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<onlyinclude>This is a major feature and bugfix release which adds support for [http://www.nmr-relax.com/manual/structure_read_gaussian.html 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]] [[:Category:relaxation dispersion|relaxation dispersion]] models, R<sub>1ρ</sub> 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 [http://www.nmr-relax.com/manual/spectrum_read_intensities.html 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.</onlyinclude>== Description ==
→Bugfixes: Switch to the {{relax developer list}} template to avoid dead Gna! links.
{{lowercase title}}
{{infobox relax release| version = Description 3.1.1| prev =3.1.0| next = 3.1.2| keywords = Gaussian structures, relax library, relaxation dispersion | type = Major feature and bugfix| date = 10 December 2013| manual = yes}}
<section begin= Download description/>This is a major feature and bugfix release which adds support for [http://www.nmr-relax.com/manual/structure_read_gaussian.html 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]] [[:Category:relaxation dispersion analysis|relaxation dispersion]] models, R<sub>1ρ</sub> 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 [http://www.nmr-relax.com/manual/spectrum_read_intensities.html 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.<section end=description/>
== Download ==
<section begin=download/>
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).
<section end=download/>
== CHANGES file ==
<section begin= CHANGES file =metadata/>Version 3.1.1<br/>(10 December 2013, from /trunk)<br/>
http://svn.gna.org/svn/relax/tags/3.1.1
<section end=metadata/>
=== Features ===
<section begin=features/>
* Support for reading 3D structures of organic molecules from Gaussian log files using the new [http://www.nmr-relax.com/manual/structure_read_gaussian.html structure.read_gaussian user function].
* Addition of the lib.periodic_table module for storing information about the periodic table.
* Support for the loading of spins directly from peak lists.
* Support for the [http://www.nmr-relax.com/manual/spectrum_read_intensities.html reading of peak intensities from NMRPipe seriesTab formatted files] (*.ser).
<section end=features/>
=== Changes ===
<section begin== Changes ==changes/>
* Small improvement for the devel_scripts/log_converter.py script for detecting commit boundaries.
* Added many small details to the release checklist document. This is for the formatting and editing of the CHANGES file, which is used for the release announcements. Some additional details about the API documentation at http://www.nmr-relax.com/api have been added too.
* The relax_disp.spin_lock_offset user function now uses the lib.nmr module. This is for converting between ppm and rad/s units.
* The relax_disp.r2eff_read_spin user function now can handle offset data in the file. If the new offset_col argument is set and disp_point_col is not, then the file being read can contain the spin-lock offset information rather than the spin-lock field strength values. This is only for R<sub>1ρ</sub>-type data.
* Implemented GUI test which caches the [https://gna.org/bugs/?21076 bug #21076] - when loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur].
* Large redesign of the R<sub>2eff</sub>/R<sub>1ρ</sub> data structures. The five indices {Ei, Si, Mi, Oi, Di} for the experiment type, the spins of the cluster, the magnetic field strengths, the pulse offsets, and the dispersion points (nu_CPMG or nu1) respectively are now much better defined. The Oi dimension is new and allows for support of R<sub>1ρ</sub>-type data whereby both different offsets and different spin-lock field strengths have been collected. Previously only one or the other was supported, but not both together. The offset information is now included as part of the spin R<sub>2eff</sub>/R<sub>1ρ</sub> key, even if not set. To support this, the specific_analyses.relax_disp.disp_data module now has the new functions loop_exp_frq_offset(), loop_exp_frq_offset_point(), loop_exp_frq_offset_point_time(), loop_frq_offset(), loop_frq_offset_point_key(), loop_offset(), and loop_offset_point(). All of the {Ei, Si, Mi, Oi, Di} dispersion indices throughout the source tree have been changed to ei, si, mi,oi, and di respectively. And the time index ti has also been introduced. These changes hugely simplify the code.
* The relax_disp.plot_disp_curves user function can now support 150 sets per Grace graph.
* Extended reading of Sparky files to include residue names. Work in progress for [https://gna.org/support/?3044 Support Request #3044 - load spins from Sparky list].
* Expanded system test and made it pass for user function spectrum.read_spins. Work in progress for [https://gna.org/support/?3044 Support Request #3044 - load spins from Sparky list].
* Updated the GUI test to check for first ID in list. Fix for [https://gna.org/bugs/?21076 bug #21076] - When loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur].
* Added keyword dim to frontend function for spectrum.read_spins(). Work in progress for [https://gna.org/support/?3044 Support Request #3044 - load spins from Sparky list]. This is associate data with the spins of up to two dimensions.
* Implemented system test for reading spins from NMRPipe SeriesTab formatted file. Work in progress for [https://gna.org/support/?3044 Support Request #3044 - load spins from Sparky list].
* Removed a printout from the Relax_disp.test_r1rho_kjaergaard GUI test as this is fatal for Python 3.
* Python 3 fixes for the relax_disp.r2eff_read_spin user function. The check for the dispersion point column now only runs if that argument is set. In addition, the offset column is now also being checked.
<section end=changes/>
=== Bugfixes ===
<section begin== Bugfixes ==bugfixes/>
* Fix for the sample_scripts/relax_disp/R1rho_analysis.py sample script. This was identified by Justin Lecher <jlec att gentoo doot org> in the post http://article.gmane.org/gmane.science.nmr.relax.devel/4748 (Message-ID:<52984043.3030808@gentoo.org>), or the threaded view http://thread.gmane.org/gmane.science.nmr.relax.announce/46/focus=4748. The problem was some extra commas which should not have been there.
* Bug fixes for the non-functional R1rho_analysis.py relaxation dispersion sample script. This script was horribly broken, but it should now work. It can even be executed from the base relax directory or from within the sample_scripts/relax_disp/ directory and perform the full analysis (assuming write access to the relax source directory).
* Fix for a number of PNG files for NESSY and Bruker icons for broken IDAT entries. This problem was identified by Justin Lecher <jlec att gentoo doot org> in the post http://article.gmane.org/gmane.science.nmr.relax.devel/4750 (Message-ID:<5298572C.5010409@gentoo.org>), or in the threaded view http://thread.gmane.org/gmane.science.nmr.relax.announce/46/focus=4750. As a result those icons are missing in the GUI. This was fixed using the pngcrush tool.
* Fix for a typo in a model name in the cpmg_analysis.py relaxation dispersion sample script.
* Fix for [https://gna.org/bugs/?21309 bug #21309], the [[R2eff]] dispersion model failure when peak intensity data is missing]. The problem was that the check for missing data in the _calculate_r2eff() private API method was accidentally deleted in the relax_disp branch. See the commit at http://article.gmane.org/gmane.science.nmr.relax.scm/19261 and the accidental deletion at http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?view=diff&r1=21504&r2=21505&pathrev=21505.* Another fix for [https://gna.org/bugs/?21309 bug #21309], the [[R2eff]] dispersion model failure when peak intensity data is missing]. This second problem is only for the numeric CPMG models for when all data at one magnetic field strength is missing. When the relaxation dispersion target function is being set up, the creation of the self.power data structure holding the number of CPMG blocks fails. The problem is that the relaxation time for the missing field strength is set to NaN. This is now caught using lib.float.isNaN().* Loosened a check in the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. This is to allow this test to pass on certain Mac OS X machines. It was reported by {{relax developer link|username=tlinnet|text=Troels }} in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/4773/focus=4774.
* Basic fix for the Relax_disp.test_r2eff_read_spin system test - the CPMG frequencies are now set. This was identified in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/4773/focus=4774.
* Fixes for the parameters in the Relax_disp.test_ns_mmq_3site system test script.
* Fix for optimisation of Dr. Flemming Hansen's CPMG data to the [[NS CPMG 2-site star]] dispersion model. Changed so assertAlmostEqual matches 2 digits. Fix for [https://gna.org/bugs/?21322 bug #21322 - 5x Test suite fail for version 3.1.0, reported for system CentOS 2.6.32-358.18.1.el6.x86_64].
* Bug fixes for the dispersion analysis when certain data sets are completely missing.
* Fix for loading a seriesTab formatted intensity, and getting the ID for the following GUI elements. Fix for [https://gna.org/bugs/?21076 bug #21076] - when loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur].
* Fix for the [http://www.nmr-relax.com/manual/relax_disp_r2eff_read_spin.html relax_disp.r2eff_read_spin user function]. The offsets are now converted to ppm prior to finding the R<sub>2eff</sub>/R<sub>1ρ</sub> key.
<section end=bugfixes/>
== Links ==
<section begin= Links =links/>
For reference, the following links are also part of the announcement for this release:
* [http://wiki.nmr-relax.com/Relax_3.1.1 Official release notes]
* [https://{{gna link|url=gna.org/forum/forum.php?forum_id=2421 2423|text=Gna! news item]}}
* [http://article.gmane.org/gmane.science.nmr.relax.announce/47 Gmane]
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00041.html Mail Archive]
* [https://mail.gna.org/public/relax-announce/2013-12/msg00000.html Local archives]
* [http://marc.info/?l=relax-announce&m=138672072911100&w=2 MARC]
<section end=links/>
== Announcements ==
{{:relax release announcements}}
== See also ==
* [http://www.nmr-relax.com/api/3.1/ The relax 3.1 API documentation]{{:relax release see also}}[[Category:MMQ CPMG data]][[Category:NMRPipe]][[Category:Release_NotesRelaxation dispersion analysis]]