Relax 3.3.5 - Revision history

Bugman: Switch to the {{gna task link}} template to remove dead Gna! links.

2020-10-16T13:37:44Z

Switch to the {{gna task link}} template to remove dead Gna! links.

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

2020-10-08T21:17:27Z

Links: Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: Increased the sectioning depth.

2015-11-03T10:25:51Z

Increased the sectioning depth.

Bugman: Added the 'manual' parameter to {{infobox relax release}}.

2015-10-22T13:28:42Z

Added the 'manual' parameter to {{infobox relax release}}.

Bugman: Infobox renaming fix.

2015-10-21T16:51:05Z

Infobox renaming fix.

Bugman: Added an infobox.

2015-10-21T15:48:48Z

Added an infobox.

Bugman: /* Links */ Fix for the MARC link.

2015-01-29T12:40:44Z

Links: Fix for the MARC link.

Bugman: Updated the links section for the relax 3.3.5 release announcements.

2015-01-28T08:50:32Z

Updated the links section for the relax 3.3.5 release announcements.

Bugman: Link fix.

2015-01-28T08:45:59Z

Link fix.

Bugman: Completed the API documentation linking.

2015-01-28T08:42:17Z

Completed the API documentation linking.

Show changes

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 * Improvements for the [http://www.nmr-relax.com/manual/pcs_corr_plot.html pcs.corr_plot user function] - the plot range is now determined by the data.
 * Improvements for the [http://www.nmr-relax.com/manual/rdc_corr_plot.html rdc.corr_plot user function] - the plot range is now determined by the data.
-* Added save state for testing implementation of error analysis.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Added save state for testing implementation of error analysis.  {{gna task link|?7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Simplification of [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual], to just test the creation of Monte-Carlo data where errors are drawn from the reduced &chi;<sup>2</sup> distribution.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Simplification of [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual], to just test the creation of Monte-Carlo data where errors are drawn from the reduced &chi;<sup>2</sup> distribution.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Extension of the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function] to draw errors from the reduced &chi;<sup>2</sup> Gauss distribution as found by best fit.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Extension of the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function] to draw errors from the reduced &chi;<sup>2</sup> Gauss distribution as found by best fit.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Adding to backend of [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html pipe_control.error_analysis()], to modify data point as error drawn from the reduced &chi;<sup>2</sup> Gauss distribution.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Adding to backend of [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html pipe_control.error_analysis()], to modify data point as error drawn from the reduced &chi;<sup>2</sup> Gauss distribution.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Adding empty API method to return errors from the reduced &chi;<sup>2</sup> distribution.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Adding empty API method to return errors from the reduced &chi;<sup>2</sup> distribution.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Added API function in relaxation dispersion to return error structure from the reduced &chi;<sup>2</sup> distribution.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Added API function in relaxation dispersion to return error structure from the reduced &chi;<sup>2</sup> distribution.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Temporary test of making a confidence interval as described in fitting guide.  This is [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#x_test_task_7882_kex_conf system test Relax_disp.x_test_task_7882_kex_conf], which is not activated by default.  Running the test, interestingly shows, there is a possibility for a lower global k<sub>ex</sub>.  But the value only differ from k<sub>ex</sub>=1826 to k<sub>ex</sub>=1813.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Temporary test of making a confidence interval as described in fitting guide.  This is [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#x_test_task_7882_kex_conf system test Relax_disp.x_test_task_7882_kex_conf], which is not activated by default.  Running the test, interestingly shows, there is a possibility for a lower global k<sub>ex</sub>.  But the value only differ from k<sub>ex</sub>=1826 to k<sub>ex</sub>=1813.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Change to [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#x_test_task_7882_kex_conf system test Relax_disp.x_test_task_7882_kex_conf()].  This is just a temporary system test, to check for local minima.  This is method in regression book of Graphpad: http://www.graphpad.com/faq/file/Prism4RegressionBook.pdf Page: 109-111.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Change to [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#x_test_task_7882_kex_conf system test Relax_disp.x_test_task_7882_kex_conf()].  This is just a temporary system test, to check for local minima.  This is method in regression book of Graphpad: http://www.graphpad.com/faq/file/Prism4RegressionBook.pdf Page: 109-111.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Raising an error, if the [[R2eff]] model is used, and drawing errors from the fit.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Raising an error, if the [[R2eff]] model is used, and drawing errors from the fit.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* To [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual()], adding test for raise of errors, if the [[R2eff]] model is selected.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* To [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual()], adding test for raise of errors, if the [[R2eff]] model is selected.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Added test of argument "distribution" in [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()].  This is to make sure that a wrong argument is not passed into the function.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Added test of argument "distribution" in [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()].  This is to make sure that a wrong argument is not passed into the function.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Extended the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function], to allow for the definition of the STD to use in Gauss distribution.  This is for creation of Monte-Carlo simulations, where one has perhaps gained information about the expected errors of the data points, which is not measured.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Extended the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function], to allow for the definition of the STD to use in Gauss distribution.  This is for creation of Monte-Carlo simulations, where one has perhaps gained information about the expected errors of the data points, which is not measured.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* In backend [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()] added the argument 'fixed_error' to allow for fixed input of error to the Gauss distribution.  Inserted a range of checks, to make sure function behaves as expected.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* In backend [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()] added the argument 'fixed_error' to allow for fixed input of error to the Gauss distribution.  Inserted a range of checks, to make sure function behaves as expected.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Added to [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()] the creation of data points for a fixed distribution.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Added to [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()] the creation of data points for a fixed distribution.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* To [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual()], added tests for creation of Monte-Carlo data by different methods.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* To [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual()], added tests for creation of Monte-Carlo data by different methods.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* In [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()], if data is of list type or ndarray, then modify the data point according to the fixed error if the distribution is set to 'fixed'.  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* In [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()], if data is of list type or ndarray, then modify the data point according to the fixed error if the distribution is set to 'fixed'.  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
-* Expanded the STD acronym, to the meaning of standard deviation.  This is in the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function].  [https://gna.org/task/?7882 Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
+* Expanded the STD acronym, to the meaning of standard deviation.  This is in the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function].  {{gna task link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals}}.
 * Added a RelaxWarning printout to the [http://www.nmr-relax.com/api/3.3/dep_check-module.html dep_check module] if wxPython 2.8 or less is encountered.  This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7502.  The warning text is simply written to STDERR as relax starts.
 * Updated the wxPython version in the relax manual to be 2.9 or higher.  This is in the section http://www.nmr-relax.com/manual/Dependencies.html.

@@ Line 319: / Line 319: @@
 * [http://wiki.nmr-relax.com/Relax_3.3.5 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2492 Gna! news item].
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2492|text=Gna! news item}}.
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/63 Gmane mailing list archive].
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00054.html The Mail Archive].

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 }}
-= Description =
+== Description ==
 <section begin=description/>
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-= Download =
+== Download ==
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-= CHANGES file =
+== CHANGES file ==
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-== Features ==
+=== Features ===
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-== Changes ==
+=== Changes ===
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-== Bugfixes ==
+=== Bugfixes ===
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-= Links =
+== Links ==
 <section begin=links/>
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-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/3.3/ The relax 3.3 API documentation]
 {{:relax release see also}}
 [[Category:Relaxation dispersion analysis]]

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 | type    = Major feature and bugfix
 | date    = 27 January 2015
 }}

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 {{lowercase title}}
-{{relax release infobox
+{{infobox relax release
 | version = 3.3.5
 | prev    = 3.3.4

← Older revision		Revision as of 15:48, 21 October 2015
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	{{lowercase title}}		{{lowercase title}}
		+
		+	{{relax release infobox
		+	\| version = 3.3.5
		+	\| prev = 3.3.4
		+	\| next = 3.3.6
		+	\| type = Major feature and bugfix
		+	\| date = 27 January 2015
		+	}}

	= Description =		= Description =

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 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00054.html The Mail Archive].
 * [https://mail.gna.org/public/relax-announce/2015-01/msg00000.html Local archives].
-* [http://marc.info/?l=relax-announce&m=141773006429005&w=2 Mailing list ARChives (MARC)].
+* [https://marc.info/?l=relax-announce&m=142248784423361&w=2 Mailing list ARChives (MARC)].
 {{:Softpedia}}

@@ Line 309: / Line 309: @@
 For reference, the announcement for this release can also be found at following links:
-* [http://wiki.nmr-relax.com/Relax_3.3.4 Official release notes on the relax wiki].
+* [http://wiki.nmr-relax.com/Relax_3.3.5 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2483 Gna! news item].
+* [https://gna.org/forum/forum.php?forum_id=2492 Gna! news item].
-* [http://article.gmane.org/gmane.science.nmr.relax.announce/62 Gmane mailing list archive].
+* [http://article.gmane.org/gmane.science.nmr.relax.announce/63 Gmane mailing list archive].
-* [http://www.mail-archive.com/relax-announce%40gna.org/msg00053.html The Mail Archive].
+* [http://www.mail-archive.com/relax-announce%40gna.org/msg00054.html The Mail Archive].
-* [https://mail.gna.org/public/relax-announce/2014-12/msg00000.html Local archives].
+* [https://mail.gna.org/public/relax-announce/2015-01/msg00000.html Local archives].
-* [http://marc.info/?l=relax-announce&m=141773006429004&w=2 Mailing list ARChives (MARC)].
+* [http://marc.info/?l=relax-announce&m=141773006429005&w=2 Mailing list ARChives (MARC)].
 {{:Softpedia}}

@@ Line 102: / Line 102: @@
 * Shifted the atomic assembly code from the [http://www.nmr-relax.com/manual/structure_align.html structure.align user function] into its own function.  The new function [http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html#assemble_coordinates assemble_coordinates()] of the [http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html pipe_control.structure.main module] will be used to standardise the process of assembling atomic coordinates for all of the structure user functions.  This will improve the support for comparing different molecules rather than different models as missing atoms or divergent primary sequence are properly handled, and it has multi-pipe support.
 * Changed the argument order for the [http://www.nmr-relax.com/manual/structure_align.html structure.align user function].  The standardised order will now be pipes, models, molecules, atom_id, etc.
-* Converted the [http://www.nmr-relax.com/manual/structure_find_pivot.html structure.find_pivot user function] to the new pipes/models/molecules/atom_id design.  This allows the motional pivot algorithm to work on atomic coordinates from different data pipes, different structural models, and different molecules.  The change allows the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_find_pivot_molecules Structure.test_find_pivot_molecules system test] to now pass, as missing atomic data is now correctly handled.  The user function backend uses the new [[http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html#assemble_coordinates pipe_control.structure.main.assemble_coordinates() function].  The Structure.test_find_pivot and [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_find_pivot_molecules Structure.test_find_pivot_molecules] system tests have been updated for the user function argument changes.
+* Converted the [http://www.nmr-relax.com/manual/structure_find_pivot.html structure.find_pivot user function] to the new pipes/models/molecules/atom_id design.  This allows the motional pivot algorithm to work on atomic coordinates from different data pipes, different structural models, and different molecules.  The change allows the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_find_pivot_molecules Structure.test_find_pivot_molecules system test] to now pass, as missing atomic data is now correctly handled.  The user function backend uses the new [http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html#assemble_coordinates pipe_control.structure.main.assemble_coordinates() function].  The Structure.test_find_pivot and [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_find_pivot_molecules Structure.test_find_pivot_molecules] system tests have been updated for the user function argument changes.
 * Shift of the atomic coordinate assembly code into the relax library.  Most of the [http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html#assemble_coordinates pipe_control.structure.main.assemble_coordinates() function] has been shifted into the [http://www.nmr-relax.com/api/3.3/lib.structure.internal.coordinates-module.html#assemble_coord_array assemble_coord_array() function] of the new [http://www.nmr-relax.com/api/3.3/lib.structure.internal.coordinates-module.html lib.structure.internal.coordinates module].  The pipe_control function now only checks the arguments and assembles the structural objects from the relax data store, and then calls assemble_coord_array() to do all of the work.  This code abstraction increases the usefulness of the atomic coordinate assembly and allows it to be significantly expanded in the future, for example by being able to take sequence alignments into consideration.
 * Tooltip standardisation for the [http://www.nmr-relax.com/manual/structure_align.html structure.align] and [http://www.nmr-relax.com/manual/structure_find_pivot.html structure.find_pivot] user functions.