Edward d'Auvergne | 15 Dec 14:34 2015

relax version 4.0.1.

This is a major feature and bugfix release.  Features include the new
structure.pca user function for performing a principle component
analysis (PCA) of a set of structures, handling of replicated R2eff
data points in the dispersion analysis, improvements in the handling
of PDB structures, the protection against numpy ≥ 1.9 FutureWarnings
for a number of soon to change behaviours in numpy, and addition of a
deployment script for the Google Cloud Computing.  Bugfixes include an
error when loading relaxation data, the CSA constant equation in the
manual, missing information in the relax state and results files,
loading of certain state files in the GUI, running relax with no
graphical display and using matplotlib, BMRB export failure when a
spin container is missing data or parameters.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_4.0.1 .

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 compilation of the HTML version of
the relax manual (http://www.nmr-relax.com/manual/index.html).
        * Updated relax to eliminate all FutureWarnings from numpy ≥
1.9, to future-proof relax against upcoming numpy behaviour changes.
(Continue reading)

Edward d'Auvergne | 14 Oct 15:00 2015

relax version 4.0.0.

This is a major feature release for a new analysis type labelled
'frame order'.   The frame order theory aims to unify all rotational
molecular physics data sources via a single mechanical model. It is a
bridging physics theory for rigid body motions based on the
statistical mechanical ordering of reference frames.  The previous
analysis of the same name was an early iteration of this theory that
was however rudamentary and non-functional.  Its current
implementation is for analysing RDC and PCS data from an internal
alignment to interpret domain or other rigid body motions within a
molecule or molecular complex.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_4.0.0 .

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:
        * The final, complete, and correct implementation of the frame
order theory for studying rigid body motions.  This is currently for
analysing RDC and PCS data from internally aligned systems.


    Changes:
(Continue reading)

Edward d'Auvergne | 1 Oct 14:43 2015

relax version 3.3.9.

This is a minor feature release with improvements to the automatic
relaxation dispersion protocol for repeated CPMG data, support for
Monte Carlo or Bootstrap simulating RDC and PCS Q factors, a huge
speedup of Monte Carlo simulations in the N-state model analysis, and
geometric mean and standard deviation functions added to the relax
library.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.9.

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:
        * Improvements to the automatic relaxation dispersion protocol
for repeated CPMG data.
        * Support for Monte Carlo or Bootstrap simulating the RDC and
PCS Q factors.
        * Huge speedup of Monte Carlo simulations in the N-state model analysis.
        * Geometric mean and standard deviation functions added to the
relax library.

    Changes:
        * Wrote a method to store parameter data and dispersion
(Continue reading)

Edward d'Auvergne | 2 Apr 14:05 2015

relax version 3.3.8.

This is a minor bugfix release which allows the relax GUI to be used
on screens with the low resolution of 1024x768 pixels.

For the official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.8.

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:
        * Fix for the pipe_control.reset.reset() function when
resetting the GUI in non-standard contexts.  This is mainly for
debugging scripts when simulating a GUI and hence the GUI reset()
method does not exist.
        * Created a GUI memory management debugging script for the
align_tensor.init user function.  This repetitively calls the reset,
pipe.create and align_tensor.init user functions, and opening the GUI
element for setting alignment tensor elements (the Sequence window).
The pympler muppy_log file shows no memory leaks for these user
functions on Linux systems.

(Continue reading)

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)


Gmane