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)

Edward d'Auvergne | 17 Mar 16:47 2014

relax version 3.1.7.

This is a minor feature and bugfix release which includes improvements
to the relaxation dispersion chapter of the manual and the addition of
new infrastructure for R1rho data handling in the dispersion analysis.
 More details are given below.

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 amounts of new infrastructure for the R1rho relaxation
dispersion analysis type.
        * More hardware information printed out when using the
'--info' command line option.
        * The user function relax_disp.write_disp_curves now produces
text files of R2eff verses the rotating frame tilt angle theta.
        * Small improvements for the relaxation dispersion GUI
tutorial and citation chapter of the relax manual.

    Changes:
        * Added text file for the articles reference values from the
global fit in Relax_disp.test_r1rho_kjaergaard.  Regarding bug #21344,
(https://gna.org/bugs/?21344) - Handling of in sparse acquired R1rho
dataset with missing combinations of time and spin-lock field
strengths.  This is from optimisation of the Kjaergaard et al., 2013
Off-resonance R1rho relaxation dispersion experiments using the 'DPL'
(Continue reading)

Edward d'Auvergne | 28 Feb 18:30 2014

relax version 3.1.6.

This is a major feature and bugfix release.  A comprehensive tutorial
has been added to the relaxation dispersion chapter of the manual
which shows, step-by-step, the dispersion analysis in the GUI using
screenshots.  Other changes include improved PDB chain ID support, a
new mode for running a relax script and then entering the prompt UI
mode, multiple file reading by the spectrum.read_intensities user
function, and improvements to the relaxation dispersion analysis.  A
number of major bugs in the dispersion analysis concerning different
relaxation delay times for different experiments and for improved
handling of the offset have also been fixed.  A number of important
GUI bugs have also been fixed.  All users are recommended to upgrade
to this version of relax.

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:
        * Full support for PDB chain IDs in the internal structural object.
        * Improvements for the devel_scripts/python_seek.py for
finding all installed Python versions and modules.  Individual modules
can now be specified on the command line.
        * The pedantic command line option -p, --pedantic has been
renamed to -e, --escalate.
        * The new prompt command line option -p, --prompt causes the
(Continue reading)

Edward d'Auvergne | 4 Feb 18:33 2014

relax version 3.1.5.

This is a major bugfix release which fixes the complete failure of the
NOE analysis for most users,
a bug introduced in the last relax release
(https://gna.org/forum/forum.php?forum_id=2433).  All
users of relax 3.1.4 should upgrade to this 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:
        N/A

    Changes:
        * Updated the interatom.unit_vectors user function description
to add the text '3D structure'.  This is in response to the
http://thread.gmane.org/gmane.science.nmr.relax.user/1547 relax-users
mailing list message and the change is to clarify the usage of the
user function.
        * Created the Noe.test_bug_21591_noe_calculation_fail system
test.  This is to catch bug #21591 (https://gna.org/bugs/?21591)
submitted by Martin Ballaschk (https://gna.org/users/mab).  This is
the complete failure of the NOE analysis.  The peak lists attached to
the bug report have been included in the test suite to create the
system test.
(Continue reading)

Edward d'Auvergne | 31 Jan 15:07 2014

relax version 3.1.4.

This is a minor feature and bugfix release which has improvements for
the handling of structural data involving multiple molecules or models
and improved support in the NOE analysis for replicated spectra.
Included are fixes for the failure of the
structure.create_diff_tensor_pdb user function for non-spherical
diffusion tensors when no Monte Carlo simulations are present and for
the failure of the rdc.write user function for back calculated RDC
data.  Full details are given below.

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 structure.write_pdb user function now supports multiple
molecules being present.
        * Large speed optimisations for the internal structural object
when multiple models are present.
        * Improved support for replicated spectra in the NOE analysis.

    Changes:
        * Created the Frame_order.test_generate_rotor2_distribution
system test.  This is to test the Frame Order distribution generating
base script, used for creating the synthetic Frame Order test data,
and to demonstrate a failure in handling back-calculated RDC data.  To
(Continue reading)

Edward d'Auvergne | 16 Jan 17:01 2014

relax version 3.1.3.

This is a minor documentation release which includes small
improvements to the documentation of the relaxation dispersion
analysis in the manual as well as the API documentation for the
lib.dispersion package.  As the manual is available from
http://download.gna.org/relax/manual/relax.pdf, installing this newer
version of relax is not necessary.

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 parameters listed for the IT99 dispersion model
in the manual.
        * Improvements and addition of many links to the
lib.dispersion.cr72 API documentation.  This is for the API
documentation at
http://www.nmr-relax.com/api/3.1/lib.dispersion.cr72-module.html.
        * Spacing fix for the lib.dispersion.cr72 module docstring.
        * Improvements and addition of many links to the
lib.dispersion.dpl94 API documentation.  This is for the API
documentation at
(Continue reading)

Edward d'Auvergne | 13 Jan 17:31 2014

relax version 3.1.2.

This relax version is a minor bugfix release which repairs a number of
icons on newer operating systems and a solves a problem caused by
accidentally setting an incorrect spectrometer frequency.

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:
        * The average_intensity() dispersion function now accepts the
offset argument.  This is for better support of combined offset and
spin-lock varied R1rho-type data.  The argument is then passed into
the find_intensity_keys() function.
        * Improved the DPL94 dispersion model description in the manual.
        * Copied a Sparky peak list to be modified to be a Sparky file
without intensity column.
        * Modified the Sparky file to have no columns with intensity values.
        * Implemented to read spins from a SPARKY list, when no
intensity column is present.  Addition to Support Request #3044,
(https://gna.org/support/index.php?3044) - load spins from Sparky
list.
        * Created the Relax_disp.test_bug_21460_disp_cluster_fail
(Continue reading)

Edward d'Auvergne | 10 Dec 16:44 2013

relax version 3.1.1.

This is a major feature and bugfix release which adds support for
reading 3D structures of organic molecules from Gaussian log files,
the new lib.periodic_table and lib.nmr modules, the 'NS MMQ 3-site
linear', 'NS MMQ 3-site', 'NS R1rho 3-site linear', and 'NS R1rho
3-site' relaxation dispersion models, R1rho dispersion data sets where
multiple offsets and multiple spin-lock fields have been collected for
each spin, the loading of spins directly from peak lists, and the
reading of NMRPipe seriesTab files.  Due to the improvements and the
bugs fixed in the relaxation dispersion analysis, all users are
recommended to upgrade to this 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:
        * Support for reading 3D structures of organic molecules from
Gaussian log files using the new structure.read_gaussian user
function.
        * Addition of the lib.periodic_table module for storing
information about the periodic table.
        * Addition of the lib.nmr module for basic NMR related
functions.  It currently has functions for converting between ppm, Hz,
and rad.s^-1 units.
        * Many improvements to the relaxation dispersion chapter of
(Continue reading)


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