Difference between revisions of "Relax 3.2.0"

From relax wiki
Jump to navigation Jump to search
(Tracker link improvements.)
(More user function HTML manual links.)
Line 69: Line 69:
 
*  Complete rearrangement of the specific analysis code for the steady-state NOE.  This brings the code into line with the recent specific analysis code rearrangements, specifically in the specific_analyses.relax_disp package.
 
*  Complete rearrangement of the specific analysis code for the steady-state NOE.  This brings the code into line with the recent specific analysis code rearrangements, specifically in the specific_analyses.relax_disp package.
 
*  Changed the Noe auto-analysis to properly handle the peak intensity Grace plots.  This relates to [https://gna.org/bugs/?21863 bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py].  Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat' parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter.  The reference and saturated intensities will appear as two graph sets within that plot.
 
*  Changed the Noe auto-analysis to properly handle the peak intensity Grace plots.  This relates to [https://gna.org/bugs/?21863 bug #21863, the grace.write user function not being able to write ref/sat plots as described in sample script noe.py].  Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the non-existent 'ref' and 'sat' parameters, instead the 'intensities.agr' file is being produced for the peak intensity parameter.  The reference and saturated intensities will appear as two graph sets within that plot.
*  Redesign and standardisation of the peak intensity data structure throughout all analyses in relax.  The various structures 'intensities', 'intensity_err', 'intensity_sim', 'sim_intensity', and 'intensity_bc' have all been renamed.  The new structures are called 'peak_intensity', 'peak_intensity_err', 'peak_intensity_sim' and 'peak_intensity_bc'.  This allows the structure to be processed as a standard parameter in the specific analysis API.  One very visible consequence is that plots of peak intensities, as well as value files, will now have peak intensity errors.  For backwards compatibility, the relax data store method _back_compat_hook() has been modified to catch all previous peak intensity object variants and to standardise and rename these to the new object names.  As the parameter is now called 'peak_intensity' rather than 'intensities', all calls to the grace.write and value.write for this parameter have been changed in the auto-analyses, the sample scripts, the test suite and the manual.
+
*  Redesign and standardisation of the peak intensity data structure throughout all analyses in relax.  The various structures 'intensities', 'intensity_err', 'intensity_sim', 'sim_intensity', and 'intensity_bc' have all been renamed.  The new structures are called 'peak_intensity', 'peak_intensity_err', 'peak_intensity_sim' and 'peak_intensity_bc'.  This allows the structure to be processed as a standard parameter in the specific analysis API.  One very visible consequence is that plots of peak intensities, as well as value files, will now have peak intensity errors.  For backwards compatibility, the relax data store method _back_compat_hook() has been modified to catch all previous peak intensity object variants and to standardise and rename these to the new object names.  As the parameter is now called 'peak_intensity' rather than 'intensities', all calls to the [http://www.nmr-relax.com/manual/grace_write.html grace.write] and [http://www.nmr-relax.com/manual/value_write.html value.write] for this parameter have been changed in the auto-analyses, the sample scripts, the test suite and the manual.
 
*  Fix for the Noe.test_noe_analysis system test.  The grace plots of the peak intensities now have error bars.
 
*  Fix for the Noe.test_noe_analysis system test.  The grace plots of the peak intensities now have error bars.
 
*  The legends in Grace plots are now turned on by default, if the legend flags are not specified.  The Noe.test_noe_analysis system test has been updated for the change.
 
*  The legends in Grace plots are now turned on by default, if the legend flags are not specified.  The Noe.test_noe_analysis system test has been updated for the change.

Revision as of 16:31, 9 September 2014


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


References

  • [*Baldwin 2014] A. Baldwin (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).

<HarvardReferences />


See also

relax release descriptions