Edward d'Auvergne | 13 Mar 17:55 2015

relax version 3.3.7.

This is a major feature and bugfix release. New features include the
statistics.aic and statistics.model user functions, plotting API
advancements, huge speed ups for the assembly of atomic coordinates
from a large number of structures, the sorting of sequence data in the
internal structural object for better structural consistency,
conversion of the structure.mean user function to the new
pipe/model/molecule/atom_id design, and improvements to the rdc.copy
and pcs.copy user functions. Bugs fixed include the incorrect
pre-scanning of old scripts identifying the minimise.calculate user
function as the old minimise user function, Python 3 fixes, and the
failure in reading CSV files in the sequence.read user function. Many
more features and bugfixes are listed below.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.7.

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).

The full list of changes is:

    Features:
        * Creation of the statistics.aic and statistics.model user
functions for calculating and printing out different statistics.
        * Addition of new infrastructure for future support for
plotting data using Veusz (http://home.gna.org/veusz/).
(Continue reading)

Edward d'Auvergne | 5 Feb 09:42 2015

relax version 3.3.6.

This is a minor feature and bugfix release. It includes the addition
of the new structure.sequence_alignment user function which can use
the 'Central Star' multiple sequence alignment algorithm or align
based on residue numbers, saving the results in the relax data store.
The assembly of structural coordinates used by the structure.align,
structure.atomic_fluctuations, structure.com, structure.displacement,
structure.find_pivot, structure.mean, structure.rmsd,
structure.superimpose and structure.web_of_motion user functions has
been redesigned around this new user function. It will use any
pre-existing sequence alignments for the molecules of interest, use no
sequence alignment if only structural models are selected, and default
to a residue number based alignment if the
structure.sequence_alignment user function has not been used. Bug
fixes include a system test failure on Mac OS X, and I∞ parameter text
files and Grace graphs are now produced by the relaxation
curve-fitting auto-analysis for the inversion recovery and saturation
recovery experiment types. Many more details are given below.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.6.

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).

The full list of changes is:

(Continue reading)

Edward d'Auvergne | 28 Jan 09:58 2015

relax version 3.3.5.

This is a major feature and bugfix release. It fixes an important bug
in the Monte Carlo simulation error analysis in the relaxation
dispersion analysis. Features include improvements to the NMR spectral
noise error analysis, expansion of the grace.write user function to
handle both first and last point normalisation for reasonable R1
curves in saturation recovery experiments, the implementation of
Needleman-Wunsch pairwise sequence alignment algorithm using the
BLOSUM62, PAM250 and NUC 4.4 substitution matrices for more advanced
3D structural alignments via the structure.align and
structure.superimpose user functions as well as any of the other
structure user functions dealing with multiple molecules, conversion
of the structure.displacement, structure.find_pivot, structure.rmsd,
structure.superimpose and structure.web_of_motion user functions to a
new pipes/models/molecules/atom_id design to allow the user functions
to operate on different data pipes, different structural models and
different molecules, addition of the displace_id argument to the
structure.align and structure.superimpose user functions to allow
finer control over which atoms are translated and rotated by the
algorithm, large improvement for the PDB molecule identification code
affecting the structure.read_pdb user function, creation of the
lib.plotting package for assembling all of the data plotting
capabilities of relax, implementation of the new
structure.atomic_fluctuations user function for creating text output
or Gnuplot graphs of the correlation matrix of interatomic distance,
angle or parallax shift fluctuations, the implementation of ordinary
least squares fitting, and improvements for the pcs.corr_plot and
rdc.corr_plot user functions. Many more features and bugfixes are
listed below.

For the official, easy to navigate release notes, please see
(Continue reading)

Edward d'Auvergne | 4 Dec 10:35 2014

relax version 3.3.4.

This is a major feature and bugfix release, finally adding support for
the saturation recovery and inversion recovery R1 experiments and
including a major bug fix for storing multi-dimensional numpy data
structures as IEEE 754 byte arrays in the XML output of the relax
state and results files.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.4.

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).

The full list of changes is:
    Features:
        * Numerous improvements for the relax_fit.select_model user function.
        * Support for the saturation recovery experiment in the
relaxation exponential curve-fitting analysis.
        * Support for the inversion recovery experiment in the
relaxation exponential curve-fitting analysis.
        * Added a section to the start of the relaxation curve-fitting
chapter of the manual to include descriptions of all supported models.
        * Addition of a button to the R1 and R2 GUI analyses for
selecting the desired exponential curve model via the
relax_fit.select_model user function.

    Changes:
(Continue reading)

Edward d'Auvergne | 24 Nov 15:49 2014

relax version 3.3.3.

This is a major feature and bugfix release.  It fixes a failure when
loading relaxation data and adds Python 3 support for using the
NMRPipe showApod software.  Features include a large expansion for the
align_tensor.matrix_angles and align_tensor.svd user functions to
support the standard inter-matrix angles, the unitary 9D vector
notation {Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz}, and the
irreducible spherical tensor 5D basis set of {A-2, A-1, A0, A1, A2}
for correctly calculating the inter-tensor angles, singular values and
condition numbers.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.3.

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).

The full list of changes is:

    Features:
        * Implemented the lib.geometry.vectors.vector_angle_atan2()
relax library function.  This is for calculating the inter-vector
angle using the more numerically stable atan2() formula.
        * Implemented the lib.geometry.vectors.vector_angle_acos()
relax library function.  This is used to calculate the inter-vector
angle using the arccos of the dot product formula.  The function has
been introduced into the relax library as the calculation is repeated
(Continue reading)

Edward d'Auvergne | 14 Nov 16:34 2014

relax version 3.3.2

This is a minor feature and bugfix release.  It includes improvements
to the readability of the HTML version of the manual
(http://www.nmr-relax.com/manual/index.html), improved printouts
throughout the program, numerous GUI enhancements, and far greater
Python 3 support.  Please see below for a full listing of all the new
features and bugfixes.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.2.

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).

The full list of changes is:

    Features:
        * Many improvements for the HTML version of the manual at
http://www.nmr-relax.com/manual/index.html.
        * Improved sectioning printouts in the model-free
dauvergne_protocol auto-analysis.
        * Significant improvements for the relax controller window.
        * All wizards and user functions in the relax GUI now have
focus so that keyboard is active without requiring a mouse click.
        * The ESC key will now close the relax controller window and
all user function windows.
        * The structure.load_spins user function can now load spins
(Continue reading)

Edward d'Auvergne | 9 Oct 16:56 2014

relax version 3.3.1.

This is a minor feature and bugfix release.  It includes the addition
of the error_analysis.covariance_matrix, structure.align, and
structure.mean user functions and expanded functionality for the
structure.com and structure.delete user functions.  Many operations
involving the internal structural object are now orders of magnitude
faster, with the interatom.define user function showing the greatest
speed ups.  There are also improvements for helping to upgrade relax
scripts to newer relax versions.  The numdifftools package is now
bundled with relax for allowing numerical gradient, Hessian and
Jacobian matrices to be calculated.  And the release includes the
start of a new protocol for iteratively analysing repetitive
relaxation dispersion experiments.

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).

The full list of changes is:

    Features:
        * Initial auto-analysis support for a highly repetitive
protocol for analysing relaxation dispersion data.
        * Addition of the docs/user_function_changes.txt file which
documents all user function changes from relax 1.0.1 to 3.3.1 to help
with upgrading scripts to newer relax versions.
        * Updated the translation table used to identify no longer
existing user functions and explain what the new user function is
(Continue reading)

Edward d'Auvergne | 5 Sep 12:17 2014

relax version 3.3.0.

This is a major feature release which includes a huge number of
changes, as can be seen below.  The most important change is an
incredible speed up of all relaxation dispersion models.  See the
table below for a comparison to the previous relax 3.2.3 release.  The
maximum possible advantage of linear algebra operations are used to
eliminate all of the slow Python looping and to obtain the ultimate
algorithms for speed.  As this is using NumPy, conversion to C or
FORTRAN will not result in any significant speed advantage.  With
these huge speed ups, relax should now be one of the fastest software
packages for analysing relaxation dispersion phenomena.

Other important features include the implementation of a zooming grid
search (http://www.nmr-relax.com/manual/minimise_grid_zoom.html)
algorithm for use in all analysis types, expanded plotting
capabilities for R1rho values in the relaxation dispersion analysis
(http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html),
the ability to optimise the R1 parameter in all off-resonance
dispersion models
(http://www.nmr-relax.com/manual/relax_disp_r1_fit.html), proper
minimisation statistics resetting by the minimisation user functions,
and a large expansion of the periodic table information for all
elements in the relax library for correctly estimating molecular
masses.  Additional features are that there is better tab completion
support in the prompt UI for Mac OS X, the addition of the time user
function for printing the current date and time
(http://www.nmr-relax.com/manual/time.html), the value.copy user
function accepting a force argument for overwriting values
(http://www.nmr-relax.com/manual/value_copy.html), model nesting in
the dispersion auto-analysis has been extended, the spin-lock offset
is now shown in the dispersion analysis in the GUI, the
(Continue reading)

Edward d'Auvergne | 3 Jul 14:06 2014

relax version 3.2.3.

This is a major bugfix release and the first requiring numpy >= 1.6 to
allow for faster calculations for certain analyses.  There have been
improvements to the GUI user functions, the ^[[?1034h escape code is
finally suppressed on Linux systems, and the structure.com user
function has been added.  Bugfixes include the proper handling of R20A
and R20B parameters in the relaxation dispersion models, the 'IT99'
dispersion model tex parameter was incorrectly handled, the 'LM63
3-site' dispersion models had a fatal mistake in its equations, files
with multiple extensions (for example *.pdb.gz) are now correctly
handled, and closing the free file format window in Mac OS X systems
caused the GUI to freeze.  Full details can be found below.

For this release, the Mac OS X framework used to build the universal
3-way (ppc, i386, x86_64) binaries for the stand-alone relax
application has been updated.  The relax application now bundles
Python 2.7.8, numpy 1.8.1, scipy 0.14.0, nose 1.3.3, wxPython 2.9.3.1
osx-cocoa (classic), matplotlib 1.3.1, epydoc 3.0.1, mpi4py 1.3.1 and
py2app 0.8.1.  This should result in better formatted relax state and
results files and give access to more advanced packages for power
users to take advantage of.

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).

The full list of changes is:

(Continue reading)

Edward d'Auvergne | 5 Jun 16:09 2014

relax version 3.2.2.

This is a major feature and bugfix release.  It includes a large speed
up of all analytic relaxation dispersion models, the correct handling
of edge case failures in all models of the dispersion analysis, a
number of fixes for the handling of list-type data in the GUI user
function windows including the fatal GUI crashes on Mac OS X systems,
and many other bug fixes.  Please see below for a full list of
features, changes and bugfixes.  All users of the dispersion analysis,
the relax GUI, or Mac OS X systems are recommended to upgrade to this
newest version.

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).

The full list of changes is:

    Features:
        * Large speedups of all analytical relaxation dispersion
models by converting the R2eff calculations and value error checking
from single values to numpy arrays.
        * Edge cases where function failures occur are now properly
handled for all analytical relaxation dispersion models.
        * Completion of the frame_order.pdb_model user function
backend for the frame order PDB representation.
        * relax will now detect when files with *.gz or *.bz2 file
extensions are being created and automatically gzip or bzip compress
the file.
(Continue reading)

Edward d'Auvergne | 23 May 15:58 2014

relax version 3.2.1

This is a major bugfix release which includes the equations for the
"B14" and "B14 full" relaxation dispersion models, from Baldwin 2014
and introduced with relax version 3.2.0, now being calculated
correctly, the 'NS CPMG 2-site expanded' model correctly handling edge
cases where no exchange is expected, and the structure.delete user
function correctly operating when multiple models are loaded into the
data store.

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).

The full list of changes is:

    Features:
        * N/A

    Changes:
        * Punctuation fixes throughout the CHANGES document.
        * Modified system test
Relax_disp.test_cpmg_synthetic_ns3d_to_cr72 to catch bug #22017:
(https://gna.org/bugs/index.php?22017) LinAlgError, for all numerical
CPMG models.  System test was renamed from test_cpmg_synthetic_cr72 to
test_cpmg_synthetic_ns3d_to_cr72, to reflect which model create the
data and which model fits the data.
        * Modified cpmg_synthetic script to first create all time
structures before doing back-calculation.  Bug #22017:
(Continue reading)


Gmane