relax 1.2.4

Description

This is a long overdue release which includes many new features, changes, and bugfixes. Molmol macros which plot parameter values onto the structure using arbitrary colour gradients through the X11 colours, Molmol colours, or RGB vectors can now be created by the program. A test suite has been added to aid in debugging and checking that new code does not break the functionality of the program. The relax manual has been significantly updated. Hyperlinks are now present. The chapter Open source infrastructure has been added and the development chapter has been rewritten. Hybrid runs are now supported. Half the protein can be analysed in one run, the other half in another, and then the two combined into one hybrid run.

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 1.2.4
(2 May 2006, from /1.2)
http://svn.gna.org/svn/relax/tags/1.2.4

Features

• Added elimination of Monte Carlo simulations to the sample scripts.
• Creation of the relax test suite 'relax --test-suite'.
• Creation of the committers file.
• The hyperref LaTeX package is now used in the relax manual.
• Addition of a chapter called Open source infrastructure.
• Rewrite of the Development of relax chapter.
• Addition of the user function run.hybridise. (task #3122)
• The user function relax_data.read no longer deselects residues when no data is encountered. (bug #5501)
• Residues are deselected by the user functions grid_search, calc, and minimise if k > n or if there is less than 3 data sets. (bug #5501)
• Mapping parameter values onto the structure through Molmol macros. (task #3146)
• Added support for arbitrary colour gradients in the Molmol macros. (task #3146)
• Addition of a file for colour operations. All X11 colours and all Molmol colours can be selected by name. (task #3146)

Changes

• The 'full_analysis.py' sample script now only searches over 6⁶ rather than 11⁶ grid points for the ellipsoid diffusion tensor to speed up the analysis.
• Updated the manual to replace the references to 'make' with 'sconstruct'.
• Extension of the installation chapter.
• Changed the square and round brackets to curly brackets and replaced ':' with '=' in the user function docstrings.
• All the model-free Molmol functions have been moved into their own class Molmol.
• The null device can now be opened instead of a file for writing by passing 'devnull' as the name.
• Updated the release checklist so that the directory 'relax-x.x.x' is included in the distributions rather than just 'relax'.
• Removed the bugs file 'docs/BUGS'.

Bugfixes

• Small bugs in the sconstruct script have been removed.
• The value reading function can now handle rows which contain no data.
• The ellipsoid diffusion tensor was being incorrectly initialised in the 'full_analysis.py' script.
• Another Numeric version issue. The model m0 with no parameters which used to be handled okay by the grid search and minimisation code was failing due to changes in Numeric.
• In certain situations, the angle folding function which is called after model-free minimisation used the wrong run name.
• Fixed the -fPIC option segfault problem on some Linux systems. (bug #5473)
• Changed the τ_m grid search which was between 6-12 ns to be between 1-12 ns.
• Fixed some grammar in the intro chapter of the manual.
• Fixed a bug in the model-free sample script in the spheroid diffusion tensor function.
• Removed the spaces in front of the \index{} commands from the manual LaTeX source files.
• The diffusion parameters D_iso, D_⊥, D_∥, D_ratio, D_x, D_y, and D_z are generated on the fly. (bug #5559)
• Fixed the spacing after 'Gna!' in the manual.
• The grace.write user function now plots the associated errors. (bug #5659)
• Fix to the parameter errors not being scaled in the value.read user function. (bug #5670)
• Parameter errors were not always included in the results file. (bug #5660)
• Removed the memory leak in the relaxation curve-fitting C modules. (bug #5602)
• The user function value.set no longer raises RelaxError in spectral density mapping runs. (bug #5698)
• Fix to the broken Molmol pipe. (bug #5752)
• Fix of the failure of molmol.view when the PDB is missing. (bug #5753)
• Fix to the failure of relax_data.read when relaxation data is missing. (bug #5805)

Links

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

• Official release notes
• Gna! news item
• Gmane
• Mail archive
• Local archives
• MARC

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

• The combined release notes for all relax versions (warning, this is very large).
• The combined release descriptions for all relax versions.
• The combined release metadata for all relax versions.
• The combined release features for all relax versions.
• The combined release changes for all relax versions (warning, this is very large).
• The combined release bugfixes for all relax versions.
• The combined release announcement links for all relax versions.