Difference between revisions of "Relax 3.3.6"

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(One more API documentation link)
(HTML formatting for the Diso parameter.)
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* 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].
 
* 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>.
 
* 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.
 
* 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.
 
* 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.

Revision as of 08:28, 5 February 2015


Description

This is a minor feature and bugfix release. It includes the addition of the new 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 structure.align, structure.atomic_fluctuations, structure.com, structure.displacement, structure.find_pivot, structure.mean, structure.rmsd, structure.superimpose and 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 default to a residue number based alignment if the structure.sequence_alignment user function has not been used. This version also fixes a system test failure on Mac OS X and I parameter text files and Grace graphs are produced by the relaxation curve-fitting auto-analysis for the inversion recovery and saturation recovery experiment types.


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 3.3.6
(4 February 2015, from /trunk)
http://svn.gna.org/svn/relax/tags/3.3.6


Features

  • The 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.
  • Large speed up of the molecule, residue, and spin selection object, affecting all parts of relax.
  • 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 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'.
  • More advanced support for different numpy number types in the 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 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 structure.align, structure.atomic_fluctuations, structure.com, structure.displacement, structure.find_pivot, structure.mean, structure.rmsd, structure.superimpose and structure.web_of_motion user functions.
  • Large improvements in the memory management for all parts of the GUI.


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