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)

Edward d'Auvergne | 28 Nov 15:50 2013

relax version 3.1.0.

After four years of development by numerous NMR spectroscopists, the
relaxation dispersion analysis in relax is finally ready for release!
This support is complete and includes almost all analytic and numeric
dispersion models in existence.  These have been labelled as 'R2eff',
'No Rex', 'LM63', 'LM63 3-site', 'CR72', 'IT99', 'TSMFK01', 'NS CPMG
2-site expanded', 'NS CPMG 2-site 3D', 'NS CPMG 2-site star', 'M61',
'DPL94', 'TP02', 'TAP03', 'MP05', 'NS R1rho 2-site', 'MQ CR72', and
'MMQ 2-site', mainly named after the authors and publication date.  It
includes support for single, zero, double, and multiple quantum CPMG
data, including combined proton-heteronuclear data, and off-resonance
R1rho data.  An automated protocol has been developed to simplify the
analysis and a GUI has been designed around this auto-analysis.
Calculations have been parallelised at the spin cluster and Monte
Carlo simulation level for speed.

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 (note this list is huge as it covers 4
years of development by numerous authors):

    Features:
        * Full support for the analysis of relaxation dispersion data
in the prompt, scripting, and graphical user interfaces.
        * Support for single quantum (SQ), zero quantum (ZQ), double
quantum (DQ), and multiple quantum (MQ) CPMG-type data.
(Continue reading)

Edward d'Auvergne | 26 Nov 20:02 2013

relax version 3.0.2.

This version is a minor feature and bugfix release which includes
better pseudo-atom support, support of the value.write user function
to allow model information to be written to file, improvements to the
2D Grace plots, and fixes for missing log messages when running on a
cluster using OpenMPI.

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).

    Features:
        * Much better pseudo-atom support, including not requiring
tetrahedral geometry.
        * The value.write user function can now create files with
non-numeric data, such as the models for each spin.
        * Improvements to the 2D Grace plotting from the grace.write
user function including full support for multiple graphs and the
setting of the axes to the zero point.

    Changes:
        * Updated the Release Checklist document rsync instructions to
allow resumed uploads.  This is needed if the internet connection has
been cut, as uploading can take a long time.
        * The test_suite.clean_up.deletion() function can now handle
the case of missing files and directories.  This problem was occurring
in the relax_disp branch for some of the system tests.
        * Created the is_int() and is_num() functions for the
(Continue reading)

Edward d'Auvergne | 18 Oct 09:10 2013

relax version 3.0.1.

This version is a minor feature and bugfix release.  The handling of
peak lists has been enhanced and chemical shifts can now be read into
relax, there are a number of improvements throughout the GUI, and a
number of minor bugs have been solved.  If these changes affect you,
please upgrade to this latest 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).

    Features:
        * Improved handling of peak lists.
        * Simplification of the user function GUI elements for those
associated with the free file format.
        * Support for the reading of chemical shifts into the relax
data store with the new  chemical_shift.read user function.
        * Improvements to the appearance of the GUI by using more unicode.
        * Redesign of the model list GUI element used in the
model-free analysis.

    Changes:
        * The font size is no longer set for the latex2html compiled
user manual.
        * A number of updates and improvements to the document
explaining how to setup a Mac OS X framework.  This Framework Python
setup is used to build the binary distribution files.
        * Updated the Mac Framework testing script to handled 4-way
(Continue reading)

Edward d'Auvergne | 7 Aug 18:13 2013

relax version 3.0.0.

This is the first release of the new relax 3 series.  This release
marks a major shift of relax towards becoming a scientific computing
environment specialised for the study of molecular dynamics using
experimental biophysical data.  It is designed to be a replacement for
numerical computational environments such as GNU Octave, MATLAB,
Mathematica, Maple, etc.  From the perspective of a user, however, not
much has changed.  There are only a few modifications to the prompt,
script, or graphical user interfaces.  Most changes are for the power
user as they are rather in the backend.  The infrastructure changes
are comprehensive and include the reorganisation of most of the relax
code base, a large expansion of the relax library, and general
improvements and fixes to the user manual, the GUI, and the whole code
base.  The huge number of changes can be seen 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:
        * Huge amounts of code throughout the relax codebase has been
shifted into independent functions in the relax library.
        * Many new functions added to the relax library.
        * Complete rearrangement of the relax package and module layout.
        * Clean up and improvements to the relaxation curve-fitting C
module including the removal of a severe memory leak eating up all the
(Continue reading)


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