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For reference* [*d'Auvergne and Gooley, the following links are also part of the announcement for this release2008a] {{#lst:Citations|dAuvergneGooley08a}}* [http://wiki.nmr-relax.com/Relax_3.1.7 Official release notes*d'Auvergne and Gooley, 2008b]* [https{{#lst://gna.org/forum/forum.php?forum_id=2448 Gna! news item]Citations|dAuvergneGooley08b}}* [http://article.gmane.org/gmane.science.nmr.relax.announce/53 Gmane]* [http://www.mail-archive.com/relax-announce%40gna.org/msg00047.html Mail Archived'Auvergne and Gooley, 2008c]* [https{{#lst://mail.gna.org/public/relax-announce/2014-03/msg00001.html Local archives]Citations|dAuvergneGooley08c}}* [http:/<HarvardReferences/marc.info/?l=relax-announce&m=139509874209089&w=2 MARC]>
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{{infobox relax release| version = Description 3.1.7| prev =3.1.6| next = 3.2.0| keywords = Manual, relaxation dispersion| type = Minor feature and bugfix| date = 17 March 2014| manual = yes}}
== Description == <onlyincludesection begin=description/>
This is a minor feature and bugfix release which includes improvements to the [http://www.nmr-relax.com/manual/Relaxation_dispersion.html relaxation dispersion chapter of the manual] and the addition of new infrastructure for R<sub>1ρ</sub> data handling in the dispersion analysis. More details are given below.
<section end=description/onlyinclude>
== 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 3.1.7<br/>(17 March 2014, from /trunk)<br/>
http://svn.gna.org/svn/relax/tags/3.1.7
<section end=metadata/>
=== Features ===
<section begin=features/>
* Large amounts of new infrastructure for the R<sub>1ρ</sub> relaxation dispersion analysis type.
* More hardware information printed out when using the '--info' command line option.
* The [http://www.nmr-relax.com/manual/relax_disp_write_disp_curves.html user function relax_disp.write_disp_curves] now produces text files of R<sub>2eff</sub> verses the rotating frame tilt angle θ.
* Small improvements for the [http://www.nmr-relax.com/manual/relaxation_dispersion_auto_analysis_in_GUI.html relaxation dispersion GUI tutorial] and [http://www.nmr-relax.com/manual/Preface_citing_relax.html citation chapter] of the relax manual.
<section end=features/>
=== Changes ===
<section begin=changes/>
* Added text file for the articles reference values from the global fit in Relax_disp.test_r1rho_kjaergaard. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths]. This is from optimisation of the Kjaergaard et al., 2013 Off-resonance R<sub>1ρ</sub> relaxation dispersion experiments using the 'DPL' model. This uses the data from Kjaergaard's paper at DOI: http://dx.doi.org/10.1021/bi4001062.
* Replaced "_" with "-" in text file with global fit residues. Regarding [https://gna.org/bugs/?21344 bug #21344, handling of in sparse acquired R<sub>1ρ</sub> dataset with missing combinations of time and spin-lock field strengths].
* Added the OMP relaxation rates and compressed PDB file to the repository. This is to allow users to have a full data set to perform a test model-free analysis with.
* Added a sample_script to generate θ values for R<sub>1ρ</sub> data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. The script is explained at the wiki: http://wiki.nmr-relax.com/Sample_scripts.relax_disp.return_offset_data.
* Created a new citation for relax [d'Auvergne and Gooley, 2008c] which concatenates both the d'Auvergne and Gooley 2008 papers[d'Auvergne and Gooley, 2008a][d'Auvergne and Gooley, 2008b]. This is to show to those who are unaware of back-to-back paper concatenation rules how to cite both papers using one reference, saving a lot of space.
* Added lib.rotating_frame module containing functions related to rotating frame NMR calculations. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Added rotating_frame to lib.__init__.py. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Fixed unpacking of return from function calls of return_offset_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Made specific_analysis.relax_disp.return_offset_data return "w_eff" - the effective field in rotating frame in rad/s. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Fixed unpacking of return from function calls of return_offset_data, since ω<sub>eff</sub> is now also returned. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Moved calc_rotating_frame_params() to specific_analysis.relax_disp.disp_data. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is in a response to message: http://www.mail-archive.com/relax-devel@gna.org/msg05080.html.
* Started unit test for _specific_analysis._relax_disp.test_disp_data.test_calc_rotating_frame_params. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is in response to message: http://www.mail-archive.com/relax-devel@gna.org/msg05080.html.
* Extended API function in specific_analysis.relax_disp.api to calculate and return values for parameter θ when this is requested. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. Implemented according to http://www.mail-archive.com/relax-devel@gna.org/msg05082.html.
* Variable renaming and closing of files in unit test test_value_write_calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Extended unit test test_value_write_calc_rotating_frame_params() to also test writing of ω<sub>eff</sub> values. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Fixed typo and removed grace string for parameter description of θ. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Added parameter 'w_eff', the effective field in rotating frame calculation to dispersion API. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Added handling of calculating ω<sub>eff</sub> in dispersion API. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].* Added unit to parameter description of θ and ω<sub>eff</sub>. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Fix for field count and added check for R<sub>1ρ</sub> type in calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Added grace string to parameter description of θ and ω<sub>eff</sub>. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].* Fixed code duplication in relax_disp API, for calculation of θ and ω<sub>eff</sub>. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Removed unused lines of code in unit test test_return_offset_data(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Moved unit test of value writing of calc_rotating_frame_params() into separate system tests. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Added system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is to test the auto_analysis value.write function to write θ and ω<sub>eff</sub> values for an R<sub>1ρ</sub> setup.* Added writing of parameters θ and ω<sub>eff</sub> for an auto-analysis if model in MODEL_LIST_R1RHO_FULL. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Added return of None values for function calc_rotating_frame_params() if spin is not selected. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Extended system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis() to test the writing of θ values. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Hardcoded the writing of R<sub>2eff</sub> as function of the tilt angle θ, when using the [http://www.nmr-relax.com/manual/relax_disp_write_disp_curves.html user function relax_disp.write_disp_curves] . Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. θ values per spin will be written if the spin.model is in the list MODEL_LIST_R1RHO_FULL.
* Fix for return of None tuble in calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Fix for correct use of assertNotEqual or assertEqual in Relax_disp system tests. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Hardcoded contents of writing of parameters θ and ω<sub>eff</sub> in system test Relax_disp.test_value_write_calc_rotating_frame_params_auto_analysis(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This is to better support testing of key ordering and different architectures, etc.
* Fixed code duplication in specific_analysis.relax_disp.disp_data.write_disp_curves(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Modified system test of hardcoded values of θ and ω<sub>eff</sub> to match precision to 14 digits. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Fix for handling the writing of theta.out and w_eff.out in relax_disp auto_analysis, when model is not of R<sub>1ρ</sub> type. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This was discovered using the system tests.
* Fix for calculating the θ angle describing the tilted rotating frame relative to the laboratory, when omega1 / Delta_omega is negative. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This follows discussion in: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.
* Modified unit and system test to reflect new calculation of rotating frame tilt angle θ. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>]. This was discussed in thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5205.
* Added interpolation calculation of θ and ω<sub>eff</sub>, when dispersion points are interpolated. Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
* Added printout of Ω, the average resonance offset, in calc_rotating_frame_params(). Regarding [https://gna.org/support/?3124 sr #3124, Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>].
<section end=changes/>
=== Bugfixes ===
<section begin== Bugfixes ==bugfixes/>
* Typo fix for text in the model-free GUI auto-analysis. The maximum iterations for the protocol was misspelled in the GUI. This was spotted by Hessam Nasrollah.
* Fix for one of the frame order system tests when using the Mac OS X application binary. The problem was that the 'shared_data' directory could not be found as it was not included in the test_suite package __all__ list.
* Fix for [https://gna.org/bugs/?21754 bug #21754, the failure of the grace.view user function on MS Windows in opening a file in qtgrace when the path includes spaces], as reported by Mengjun Xue (mengjun dott xue att mailbox dott tu-berlin dott de). The fix was to run the program with the file name in double quotes.
* Fix for [https://gna.org/bugs/?21763 bug #21763, the problem of the chi2 value not being visible in the parameter list of the grace.write and value.write user functions in the GUI]. The problem was that when asking for the parameter name list, the minimisation parameters were not being asked for.
<section end=bugfixes/>
== Links ==
<section begin=links/>
For reference, the announcement for this release can also be found at following links:
* [http://wiki.nmr-relax.com/Relax_3.1.7 Official release notes on the relax wiki].
* {{gna link|url=gna.org/forum/forum.php?forum_id=2448|text=Gna! news item}}.
* [http://article.gmane.org/gmane.science.nmr.relax.announce/53 Gmane mailing list archive].
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00047.html The Mail Archive].
* [https://mail.gna.org/public/relax-announce/2014-03/msg00001.html Local archives].
* [http://marc.info/?l=relax-announce&m=139509874209089&w=2 Mailing list ARChives (MARC)].
{{:Softpedia}}
<section end=links/>
== Announcements ==
{{:relax release announcements}}
= Links = References ==
== See also ==
* [http://www.nmr-relax.com/api/3.1/ The relax 3.1 API documentation]{{:relax release see also}}[[Category:Release_NotesRelaxation dispersion analysis]]