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{{infobox relax release| version = 3.3.6| prev = 3.3.5| next = 3.3.7| type = Minor feature and bugfix| date = 4 February 2015| manual = yes}} == Description ==
<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, but 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 Bug fixes include a system test failure on Mac OS X , and I<sub>∞</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/>
== Download ==
<section begin=download/>
<section end=download/>
== CHANGES file ==
<section begin=metadata/>
<section end=metadata/>
=== Features ===
<section begin=features/>
* 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.
* 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 [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].
* The assembly of common atomic coordinates by the structure user functions now takes sequence alignments into account. The logic is to first use a sequence alignment from the relax data store if present, use no sequence alignment if coordinates only come from structural models, or fall back to a residue number based alignment. This affects 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.
<section end=features/>
=== Changes ===
<section begin=changes/>
* 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 [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 [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].
* 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> ≤ D<sub>y</sub> ≤ 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 D<sub>iso</sub> value is now set to the real final DisoD<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.
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>
<section end=bugfixes/>
== Links ==
<section begin=links/>
* [http://wiki.nmr-relax.com/Relax_3.3.6 Official release notes on the relax wiki].
* [https://{{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].
* [https://mail.gna.org/public/relax-announce/2015-02/msg00000.html Local archives].
* [https://marc.info/?l=relax-announce&m=142248784423362142326608230935&w=2 Mailing list ARChives (MARC)].
{{:Softpedia}}
<section end=links/>
== Announcements ==
{{:relax release announcements}}
== See also ==
* [http://www.nmr-relax.com/api/3.3/ The relax 3.3 API documentation]
{{:relax release see also}}
[[Category:Relaxation dispersion analysis]]