Difference between revisions of "Relax 3.3.9"

From relax wiki
Jump to navigation Jump to search
(Infobox renaming fix.)
m (Switch to the {{gna task link}} template to remove dead Gna! links.)
 
(3 intermediate revisions by the same user not shown)
Line 2: Line 2:
  
 
{{infobox relax release
 
{{infobox relax release
| version = 3.3.9
+
| version = 3.3.9
| prev   = 3.3.8
+
| prev     = 3.3.8
| next   = 4.0.0
+
| next     = 4.0.0
| type   = Minor feature
+
| keywords = N-state model, relaxation dispersion
| date   = 30 September 2015
+
| type     = Minor feature
 +
| date     = 30 September 2015
 +
| manual  = yes
 
}}
 
}}
  
= Description =
+
== Description ==
  
 
<section begin=description/>
 
<section begin=description/>
Line 15: Line 17:
 
<section end=description/>
 
<section end=description/>
  
= Download =
+
== Download ==
  
 
<section begin=download/>
 
<section begin=download/>
Line 21: Line 23:
 
<section end=download/>
 
<section end=download/>
  
= CHANGES file =
+
== CHANGES file ==
  
 
<section begin=metadata/>
 
<section begin=metadata/>
Line 29: Line 31:
 
<section end=metadata/>
 
<section end=metadata/>
  
== Features ==
+
=== Features ===
  
 
<section begin=features/>
 
<section begin=features/>
Line 38: Line 40:
 
<section end=features/>
 
<section end=features/>
  
== Changes ==
+
=== Changes ===
  
 
<section begin=changes/>
 
<section begin=changes/>
* Wrote a method to store parameter data and dispersion curves, for the protocol of repeated CPMG analysis.  This is to prepare for analysis in other programs.  The method loops through the data pipes, and writes the data out.  It then writes a bash script that will concatenate the data in an matrix array style, for reading and processing in other programs.  [https://gna.org/task/?7826 Task #7826: Write an Python class for the repeated analysis of dispersion data].
+
* Wrote a method to store parameter data and dispersion curves, for the protocol of repeated CPMG analysis.  This is to prepare for analysis in other programs.  The method loops through the data pipes, and writes the data out.  It then writes a bash script that will concatenate the data in an matrix array style, for reading and processing in other programs.  {{gna task link|7826|text=Task #7826: Write an Python class for the repeated analysis of dispersion data}}.
* Added to write out a collection script for &chi;<sup>2</sup> and rate parameters.  [https://gna.org/task/?7826 Task #7826: Write an Python class for the repeated analysis of dispersion data].
+
* Added to write out a collection script for &chi;<sup>2</sup> and rate parameters.  {{gna task link|7826|text=Task #7826: Write an Python class for the repeated analysis of dispersion data}}.
* In the collection bash script, removes spins which have not been fitted.  [https://gna.org/task/?7826 Task #7826: Write an Python class for the repeated analysis of dispersion data].
+
* In the collection bash script, removes spins which have not been fitted.  {{gna task link|7826|text=Task #7826: Write an Python class for the repeated analysis of dispersion data}}.
* Fix for use of " instead of ' in bash script.  [https://gna.org/task/?7826 Task #7826: Write an Python class for the repeated analysis of dispersion data].
+
* Fix for use of " instead of ' in bash script.  {{gna task link|7826|text=Task #7826: Write an Python class for the repeated analysis of dispersion data}}.
* Adding option to [http://www.nmr-relax.com/api/3.3/auto_analyses.relax_disp_repeat_cpmg.Relax_disp_rep-class.html#minimise_execute minimise class function], to perform Monte Carlo error analysis.  [https://gna.org/task/?7826 Task #7826: Write an Python class for the repeated analysis of dispersion data].
+
* Adding option to [http://www.nmr-relax.com/api/3.3/auto_analyses.relax_disp_repeat_cpmg.Relax_disp_rep-class.html#minimise_execute minimise class function], to perform Monte Carlo error analysis.  {{gna task link|7826|text=Task #7826: Write an Python class for the repeated analysis of dispersion data}}.
* Printout when minimising Monte Carlo simulations.  [https://gna.org/task/?7826 Task #7826: Write an Python class for the repeated analysis of dispersion data].
+
* Printout when minimising Monte Carlo simulations.  {{gna task link|7826|text=Task #7826: Write an Python class for the repeated analysis of dispersion data}}.
 
* Added additional test to [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_bug_23186_cluster_error_calc_dw system test Relax_disp.test_bug_23186_cluster_error_calc_dw()] to prove that Bug #23619 is invalid.  [https://gna.org/bugs/?23619 Bug #23619: Stored chi2 sim values from Monte Carlo simulations does not equal normal chi2 values].
 
* Added additional test to [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_bug_23186_cluster_error_calc_dw system test Relax_disp.test_bug_23186_cluster_error_calc_dw()] to prove that Bug #23619 is invalid.  [https://gna.org/bugs/?23619 Bug #23619: Stored chi2 sim values from Monte Carlo simulations does not equal normal chi2 values].
* Small fix for the shell script to collect data files, and not use the program "column" in the end.  The line width becomes to large to handle for column.  [https://gna.org/task/?7826 Task #7826: Write an Python class for the repeated analysis of dispersion data].
+
* Small fix for the shell script to collect data files, and not use the program "column" in the end.  The line width becomes to large to handle for column.  {{gna task link|7826|text=Task #7826: Write an Python class for the repeated analysis of dispersion data}}.
 
* Added a unit test that triggers the bug.  Test added in [http://www.nmr-relax.com/api/3.3/test_suite.unit_tests.spin_testing_base.Spin_base_class-class.html#test_delete_spin_all test_delete_spin_all], and can be accessed with: relax -u _pipe_control.test_spin.  [https://gna.org/bugs/?23642 Bug #23642: When deleting all spins for a residue, an empty placeholder is where select=True].
 
* Added a unit test that triggers the bug.  Test added in [http://www.nmr-relax.com/api/3.3/test_suite.unit_tests.spin_testing_base.Spin_base_class-class.html#test_delete_spin_all test_delete_spin_all], and can be accessed with: relax -u _pipe_control.test_spin.  [https://gna.org/bugs/?23642 Bug #23642: When deleting all spins for a residue, an empty placeholder is where select=True].
 
* Added sample data and analysis script, that will eventually show that there is not much difference in the sample statistics used for comparing the output of two very similar datasets.  This is a multiple comparison test with many T-tests at once, where the familywise error is controlled by the Holm method.  Even if the values are close to equal, and within the standard deviation, this procedure will reject up to 20% of the null hypothesis.  This is not deemed as a suitable method.  [https://gna.org/bugs/?23644 Bug #23644: monte_carlo.error_analysis() does not update the mean value/expectation value from simulations].
 
* Added sample data and analysis script, that will eventually show that there is not much difference in the sample statistics used for comparing the output of two very similar datasets.  This is a multiple comparison test with many T-tests at once, where the familywise error is controlled by the Holm method.  Even if the values are close to equal, and within the standard deviation, this procedure will reject up to 20% of the null hypothesis.  This is not deemed as a suitable method.  [https://gna.org/bugs/?23644 Bug #23644: monte_carlo.error_analysis() does not update the mean value/expectation value from simulations].
Line 60: Line 62:
 
* Created a simple unit test for the new [http://www.nmr-relax.com/api/3.3/lib.statistics-module.html#geometric_mean lib.statistics.geometric_mean() function].
 
* Created a simple unit test for the new [http://www.nmr-relax.com/api/3.3/lib.statistics-module.html#geometric_mean lib.statistics.geometric_mean() function].
 
* Added a unit test for the new [http://www.nmr-relax.com/api/3.3/lib.statistics-module.html#geometric_std lib.statistics.geometric_std() function].
 
* Added a unit test for the new [http://www.nmr-relax.com/api/3.3/lib.statistics-module.html#geometric_std lib.statistics.geometric_std() function].
* Made a summarize function to compare results.  [https://gna.org/task/?7826 Task #7826: Write an Python class for the repeated analysis of dispersion data].
+
* Made a summarize function to compare results.  {{gna task link|7826|text=Task #7826: Write an Python class for the repeated analysis of dispersion data}}.
 
<section end=changes/>
 
<section end=changes/>
  
== Bugfixes ==
+
=== Bugfixes ===
  
 
<section begin=bugfixes/>
 
<section begin=bugfixes/>
Line 69: Line 71:
 
<section end=bugfixes/>
 
<section end=bugfixes/>
  
= Links =
+
== Links ==
  
 
<section begin=links/>
 
<section begin=links/>
Line 75: Line 77:
  
 
* [http://wiki.nmr-relax.com/Relax_3.3.9 Official release notes on the relax wiki].
 
* [http://wiki.nmr-relax.com/Relax_3.3.9 Official release notes on the relax wiki].
* [https://gna.org/forum/forum.php?forum_id=2513 Gna! news item].
+
* {{gna link|url=gna.org/forum/forum.php?forum_id=2513|text=Gna! news item}}.
 
* [http://article.gmane.org/gmane.science.nmr.relax.announce/67 Gmane mailing list archive].
 
* [http://article.gmane.org/gmane.science.nmr.relax.announce/67 Gmane mailing list archive].
 
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00058.html The Mail Archive].
 
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00058.html The Mail Archive].
Line 84: Line 86:
 
<section end=links/>
 
<section end=links/>
  
= Announcements =
+
== Announcements ==
  
 
{{:relax release announcements}}
 
{{:relax release announcements}}
  
  
= See also =
+
== 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 13:43, 16 October 2020


Official relax releases
relax logo
relax version 3.3.9
Previous version Next version
← relax 3.3.8 relax 4.0.0 →

Keywords N-state model, relaxation dispersion
Release type Minor feature
Release date 30 September 2015

The PDF version of the relax 3.3.9 user manual The relax 3.3.9 user manual

Description

This is a minor feature release with improvements to the automatic relaxation dispersion protocol for repeated CPMG data, support for Monte Carlo or Bootstrap simulating RDC and PCS Q factors, a huge speedup of Monte Carlo simulations in the N-state model analysis, and geometric mean and standard deviation functions added to the relax library.


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 3.3.9
(30 September 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.9


Features

  • Improvements to the automatic relaxation dispersion protocol for repeated CPMG data.
  • Support for Monte Carlo or Bootstrap simulating the RDC and PCS Q factors.
  • Huge speedup of Monte Carlo simulations in the N-state model analysis.
  • Geometric mean and standard deviation functions added to the relax library.


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