sub>ex</sub>].
Line 665: Line 675:
 
*  Fix for [https://gna.org/bugs/?22039 bug #22039, the printing out of Dpar twice by the diffusion_tensor.display user function].  The solution is given in the original bug report.
 
*  Fix for [https://gna.org/bugs/?22039 bug #22039, the printing out of Dpar twice by the diffusion_tensor.display user function].  The solution is given in the original bug report.
 
*  Fix for [https://gna.org/bugs/?22041 bug #22041, the PDB atom serial number error from the structure.write_pdb user function].  The problem is that the [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] preserves the atom numbering from the original structure and uses that for the atom serial number.  However the atom serial number must be replaced with sequential values to produce a valid PDB file.  This is fatal for any CONECT records.
 
*  Fix for [https://gna.org/bugs/?22041 bug #22041, the PDB atom serial number error from the structure.write_pdb user function].  The problem is that the [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] preserves the atom numbering from the original structure and uses that for the atom serial number.  However the atom serial number must be replaced with sequential values to produce a valid PDB file.  This is fatal for any CONECT records.
*  Fix for the chain-reaction failures in the test suite.  This fixes [https://gna.org/bugs/?22055 bug #22055, the processor.run_queue() not cleaning up in uni_processor - chain-reaction failures in the test suite].  The fix was insanely simple, just implementing what was mentioned Gary Thompson's FIXME comment in the run_queue() method of the uni-processor object.  The queue execution code has been placed inside a 'try' statement and the queue cleaning up code in a 'finally' statement.  This closes a painfully difficult to find bug that has been in relax since 2006, though only affecting relax developers.
+
*  Fix for the chain-reaction failures in the test suite.  This fixes [https://gna.org/bugs/?22055 bug #22055, the processor.run_queue() not cleaning up in uni_processor - chain-reaction failures in the test suite].  The fix was insanely simple, just implementing what was mentioned {{relax developer link|username=varioustoxins|text=Gary Thompson's}} FIXME comment in the run_queue() method of the uni-processor object.  The queue execution code has been placed inside a 'try' statement and the queue cleaning up code in a 'finally' statement.  This closes a painfully difficult to find bug that has been in relax since 2006, though only affecting relax developers.
 
<section end=bugfixes/>
 
<section end=bugfixes/>
  
= Links =
+
== Links ==
  
 
<section begin=links/>
 
<section begin=links/>
For reference, the following links are also part of the announcement for this release:
+
For reference, the announcement for this release can also be found at following links:
* [http://wiki.nmr-relax.com/Relax_3.2.0 Official release notes]
+
 
* [https://gna.org/forum/forum.php?forum_id=2461 Gna! news item]
+
* [http://wiki.nmr-relax.com/Relax_3.2.0 Official release notes on the relax wiki].
* [http://article.gmane.org/gmane.science.nmr.relax.announce/54 Gmane]
+
* {{gna link|url=gna.org/forum/forum.php?forum_id=2461|text=Gna! news item}}.
* [https://mail.gna.org/public/relax-announce/2014-05/msg00000.html Local archives]
+
* [http://article.gmane.org/gmane.science.nmr.relax.announce/54 Gmane mailing list archive].
* [http://marc.info/?l=relax-announce&m=140071233101164&w=2 MARC]
+
* [https://mail.gna.org/public/relax-announce/2014-05/msg00000.html Local archives].
 +
* [http://marc.info/?l=relax-announce&m=140071233101164&w=2 Mailing list ARChives (MARC)].
 +
 
 +
{{:Softpedia}}
 
<section end=links/>
 
<section end=links/>
  
= Announcements =
+
== Announcements ==
  
 
{{:relax release announcements}}
 
{{:relax release announcements}}
  
  
= References =
+
== References ==
  
 
<section start=references/>
 
<section start=references/>
* [*Baldwin 2014] A. Baldwin (2014).  An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange.  ''J. Magn. Reson.'', '''244''', 114-124.  (DOI: [http://dx.doi.org/10.1016/j.jmr.2014.02.023 10.1016/j.jmr.2014.02.023]).
+
* [*Baldwin 2014] {{#lst:Citations|Baldwin14}}
 +
* [*d'Auvergne and Gooley, 2007] {{#lst:Citations|dAuvergneGooley07}}
 +
* [*d'Auvergne and Gooley, 2008b] {{#lst:Citations|dAuvergneGooley08b}}
 
<section end=references/>
 
<section end=references/>
 
<HarvardReferences />
 
<HarvardReferences />
  
 +
== See also ==
  
= See also =
+
* [http://www.nmr-relax.com/api/3.2/ The relax 3.2 API documentation]
 
 
 
{{:relax release see also}}
 
{{:relax release see also}}
 
[[Category:N-state model analysis]]
 
[[Category:N-state model analysis]]
 
[[Category:Relaxation dispersion analysis]]
 
[[Category:Relaxation dispersion analysis]]

Latest revision as of 13:58, 16 October 2020


Official relax releases
relax logo
relax version 3.2.0
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← relax 3.1.7 relax 3.2.1 →

Keywords Manual, relaxation dispersion
Release type Major feature
Release date 20 May 2014

The PDF version of the relax 3.2.0 user manual The relax 3.2.0 user manual

Description

This is a major feature release. It includes the addition of the new B14 and B14 full relaxation dispersion models [Baldwin 2014], a complete rearrangement of the module layout of the specific analyses packages, a number of new user functions, documentation improvements including the addition of a new chapter to the manual for the N-state model or ensemble analysis, and numerous of other features. This is also a major bugfix release, so all users are recommended to upgrade. This is essential if you are using the new relaxation dispersion analysis in relax as a severe bug in the error calculation has been corrected. See below for a comprehensive list of new features, the rather large number of changes, and the long list of all bugs fixed.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 3.2.0
(20 May 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.2.0


Features

  • Addition of the vector_angle() relax library function for calculating the signed or directional angle between two vectors.
  • Huge speed up of the interatom.define user function.
  • For improved feedback, a busy cursor is shown in the GUI when executing user functions.
  • The steady-state NOE auto-analysis now produces a 2D Grace plot of the reference and saturated spectra peak intensity values.
  • Complete redesign of the specific analyses backend, simplifying and cleaning up this internal API and making it easier for users to add completely new analysis types to relax.
  • Parametric reduction of the rotor frame order model, eliminating one redundant parameter hence simplifying optimisation.
  • Large improvement for the lib.software.grace module. The '*_err' and '*_bc' parameter names for the parameter error and back-calculated parameters respectively are now supported, allowing these values to be easily plotted.
  • Expansion of the value.set user function to handle parameters which consist of lists of values. The index argument has been added to allow the index of the list to be specified, and this is then propagated into the specific analysis API.
  • Improvements for the parameter definitions in all analysis types. This allows for better output in 2D plots and text files.
  • Implemented linear constraints for the frame order analysis. This uses the log-barrier constraint algorithm in the minfx library to provide constraints without requiring gradients.
  • Improved and expanded the relax command line options for debugging.
  • Full independence of the relax library so that it can be used outside of relax.
  • The addition of a relaxation dispersion user function for setting the R20 values to the minimum R2eff value.
  • Expanded capabilities for the relax_disp.sherekhan_input user function.
  • Implementation of the B14 and B14 full relaxation dispersion CPMG models for 2-site exchange for all time scales (from the new paper [Baldwin 2014] at http://dx.doi.org/10.1016/j.jmr.2014.02.023).
  • Large improvements to the relax HTML manual including fixes for URLs, bibliography entries, links, and tables.
  • Support for multiple point creation for the OpenDX chi-squared space mapping user function.
  • Automatic determination of reasonable initial contour levels for the OpenDX mapping user function.
  • Addition of a new chapter to the manual for the N-state model or ensemble analysis.
  • Creation of the new pymol.frame_order user function for visualising results.
  • Expansion of the Grace 2D data plotting capabilities.


Changes


Bugfixes


Links

For reference, the announcement for this release can also be found at following links:

Softpedia also has information about the newest relax releases:


Announcements

If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.


References

  • [*Baldwin 2014] Baldwin A. J. (2014). An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange. J. Magn. Reson., 244, 114-124. (DOI: 10.1016/j.jmr.2014.02.023)
  • [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. Mol. BioSyst., 3(7), 483-494. (DOI: 10.1039/b702202f)
  • [*d'Auvergne and Gooley, 2008b] d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133. (DOI: 10.1007/s10858-007-9213-3)

<HarvardReferences />

See also