relax 3.3.6

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Revision as of 22:13, 4 February 2015 by Bugman (talk | contribs) (→‎Features: Updated the feature list, copying from the CHANGES file.)
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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 Iinf 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


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