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{{infobox relax release| version = 3.3.5| prev = 3.3.4| next = 3.3.6| type = Major feature and bugfix| date = 27 January 2015| manual = yes}} == Description ==
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== Download ==
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== CHANGES file ==
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=== Features ===
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=== Changes ===
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* Shifted the atomic assembly code from the [http://www.nmr-relax.com/manual/structure_align.html structure.align user function] into its own function. The new function [http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html#assemble_coordinates assemble_coordinates()] of the [http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html pipe_control.structure.main module] will be used to standardise the process of assembling atomic coordinates for all of the structure user functions. This will improve the support for comparing different molecules rather than different models as missing atoms or divergent primary sequence are properly handled, and it has multi-pipe support.
* Changed the argument order for the [http://www.nmr-relax.com/manual/structure_align.html structure.align user function]. The standardised order will now be pipes, models, molecules, atom_id, etc.
* Converted the [http://www.nmr-relax.com/manual/structure_find_pivot.html structure.find_pivot user function] to the new pipes/models/molecules/atom_id design. This allows the motional pivot algorithm to work on atomic coordinates from different data pipes, different structural models, and different molecules. The change allows the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_find_pivot_molecules Structure.test_find_pivot_molecules system test] to now pass, as missing atomic data is now correctly handled. The user function backend uses the new [[http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html#assemble_coordinates pipe_control.structure.main.assemble_coordinates() function]. The Structure.test_find_pivot and [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.structure.Structure-class.html#test_find_pivot_molecules Structure.test_find_pivot_molecules] system tests have been updated for the user function argument changes.
* Shift of the atomic coordinate assembly code into the relax library. Most of the [http://www.nmr-relax.com/api/3.3/pipe_control.structure.main-module.html#assemble_coordinates pipe_control.structure.main.assemble_coordinates() function] has been shifted into the [http://www.nmr-relax.com/api/3.3/lib.structure.internal.coordinates-module.html#assemble_coord_array assemble_coord_array() function] of the new [http://www.nmr-relax.com/api/3.3/lib.structure.internal.coordinates-module.html lib.structure.internal.coordinates module]. The pipe_control function now only checks the arguments and assembles the structural objects from the relax data store, and then calls assemble_coord_array() to do all of the work. This code abstraction increases the usefulness of the atomic coordinate assembly and allows it to be significantly expanded in the future, for example by being able to take sequence alignments into consideration.
* Tooltip standardisation for the [http://www.nmr-relax.com/manual/structure_align.html structure.align] and [http://www.nmr-relax.com/manual/structure_find_pivot.html structure.find_pivot] user functions.
* Improvements for the [http://www.nmr-relax.com/manual/pcs_corr_plot.html pcs.corr_plot user function] - the plot range is now determined by the data.
* Improvements for the [http://www.nmr-relax.com/manual/rdc_corr_plot.html rdc.corr_plot user function] - the plot range is now determined by the data.
* Added save state for testing implementation of error analysis. [https://{{gna.org/task/link|?7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Simplification of [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual], to just test the creation of Monte-Carlo data where errors are drawn from the reduced χ<sup>2</sup> distribution. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Extension of the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function] to draw errors from the reduced χ<sup>2</sup> Gauss distribution as found by best fit. [https://{{gna.org/task/?7882 link|7882|text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Adding to backend of [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html pipe_control.error_analysis()], to modify data point as error drawn from the reduced χ<sup>2</sup> Gauss distribution. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Adding empty API method to return errors from the reduced χ<sup>2</sup> distribution. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Added API function in relaxation dispersion to return error structure from the reduced χ<sup>2</sup> distribution. [https://gna.org/{{gna task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Temporary test of making a confidence interval as described in fitting guide. This is [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#x_test_task_7882_kex_conf system test Relax_disp.x_test_task_7882_kex_conf], which is not activated by default. Running the test, interestingly shows, there is a possibility for a lower global k<sub>ex</sub>. But the value only differ from k<sub>ex</sub>=1826 to k<sub>ex</sub>=1813. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Change to [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#x_test_task_7882_kex_conf system test Relax_disp.x_test_task_7882_kex_conf()]. This is just a temporary system test, to check for local minima. This is method in regression book of Graphpad: http://www.graphpad.com/faq/file/Prism4RegressionBook.pdf Page: 109-111. [https://{{gna.org/task/?task link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Raising an error, if the [[R2eff]] model is used, and drawing errors from the fit. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* To [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual()], adding test for raise of errors, if the [[R2eff]] model is selected. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Added test of argument "distribution" in [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()]. This is to make sure that a wrong argument is not passed into the function. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Extended the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function], to allow for the definition of the STD to use in Gauss distribution. This is for creation of Monte-Carlo simulations, where one has perhaps gained information about the expected errors of the data points, which is not measured. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* In backend [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()] added the argument 'fixed_error' to allow for fixed input of error to the Gauss distribution. Inserted a range of checks, to make sure function behaves as expected. [https://{{gna.org/task/?task link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Added to [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()] the creation of data points for a fixed distribution. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* To [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_task_7882_monte_carlo_std_residual system test Relax_disp.test_task_7882_monte_carlo_std_residual()], added tests for creation of Monte-Carlo data by different methods. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* In [http://www.nmr-relax.com/api/3.3/pipe_control.error_analysis-module.html#monte_carlo_create_data pipe_control.error_analysis.monte_carlo_create_data()], if data is of list type or ndarray, then modify the data point according to the fixed error if the distribution is set to 'fixed'. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.* Expanded the STD acronym, to the meaning of standard deviation. This is in the [http://www.nmr-relax.com/manual/monte_carlo_create_data.html monte_carlo.create_data user function]. [https://{{gna.org/task/?link|7882 |text=Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals]}}.
* Added a RelaxWarning printout to the [http://www.nmr-relax.com/api/3.3/dep_check-module.html dep_check module] if wxPython 2.8 or less is encountered. This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7502. The warning text is simply written to STDERR as relax starts.
* Updated the wxPython version in the relax manual to be 2.9 or higher. This is in the section http://www.nmr-relax.com/manual/Dependencies.html.
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=== Bugfixes ===
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== Links ==
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For reference, the announcement for this release can also be found at following links:
* [http://wiki.nmr-relax.com/Relax_3.3.4 5 Official release notes on the relax wiki].* [https://{{gna link|url=gna.org/forum/forum.php?forum_id=2483 2492|text=Gna! news item]}}.* [http://article.gmane.org/gmane.science.nmr.relax.announce/62 63 Gmane mailing list archive].* [http://www.mail-archive.com/relax-announce%40gna.org/msg00053msg00054.html The Mail Archive].* [https://mail.gna.org/public/relax-announce/20142015-1201/msg00000.html Local archives].* [httphttps://marc.info/?l=relax-announce&m=141773006429004142248784423361&w=2 Mailing list ARChives (MARC)].
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== Announcements ==
{{:relax release announcements}}
== See also ==
* [http://www.nmr-relax.com/api/3.3/ The relax 3.3 API documentation]
{{:relax release see also}}
[[Category:Relaxation dispersion analysis]]