Relax 3.3.6 - Revision history

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

2020-10-08T21:15:29Z

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

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

2015-10-22T13:47:24Z

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

Bugman: Increased the sectioning depth.

2015-10-22T13:46:47Z

Increased the sectioning depth.

Bugman: Infobox renaming fix.

2015-10-21T16:50:45Z

Infobox renaming fix.

Bugman: Added an infobox.

2015-10-21T15:47:20Z

Added an infobox.

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

2015-02-09T10:25:16Z

Links: Fix for the MARC link.

Bugman: /* Description */ More editing.

2015-02-05T08:40:19Z

Description: More editing.

Bugman: /* Description */ Small edit.

2015-02-05T08:38:01Z

Description: Small edit.

Bugman: Links to wikipedia for the MSA algorithms.

2015-02-05T08:35:03Z

Links to wikipedia for the MSA algorithms.

Bugman: HTML formatting for the Diso parameter.

2015-02-05T08:28:42Z

HTML formatting for the Diso parameter.

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 * [http://wiki.nmr-relax.com/Relax_3.3.6 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2493 Gna! news item].
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2493|text=Gna! news item}}.
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/64 Gmane mailing list archive].
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00055.html The Mail Archive].

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 | type    = Minor feature and bugfix
 | date    = 4 February 2015
 }}

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-= Description =
+== Description ==
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-= Download =
+== Download ==
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+== CHANGES file ==
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-== Features ==
+=== Features ===
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-== Changes ==
+=== Changes ===
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-== Bugfixes ==
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-= Links =
+== 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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 {{lowercase title}}
-{{relax release infobox
+{{infobox relax release
 | version = 3.3.6
 | prev    = 3.3.5

← Older revision		Revision as of 15:47, 21 October 2015
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	{{lowercase title}}		{{lowercase title}}
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		+	{{relax release infobox
		+	\| version = 3.3.6
		+	\| prev = 3.3.5
		+	\| next = 3.3.7
		+	\| type = Minor feature and bugfix
		+	\| date = 4 February 2015
		+	}}

	= Description =		= Description =

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 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00055.html The Mail Archive].
 * [https://mail.gna.org/public/relax-announce/2015-02/msg00000.html Local archives].
-* [https://marc.info/?l=relax-announce&m=142248784423362&w=2 Mailing list ARChives (MARC)].
+* [https://marc.info/?l=relax-announce&m=142326608230935&w=2 Mailing list ARChives (MARC)].
 {{:Softpedia}}

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 <section begin=description/>
-This is a minor feature and bugfix release.  It includes the addition of the new [http://www.nmr-relax.com/manual/structure_sequence_alignment.html structure.sequence_alignment user function] which can use the 'Central Star' multiple sequence alignment algorithm or align based on residue numbers, saving the results in the relax data store.  The assembly of structural coordinates used by the [http://www.nmr-relax.com/manual/structure_align.html structure.align], [http://www.nmr-relax.com/manual/structure_atomic_fluctuations.html structure.atomic_fluctuations], [http://www.nmr-relax.com/manual/structure_com.html structure.com], [http://www.nmr-relax.com/manual/structure_displacement.html structure.displacement], [http://www.nmr-relax.com/manual/structure_find_pivot.html structure.find_pivot], [http://www.nmr-relax.com/manual/structure_mean.html structure.mean], [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd], [http://www.nmr-relax.com/manual/structure_superimpose.html structure.superimpose] and [http://www.nmr-relax.com/manual/structure_web_of_motion.html structure.web_of_motion] user functions has been redesigned around this new user function.  It will use any pre-existing sequence alignments for the molecules of interest, use no sequence alignment if only structural models are selected, and default to a residue number based alignment if the [http://www.nmr-relax.com/manual/structure_sequence_alignment.html structure.sequence_alignment user function] has not been used.  This version also fixes a system test failure on Mac OS X and I<sub>&infin;</sub> parameter text files and Grace graphs are produced by the relaxation curve-fitting auto-analysis for the inversion recovery and saturation recovery experiment types.
+This is a minor feature and bugfix release.  It includes the addition of the new [http://www.nmr-relax.com/manual/structure_sequence_alignment.html structure.sequence_alignment user function] which can use the 'Central Star' multiple sequence alignment algorithm or align based on residue numbers, saving the results in the relax data store.  The assembly of structural coordinates used by the [http://www.nmr-relax.com/manual/structure_align.html structure.align], [http://www.nmr-relax.com/manual/structure_atomic_fluctuations.html structure.atomic_fluctuations], [http://www.nmr-relax.com/manual/structure_com.html structure.com], [http://www.nmr-relax.com/manual/structure_displacement.html structure.displacement], [http://www.nmr-relax.com/manual/structure_find_pivot.html structure.find_pivot], [http://www.nmr-relax.com/manual/structure_mean.html structure.mean], [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd], [http://www.nmr-relax.com/manual/structure_superimpose.html structure.superimpose] and [http://www.nmr-relax.com/manual/structure_web_of_motion.html structure.web_of_motion] user functions has been redesigned around this new user function.  It will use any pre-existing sequence alignments for the molecules of interest, use no sequence alignment if only structural models are selected, and default to a residue number based alignment if the [http://www.nmr-relax.com/manual/structure_sequence_alignment.html structure.sequence_alignment user function] has not been used.  Bug fixes include a system test failure on Mac OS X, and I<sub>&infin;</sub> parameter text files and Grace graphs are now produced by the relaxation curve-fitting auto-analysis for the inversion recovery and saturation recovery experiment types.  Many more details are given below.
 <section end=description/>

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 <section begin=features/>
-* The Needleman-Wunsch sequence alignment algorithm now calculates an alignment score.
+* The [https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm Needleman-Wunsch sequence alignment algorithm] now calculates an alignment score.
 * Implementation of the central star multiple sequence alignment (MSA) algorithm.
 * Implementation of a reside number based multiple sequence alignment (MSA) algorithm.
@@ Line 30: / Line 30: @@
 * Sequence alignments are now saved in the relax data store.
 * Important formatting improvement for the description in the GUI user function windows, removing excess empty lines after lists.
-* Creation of the [http://www.nmr-relax.com/manual/structure_sequence_alignment.html structure.sequence_alignment user function].  The MSA algorithm can be set to either 'Central Star' or 'residue number', the pairwise sequence alignment algorithm to 'NW70' for the Needleman-Wunsch algorithm, and the substitution matrix to one of 'BLOSUM62', 'PAM250', or 'NUC 4.4'.
+* Creation of the [http://www.nmr-relax.com/manual/structure_sequence_alignment.html structure.sequence_alignment user function].  The [https://en.wikipedia.org/wiki/Multiple_sequence_alignment MSA algorithm] can be set to either 'Central Star' or 'residue number', the pairwise sequence alignment algorithm to 'NW70' for the [https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm Needleman-Wunsch algorithm], and the substitution matrix to one of [https://en.wikipedia.org/wiki/BLOSUM 'BLOSUM62'], [https://en.wikipedia.org/wiki/Point_accepted_mutation 'PAM250'], or 'NUC 4.4'.
 * More advanced support for different numpy number types in the [http://www.nmr-relax.com/api/3.3/lib.xml-module.html lib.xml relax library module].  This allows numpy int16, int32, float32, and float64 objects to be saved in the relax data store and retrieved from relax XML save and results files.
 * Merger of structure.align into the [http://www.nmr-relax.com/manual/structure_superimpose.html structure.superimpose user function].
@@ Line 57: / Line 57: @@
 * Import fix for the [http://www.nmr-relax.com/api/3.3/test_suite.unit_tests._lib._sequence_alignment.test_align_protein.Test_align_protein-class.html _lib._sequence_alignment.test_align_protein unit test module].
 * Added the verbosity argument to [http://www.nmr-relax.com/api/3.3/lib.sequence_alignment.align_protein-module.html#align_pairwise lib.sequence_alignment.align_protein.align_pairwise()].  If set to zero, all printouts are suppressed.
-* The Needleman-Wunsch sequence alignment algorithm now calculates and returns an alignment score.  This is in the [http://www.nmr-relax.com/api/3.3/lib.sequence_alignment.needleman_wunsch-module.html#needleman_wunsch_align lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function].  The score is calculated as the sum of the Needleman-Wunsch matrix elements along the traceback path.
+* The [https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm Needleman-Wunsch sequence alignment algorithm] now calculates and returns an alignment score.  This is in the [http://www.nmr-relax.com/api/3.3/lib.sequence_alignment.needleman_wunsch-module.html#needleman_wunsch_align lib.sequence_alignment.needleman_wunsch.needleman_wunsch_align() function].  The score is calculated as the sum of the Needleman-Wunsch matrix elements along the traceback path.
-* The protein pairwise sequence alignment function now returns the alignment score.  This is in the [http://www.nmr-relax.com/api/3.3/lib.sequence_alignment.align_protein-module.html#align_pairwise lib.sequence_alignment.align_protein.align_pairwise() function].  The score from the Needleman-Wunsch sequence alignment algorithm is simply passed along.
+* The protein pairwise sequence alignment function now returns the alignment score.  This is in the [http://www.nmr-relax.com/api/3.3/lib.sequence_alignment.align_protein-module.html#align_pairwise lib.sequence_alignment.align_protein.align_pairwise() function].  The score from the [https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm Needleman-Wunsch sequence alignment algorithm] is simply passed along.
 * Fix for the [http://www.nmr-relax.com/api/3.3/test_suite.unit_tests._lib._sequence_alignment.test_msa.Test_msa-class.html#test_central_star Test_msa.test_central_star unit test].  This is from the [http://www.nmr-relax.com/api/3.3/test_suite.unit_tests._lib._sequence_alignment.test_msa-module.html _lib._sequence_alignment.test_msa unit test module].  Some of the real gap matrix indices were incorrect.
 * Complete implementation of the central star multiple sequence alignment algorithm.  This includes all the four major steps - pairwise alignment between all sequence pairs, finding the central sequence, iteratively aligning the sequences to the gapped central sequence, and introducing gaps in previous alignments during the iterative alignment.  The correctness of the implementation is verified by the [http://www.nmr-relax.com/api/3.3/test_suite.unit_tests._lib._sequence_alignment.test_msa.Test_msa-class.html#test_central_star Test_msa.test_central_star unit test] of the [http://www.nmr-relax.com/api/3.3/test_suite.unit_tests._lib._sequence_alignment.test_msa-module.html _lib._sequence_alignment.test_msa module].

@@ Line 130: / Line 130: @@
 * Creation of oblate spheroid diffusion relaxation data.  This will be used in the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_create_diff_tensor_pdb_oblate Structure.test_create_diff_tensor_pdb_oblate system test].
 * Fix for the oblate spheroid diffusion relaxation data.  The diffusion parameters are constrained as D<sub>x</sub> &le; D<sub>y</sub> &le; D<sub>z</sub>.
-* More fixes for the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_create_diff_tensor_pdb_oblate Structure.test_create_diff_tensor_pdb_oblate system test].  The initial Diso value is now set to the real final Diso, and the PDB file contents have been updated for the fixed oblate spheroidal diffusion relaxation data.
+* More fixes for the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_create_diff_tensor_pdb_oblate Structure.test_create_diff_tensor_pdb_oblate system test].  The initial D<sub>iso</sub> value is now set to the real final D<sub>iso</sub>, and the PDB file contents have been updated for the fixed oblate spheroidal diffusion relaxation data.
 * Updates for many of the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.diffusion_tensor.Diffusion_tensor-class.html Diffusion_tensor system tests].  This is due to the changed directory names in test_suite/shared_data/diffusion_tensor/.  The ds.diff_dir variable has been introduced to point to the correct data directory.
 * Large improvement for the [http://www.nmr-relax.com/api/3.3/test_suite.gui_tests.base_classes.GuiTestCase-class.html#tearDown GUI test tearDown() clean up method], fixing the tests on wxPython 2.8.  The user function window destruction has been shifted into a new [http://www.nmr-relax.com/api/3.3/test_suite.gui_tests.base_classes.GuiTestCase-class.html#clean_up_windows clean_up_windows() method] which is executed via wx.CallAfter() to avoid racing conditions.  In addition, the spin viewer window is destroyed between tests.  The spin viewer window change allows the GUI tests to pass on wxPython 2.8 again.  This also allows the GUI tests to progress much further on Mac OS X systems before they crash again for some other reason.  This could simply be hiding a problem in the spin viewer window.  However it is likely to be a racing problem only triggered by the super fast speed of the GUI tests and a normal user would never be able to operate the GUI on the millisecond timescale and hence may never see it.