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<section start=references/>* [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. ''Mol. BioSyst.'', '''3'''(7), 483–494. (DOI: [http{{#lst://dx.doi.org/10.1039/b702202f 10.1039/b702202f).Citations|dAuvergneGooley07}}* [*d'Auvergne and Gooley, 2008b] d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. ''J. Biomol. NMR'', '''40'''(2), 121-133. (DOI: [http{{#lst://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).<section end=references/>Citations|dAuvergneGooley08b}}
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{{infobox relax release| version = 2.1.1| prev = 2.1.0| next = 2.1.2| keywords = Manual, relaxation data| type = Major feature and bugfix| date = 21 September 2012| manual = yes}} == Description ==
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== Download ==
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== CHANGES file ==
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=== Features ===
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=== Changes ===
<section begin=changes/>
* Added a BMRB section to the end of the model-free chapter of the user manual.
* Massive expansion of the model-free chapter of the user manual including script and GUI tutorials. The model-free chapter now has step-by-step tutorials for both the prompt/script mode and GUI mode for the new automated model-free protocol (the d'Auvergne protocol)[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]. This includes a large set of screenshots for the GUI mode.
* Created the User_functions.test_value_set GUI test demonstrating the failure of the [http://www.nmr-relax.com/manual/value_set.html value.set user function].
* Modified the dauvergne_protocol sample script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] to handle tryptophan indole NE1 data.
* The graphics.fetch_icon() function argument 'format' can now be set to None. This will return the file path without the extension.
* Created the User_functions.test_structure_pdb_read GUI test for checking the sequence editor window. This new user function GUI testing class is to be used for testing out the special GUI elements not invoked within the unit testing. The test_structure_pdb_read() test specifically shows a number of failures of the sequence editor window.
* Modified the operation of the sequence GUI element to have access to the sequence editor window. This is to allow this GUI element to be blasted within the test suite.
* Improvements to the descriptions of the [http://www.nmr-relax.com/manual/structure_read_xyz.html structure.read_xyz user function] arguments.* Improvements to the descriptions of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb user function] arguments.* Added @HE1 to the spin ID list of the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function]. This is only seen in the GUI.
* Created the new generic_fns.result_files for standardising the handling of results files. This fixes the bug where results files are repetitively added to the list. All of the code touching cdp.result_files now uses this module instead.
* Updated the scripting section of the intro chapter of the user manual for non-technical users.
* Expanded the spin ID list for the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function]. This now includes the spins "@N", "@NE1", "@C", "@H", "@O", "@P", ":A@C2", ":A@C8", ":G@N1",":G@C8", ":C@C5", ":C@C5", ":U@N3", ":U@C5", ":U@C6".
* Changed the RelaxError for missing relaxation times in the relaxation curve-fitting analyses.
* Modified the test_bug_20152_read_dc_file() GUI test to catch the RelaxError. This error is because of the old PDC format.
* Re-added Dominique Marion's solvent suppression to the NMRPipe script in the curve-fitting chapter.
* A few small edits of the relaxation curve-fitting chapter. This is to reinforce the exact time of the relaxation time period.
* Added some text to explain why test only J(0) is discussed whereas the script also calculated F<sub>R<sub>2</sub></sub> and F<sub>η</sub>. This was suggested by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} in a post at:https://mail.gna.org/public/relax-devel/2012-09/msg00044.html.
* Big clean up of the Bibtex bibliography file for the relax user manual.
* Small edits of the consistency testing figure caption in the relax user manual.
* Editing of the "Values, gradients, and Hessians" chapter of the user manual to make it fit better. The context of this chapter has been specified by changing the title to "Optimisation of relaxation data -- values, gradients, and Hessians" and the intro text has been updated. As this chapter is no longer straight after the model-free chapter, this is needed.
* Made a small correction to a reference such that a superscript is correctly displayed.
* Added the bounding box and a centerline command to the code for the figure for consistency testing. This follows two remarks by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00030.html and https://mail.gna.org/public/relax-devel/2012-09/msg00032.html.* Added more text to describe the consistency testing approach. Also includes a very basic point by point protocol for consistency testing. This was proposed by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00028.html. This also follows a discussion started by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.* Added some text to describe the consistency testing example figure. This follows a discussion started by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.* Added a modified version of Figure 1 from Morin and Gagne (JBNMR, 2009 (http://dx.doi.org/10.1007/s10858-009-9381-4)). File formats are .agr (xmgrace), eps (gzipped), and png. This follows a discussion started by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.* Added a directory for placing consistency testing graphics. This follows a discussion started by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.* Corrected the bibliography entries whih were still in plain text and not as a Latex \cite call. Also renamed the MorinGagne09 entry to MorinGagne09a as there is now also MorinGagne09b. This was proposed by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00025.html.* Added the DOI to reference Morin11 and fixed indentation (10.1016/j.pnmrs.2010.12.003). This follows a comment by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00022.html.
* Deletion of the relax version LaTeX file - this is automatically created anyway.
* Added text to detail the usage of the consistency testing script. This text was modified from the corresponding text for jw_mapping. This follows a discussion started by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.* Added some text and a reference to the consistency testing chapter. This follows a discussion started by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
* Editing of the nmrPipe script in the R<sub>x</sub> curve-fitting chapter of the manual.
* Some editing of the NOE chapter of the relax user manual.
* Created a directory for screenshots of the spin viewer window operation.
* The NOE auto-analysis GUI test now checks the support for Trp indole N data as well.
* The [http://www.nmr-relax.com/manual/spectrum_read_intensities.html spectrum.read_intensities user function] now prints out a list of the intensities read in. This is for better user feedback as to what the user function has actually done.
* Created the GUI wizard _apply() method for executing the current page's _apply() method. This is for the GUI tests to simulate a click on the 'Apply' button.
* Removed a debugging print out.
* Added a new section called 'From spectra to peak intensities' to the R<sub>x</sub> fitting chapter of the manual. This adds a number of recommendations for high quality relaxation rates.
* Added the Viles et al., 2001 reference.
* Small description edit for the [http://www.nmr-relax.com/manual/relax_data_temp_control.html relax_data.temp_control user function].
* Added a LaTeX label to the NOE chapter of the user manual.
* Added a paragraph to the model-free chapter of the user manual explaining the J(ω) equation forms.
* Redesign of how the GPL license is presented to the user. The old prompt.gpl module with the version 2 of the license has been deleted. Now the text form the docs/COPYING file is passed through pydoc.pager for the './relax --licence' and the prompt mode GPL object, and is simply printed to STDOUT for the GUI help system.
* Import clean ups for the N-state model specific module.
* Added the 'unit' argument to the [http://www.nmr-relax.com/manual/dipole_pair.read_distdipole_pair_read_dist.html dipole_pair.read_dist] and [http://www.nmr-relax.com/manual/dipole_pair.set_distdipole_pair_set_dist.html dipole_pair.set_dist] user functions. This is to allow distances in Angstroms to be read into relax and converted to meters.
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=== Bugfixes ===
<section begin=bugfixes/>
* MS Windows fix - the NOE system and GUI tests are now less strict in checking the errors.
* Proper bug fix for storing the execution status of wizard and user function pages. This allows the test suite to pass again. The execution status is now properly returned from the wizard pages run synchronously (and always set to True for asynchronous calls).
* Fix for [https://gna.org/bugs/?20173 bug #20173]. The [http://www.nmr-relax.com/manual/palmer_create.html palmer.create user function] should have been checking that the diffusion tensor had been initialised. This is now being performed.
* Bug fix for the execution of wizard pages - the execution status is now observed. This fixes [https://gna.org/bugs/?20152 bug #20152]. The problem was that the execution status was being lost in the protected_exec() function. However as relax errors are caught in the GUI interpreter anyway and the status is returned normally, the protected_exec() wrapper was removed.
* Bug fix for the creation of the user function GUI pages - the (a)synchronous arg is now observed. This argument was being ignored, which in some wizards was causing user function calls to be asynchronous. This can result in racing related crashes.
* The [http://www.nmr-relax.com/manual/bruker_read.html bruker.read user function] now throws a RelaxError when old PDC files are detected. This is a partial fix for [https://gna.org/bugs/?20152 bug #20152].
* Fixed the newlines in the sample script in the consistency testing chapter.
* Fixed the bounding box for the consistency testing figure and also fixed some Latex unfriendly code. Problems were spotted by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00039.html.* Fixed a bibliography entry label problem. This was spotted by [https://gna.org/users/{{relax developer link|username=bugman |text=Edward d'Auvergne] }} in a post at:https://mail.gna.org/public/relax-devel/2012-09/msg00040.html.
* Bug fix for the creation of 2D graphs via grace.write for when many data sets exist. The algorithm for setting the Grace symbol number to be between 1 and 10 was broken!
* Fix for [https://gna.org/bugs/?20133 bug #20133] - this was simply a missing import.
* Fix for the [http://www.nmr-relax.com/manual/spin_create.html spin.create user function] documentation - the prompt examples were wrong.
* Bug fix for the generic_fns.grace.get_data() function. This was just recently introduced and was triggered by the Relax_fit.test_bug_12670_12679 system test.
* Fix for [https://gna.org/bugs/?20120 bug #20120, the bad Grace plots with multiple spin types]. The grace data assembly function was not setting the correct index for when a spin type changes to a preexisting type.
* Bug fix for the loading of peak intensities via spectrum.read_intensities. The user function could not be applied twice, preventing the loading of data from different spin systems such as Trp indole NH data.
* Another fix for the relax_data.temp_control description.
* Fix for the incomplete [http://www.nmr-relax.com/manual/relax_data_temp_control.html relax_data.temp_control user function] description.* Spell fix for the [http://www.nmr-relax.com/manual/relax_data_temp_calibration.html relax_data.temp_calibration user function] description.
* Fixes for the referencing in the J(ω) mapping chapter of the user manual.
* Fixed some citations in the newly introduced model-free J(ω) paragraph.
<section end=bugfixes/>
== Links ==
<section begin=links/>
For reference, the following links are also part of the announcement for this release:
* [http://wiki.nmr-relax.com/Relax_2.1.1 Official release notes]
* [https://{{gna link|url=gna.org/forum/forum.php?forum_id=2362 |text=Gna! news item]}}
* [http://article.gmane.org/gmane.science.nmr.relax.announce/34 Gmane]
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00030.html Mail Archive]
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== Announcements ==
{{:relax release announcements}}
== References ==
<HarvardReferences />
== See also ==
* [http://www.nmr-relax.com/api/2.1/ The relax 2.1 API documentation]
{{:relax release see also}}
[[Category:Documentation]]