Difference between revisions of "Relax 3.2.0"

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m (Switch to the {{relax developer link}} template to remove dead Gna! links.)
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*  The J(w) mapping parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
 
*  The J(w) mapping parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
 
*  The consistency testing parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
 
*  The consistency testing parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
*  The relaxation dispersion parameter setting documentation has been shifted into the parameter list object.  The documentation has also been rewritten as it originates from [https://gna.org/users/semor Sebastien Morin] back in 2009 and is now very much out of date.
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*  The relaxation dispersion parameter setting documentation has been shifted into the parameter list object.  The documentation has also been rewritten as it originates from {{relax developer link|username=semor|text=Sebastien Morin}} back in 2009 and is now very much out of date.
 
*  Deleted the relaxation curve-fitting parameter setting documentation.  This really didn't say anything.
 
*  Deleted the relaxation curve-fitting parameter setting documentation.  This really didn't say anything.
 
*  The N-state model parameter setting documentation has been shifted into the parameter list object.
 
*  The N-state model parameter setting documentation has been shifted into the parameter list object.
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*  Created the new '-r' or '--traceback' relax command line option.  If supplied, stack tracebacks will be shown for all RelaxWarnings and RelaxErrors.  This allows for finer debugging control.
 
*  Created the new '-r' or '--traceback' relax command line option.  If supplied, stack tracebacks will be shown for all RelaxWarnings and RelaxErrors.  This allows for finer debugging control.
 
*  Clean up of the debugging command line options.  The debug flag now will cause stack tracebacks to be printed on all RelaxWarnings.
 
*  Clean up of the debugging command line options.  The debug flag now will cause stack tracebacks to be printed on all RelaxWarnings.
*  Created the '--error-state' command line option for saving a pickled state when a RelaxError is raised.  This gives greater control of a powerful feature added to relax by {{gna link|gna.org/users/macraild|text=Chris MacRaild}}.  The pickled state can then be attached to bug reports or can be used to quickly load the state prior to failure when in the scripting UI mode.
+
*  Created the '--error-state' command line option for saving a pickled state when a RelaxError is raised.  This gives greater control of a powerful feature added to relax by {{relax developer link|username=macraild|text=Chris MacRaild}}.  The pickled state can then be attached to bug reports or can be used to quickly load the state prior to failure when in the scripting UI mode.
 
*  Reordered the debugging command line options and removed the '-r' shortcut.
 
*  Reordered the debugging command line options and removed the '-r' shortcut.
 
*  The lib.errors module is now really independent of relax - the compat module is no longer used.  Instead, the Python 2 and 3 versions of the pickle module are imported using try statements.
 
*  The lib.errors module is now really independent of relax - the compat module is no longer used.  Instead, the Python 2 and 3 versions of the pickle module are imported using try statements.
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*  Fix for [https://gna.org/bugs/?22039 bug #22039, the printing out of Dpar twice by the diffusion_tensor.display user function].  The solution is given in the original bug report.
 
*  Fix for [https://gna.org/bugs/?22039 bug #22039, the printing out of Dpar twice by the diffusion_tensor.display user function].  The solution is given in the original bug report.
 
*  Fix for [https://gna.org/bugs/?22041 bug #22041, the PDB atom serial number error from the structure.write_pdb user function].  The problem is that the [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] preserves the atom numbering from the original structure and uses that for the atom serial number.  However the atom serial number must be replaced with sequential values to produce a valid PDB file.  This is fatal for any CONECT records.
 
*  Fix for [https://gna.org/bugs/?22041 bug #22041, the PDB atom serial number error from the structure.write_pdb user function].  The problem is that the [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] preserves the atom numbering from the original structure and uses that for the atom serial number.  However the atom serial number must be replaced with sequential values to produce a valid PDB file.  This is fatal for any CONECT records.
*  Fix for the chain-reaction failures in the test suite.  This fixes [https://gna.org/bugs/?22055 bug #22055, the processor.run_queue() not cleaning up in uni_processor - chain-reaction failures in the test suite].  The fix was insanely simple, just implementing what was mentioned {{gna link|url=gna.org/users/varioustoxins|text=Gary Thompson's}} FIXME comment in the run_queue() method of the uni-processor object.  The queue execution code has been placed inside a 'try' statement and the queue cleaning up code in a 'finally' statement.  This closes a painfully difficult to find bug that has been in relax since 2006, though only affecting relax developers.
+
*  Fix for the chain-reaction failures in the test suite.  This fixes [https://gna.org/bugs/?22055 bug #22055, the processor.run_queue() not cleaning up in uni_processor - chain-reaction failures in the test suite].  The fix was insanely simple, just implementing what was mentioned {{relax developer link|username=varioustoxins|text=Gary Thompson's}} FIXME comment in the run_queue() method of the uni-processor object.  The queue execution code has been placed inside a 'try' statement and the queue cleaning up code in a 'finally' statement.  This closes a painfully difficult to find bug that has been in relax since 2006, though only affecting relax developers.
 
<section end=bugfixes/>
 
<section end=bugfixes/>
  

Revision as of 21:37, 15 October 2020


Official relax releases
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relax version 3.2.0
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← relax 3.1.7 relax 3.2.1 →

Keywords Manual, relaxation dispersion
Release type Major feature
Release date 20 May 2014

The PDF version of the relax 3.2.0 user manual The relax 3.2.0 user manual

Description

This is a major feature release. It includes the addition of the new B14 and B14 full relaxation dispersion models [Baldwin 2014], a complete rearrangement of the module layout of the specific analyses packages, a number of new user functions, documentation improvements including the addition of a new chapter to the manual for the N-state model or ensemble analysis, and numerous of other features. This is also a major bugfix release, so all users are recommended to upgrade. This is essential if you are using the new relaxation dispersion analysis in relax as a severe bug in the error calculation has been corrected. See below for a comprehensive list of new features, the rather large number of changes, and the long list of all bugs fixed.


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 3.2.0
(20 May 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.2.0


Features

  • Addition of the vector_angle() relax library function for calculating the signed or directional angle between two vectors.
  • Huge speed up of the interatom.define user function.
  • For improved feedback, a busy cursor is shown in the GUI when executing user functions.
  • The steady-state NOE auto-analysis now produces a 2D Grace plot of the reference and saturated spectra peak intensity values.
  • Complete redesign of the specific analyses backend, simplifying and cleaning up this internal API and making it easier for users to add completely new analysis types to relax.
  • Parametric reduction of the rotor frame order model, eliminating one redundant parameter hence simplifying optimisation.
  • Large improvement for the lib.software.grace module. The '*_err' and '*_bc' parameter names for the parameter error and back-calculated parameters respectively are now supported, allowing these values to be easily plotted.
  • Expansion of the value.set user function to handle parameters which consist of lists of values. The index argument has been added to allow the index of the list to be specified, and this is then propagated into the specific analysis API.
  • Improvements for the parameter definitions in all analysis types. This allows for better output in 2D plots and text files.
  • Implemented linear constraints for the frame order analysis. This uses the log-barrier constraint algorithm in the minfx library to provide constraints without requiring gradients.
  • Improved and expanded the relax command line options for debugging.
  • Full independence of the relax library so that it can be used outside of relax.
  • The addition of a relaxation dispersion user function for setting the R20 values to the minimum R2eff value.
  • Expanded capabilities for the relax_disp.sherekhan_input user function.
  • Implementation of the B14 and B14 full relaxation dispersion CPMG models for 2-site exchange for all time scales (from the new paper [Baldwin 2014] at http://dx.doi.org/10.1016/j.jmr.2014.02.023).
  • Large improvements to the relax HTML manual including fixes for URLs, bibliography entries, links, and tables.
  • Support for multiple point creation for the OpenDX chi-squared space mapping user function.
  • Automatic determination of reasonable initial contour levels for the OpenDX mapping user function.
  • Addition of a new chapter to the manual for the N-state model or ensemble analysis.
  • Creation of the new pymol.frame_order user function for visualising results.
  • Expansion of the Grace 2D data plotting capabilities.


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.


References

  • [*Baldwin 2014] Baldwin A. J. (2014). An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange. J. Magn. Reson., 244, 114-124. (DOI: 10.1016/j.jmr.2014.02.023)
  • [*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)

<HarvardReferences />

See also