relax 1.3.2

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Description

This release solves many major bugs in the final stages of model-free analysis, especially when using the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]. This version also marks the return of the NOE analysis. If you are using relax version 1.3.1, it is recommended that you upgrade to 1.3.2. Bugs which have been resolved include: problems reading PDB files; failure of the value.set, fix and value.write user functions; non-functional model elimination; model selection issues in certain situations; and various Monte Carlo simulation issues.


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 1.3.2
(8 October 2008, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.2


Features

  • The NOE analysis has been converted to the new design and is fully functional again.


Changes

  • Internal abstractions to the relax data store by using the generic_fns.pipes API.
  • Added more literature references to the 'full_analysis.py' script.
  • Eliminated Monte Carlo simulations are better identified during user function execution.


Bugfixes

  • The generation of the cone geometric object for the N-state model is fixed.
  • Fixes for the relax_curve_diff.py and latex_mf_table.py sample scripts (identified by the relax data store abstraction).
  • Fixed the reading of relax 1.2 model-free results files (identified by the relax data store abstraction).
  • Various PDB file loading issues fixed.
  • value.set no longer fails when the parameter being set already exists (bug #12406).
  • Fix for the bug whereby model elimination does nothing for model-free models. This fix may solve other model-free related issues (bug #12407).
  • Model elimination no longer fails when no diffusion tensor is loaded (bug #12408).
  • The error when loading the PDB file through the reading of the results file in the 'final' stage of the 'full_analysis.py' sample script is fixed ([https://gna.org/bugs/? 1240 bug # 9).
  • Model elimination is fixed in the 'full_analysis.py' script.
  • The fix user function works again when the element argument is set to 'all'.
  • Fix for the duplication of sequence data during model selection.
  • Monte Carlo simulations were failing due to a missing sequence error (bug #12410).
  • The model elimination error "AttributeError: 'SpinContainer' object has no attribute 'params'." has been fixed (bug #12411).
  • A missing global chi-squared value was causing failure of global model selection (bug #12412).
  • Monte Carlo simulation elimination was removing the simulation not from the affected spin but from all spins (bug #12416).
  • Fix for the failure of the value.write user function in all analysis types (bug #12418).


Links

For reference, the following links are also part of the announcement for this release:


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.


References

  • [d'Auvergne and Gooley, 2007] ^ d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. Mol. BioSyst., 3(7), 483-494. (DOI: 10.1039/b702202f)
  • [d'Auvergne and Gooley, 2008b] ^ d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133. (DOI: 10.1007/s10858-007-9213-3)


See also