Difference between revisions of "Relax 3.3.5"

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= Description =
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{{infobox relax release
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| version = 3.3.5
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| prev    = 3.3.4
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| next    = 3.3.6
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| type    = Major feature and bugfix
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| date    = 27 January 2015
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| manual  = yes
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}}
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== Description ==
  
 
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= Download =
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== Download ==
  
 
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= CHANGES file =
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== CHANGES file ==
  
 
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== Features ==
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=== Features ===
  
 
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<section end=features/>
  
== Changes ==
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=== Changes ===
  
 
<section begin=changes/>
 
<section begin=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/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.
 
* 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.
 
* 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.
 
* 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.
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== Bugfixes ==
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=== Bugfixes ===
  
 
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= Links =
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== Links ==
  
 
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<section begin=links/>
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* [http://wiki.nmr-relax.com/Relax_3.3.5 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=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://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].
 
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00054.html The Mail Archive].
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<section end=links/>
  
= Announcements =
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== Announcements ==
  
 
{{:relax release announcements}}
 
{{:relax release announcements}}
  
  
= See also =
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== See also ==
  
 
* [http://www.nmr-relax.com/api/3.3/ The relax 3.3 API documentation]
 
* [http://www.nmr-relax.com/api/3.3/ The relax 3.3 API documentation]
 
{{:relax release see also}}
 
{{:relax release see also}}
 
[[Category:Relaxation dispersion analysis]]
 
[[Category:Relaxation dispersion analysis]]

Latest revision as of 13:37, 16 October 2020


Official relax releases
relax logo
relax version 3.3.5
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← relax 3.3.4 relax 3.3.6 →

Release type Major feature and bugfix
Release date 27 January 2015

The PDF version of the relax 3.3.5 user manual The relax 3.3.5 user manual

Description

This is a major feature and bugfix release. It fixes an important bug in the Monte Carlo simulation error analysis in the relaxation dispersion analysis. Features include improvements to the NMR spectral noise error analysis, expansion of the grace.write user function to handle both first and last point normalisation for reasonable R1 curves in saturation recovery experiments, the implementation of Needleman-Wunsch pairwise sequence alignment algorithm using the BLOSUM62, PAM250 and NUC 4.4 substitution matrices for more advanced 3D structural alignments via the structure.align and structure.superimpose user functions as well as any of the other structure user functions dealing with multiple molecules, conversion of the structure.displacement, structure.find_pivot, structure.rmsd, structure.superimpose and structure.web_of_motion user functions to a new pipes/models/molecules/atom_id design to allow the user functions to operate on different data pipes, different structural models and different molecules, addition of the displace_id argument to the structure.align and structure.superimpose user functions to allow finer control over which atoms are translated and rotated by the algorithm, large improvement for the PDB molecule identification code affecting the structure.read_pdb user function, creation of the lib.plotting package for assembling all of the data plotting capabilities of relax, implementation of the new structure.atomic_fluctuations user function for creating text output or Gnuplot graphs of the correlation matrix of interatomic distance, angle or parallax shift fluctuations, the implementation of ordinary least squares fitting, and improvements for the pcs.corr_plot and rdc.corr_plot user functions. Many more features and bugfixes are listed below.


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 3.3.5
(27 January 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.5


Features


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.


See also