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.
The full list of changes is:
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
6^6 rather than 11^6 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 tm grid search which was between 6-12 ns to be
between 1-12ns.
* 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 'Diso', 'Dper', 'Dpar', 'Dratio',
'Dx', 'Dy', and 'Dz' 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)
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