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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 ==
<section begin=description/>
<section end=description/>
== Download ==
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== CHANGES file ==
<section begin=metadata/>
Version 2.1.1<br/>(21 September 2012, from /trunk)<br/>
http://svn.gna.org/svn/relax/tags/2.1.1
<section end=metadata/>
=== Features ===
<section begin=features/>
* Creation of extensive tutorials for both the script and GUI modes for the NOE, R1 R<sub>1</sub> and R2R<sub>2</sub>, model-free chapters with screenshots in of the GUI in operation.* Restored support for multiple spin types in the NOE, R1 R<sub>1</sub> and R2 R<sub>2</sub> analyses allowing, for example, tryptophan sidechain indole NE1 data to be analysed.
* The activation and expansion of the [http://www.nmr-relax.com/manual/Consistency_testing.html consistency testing chapter] to the user manual.
* The completion of the [http://www.nmr-relax.com/manual/Reduced_spectral_density_mapping.html reduced spectral density mapping chapter] of the user manual.
* Improvements to the [http://www.nmr-relax.com/manual/Alphabetical_listing_user_functions.html user function section of the user manual ] with better visual separation and the inclusion of the icons used in the GUI.
* Creation of the [http://www.nmr-relax.com/manual/relax_data_model.html relax data model chapter] of the user manual to explain how to set up data in relax in all UI modes (with screenshots in the GUI mode).
* Creation of the [http://www.nmr-relax.com/manual/Preface_citing_relax.html citations chapter] of the user manual to help users properly cite the parts of relax that they use.
* A complete rewrite of the [http://www.nmr-relax.com/manual/Relaxation_curve_fitting.html relaxation curve-fitting chapter] of the relax manual.
* General improvements and expansions throughout the user manual (the manual is now 15 Mb compared to 4.3 Mb for [[relax 2.1.0]]).
<section end=features/>
=== Changes ===
<section begin=changes/>
* Modified the model-free optimisation final printout to be more multi-processor friendly. The message saying that the optimised chi2 χ<sup>2</sup> is an improvement or not now includes the spin ID string if present. This is more informative for the multi-processor mpi4py printouts.
* Added the use of the program 'nice' to the model-free GUI tutorial in the user manual.
* Removed the out of date and useless README file for the HTML version of the user manual.
* 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.
* Improvements to the duplicate user manual title finding script.
* 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.
* Created the test_bug_20152_read_dc_file() GUI test for catching bug #20152 ([https://gna.org/bugs/?20152)bug #20152]. This includes truncated data taken from the bug report (with data for only the first 3 residues).* Set up the Bruker Dynamics Center system tests as GUI tests. This is in preparation for catching bug #20152 ([https://gna.org/bugs/?20152)bug #20152].
* 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_R2 F<sub>R<sub>2</sub></sub> and F_etaF<sub>η</sub>. This was suggested by {{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 {{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 by {{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 {{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 {{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 {{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 {{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 {{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 {{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 {{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 {{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 Rx R<sub>x</sub> curve-fitting chapter of the manual.
* Some editing of the NOE chapter of the relax user manual.
* The old R1 R<sub>1</sub> and R2 R<sub>2</sub> analysis screenshots have been shifted to the intro chapter.
* Editing of the relax data model chapter of the user manual.
* Large expansion and lots of editing of the relaxation curve-fitting chapter of the user manual. The GUI section has been added which includes step-by-step instructions on how to use relax,illustrated with screenshots at each step. There has been general editing of the whole of the chapter as well.
* Added a tonne of GUI screenshots of an R1 R<sub>1</sub> analysis. These will be used in the relaxation curve-fitting chapter of the user manual.
* Added some Grace plots from an NOE analysis for use in the user manual.
* Small edits of the relax data model chapter of the user manual.
* Large edits of the consistency testing chapter of the user manual.
* Activated the consistency testing chapter of the user manual.
* Added a LaTeX label to the J(wω) mapping chapter.
* Added the other consistency testing references to the citation chapter of the manual.
* Added the Fushman et al., 1998 reference.
* Fix for the Farrow et al., 1995 DOI number.
* Changed the order of the Rx R<sub>x</sub> curve-fitting and NOE chapters in the relax manual. This is because the NOE chapter references passages from the Rx R<sub>x</sub> curve-fitting chapter, so it's more logical to have the Rx R<sub>x</sub> curve-fitting chapter first.
* Clean up of a paragraph of the data model chapter of the user manual.
* Improved the consistency in the user manual by using the new LaTeX commands. These changes are throughout the manual and affect all the text of user functions, menu items, prompt examples, GUI elements, files, directories, etc.
* 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.
* Modified the NOE system test to catch bug #20120 ([https://gna.org/bugs/?20120)bug #20120].
* Lots of editing of the NOE chapter of the user manual.
* Significant update of the NOE chapter of the user manual. The sample script used in this chapter was incredibly out of date.
* Modified the NOE system test to test the usage of Trp indole <sup>15</sup>N data. This is to catch bug #20119 ([https://gna.org/bugs/?20119)bug #20119].* Added some Trp peak data (backbone and indole N) to the Sparky steady-state NOE peak lists. This is in preparation for the modification of the NOE system test to catch bug #20119([https://gna.org/bugs/?20119)bug #20119].
* Modified the NOE sample script to include Trp indole NH data.
* Added a step-by-step tutorial for the GUI NOE auto-analysis to the user manual. This includes 22 screenshots of all the steps.
* Added a section label.
* Added some Sparky info to the Rx R<sub>x</sub> curve-fitting chapter of the user manual.
* Allowed the raggedbottom LaTeX setting as this is better for the screenshot layout in the user manual.
* Added the nth package for the user manual LaTeX compilation.
* The NOE chapter now points to the recommendations in the Rx R<sub>x</sub> fitting chapter.* Added a new section called 'From spectra to peak intensities' to the Rx 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(wω) equation forms.
* Added a label to the data model chapter of the user manual.
* Created an initial rough version of the RSDM chapter of the user manual.
* 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_dist.html dipole_pair.read_dist ] and [http://www.nmr-relax.com/manual/dipole_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.
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>* Fix for bug #20189 ([https://gna.org/bugs/?20189)bug #20189]. The Sequence GUI element can not handle values of None.
* The citations chapter is now included in the HTML version of the user manual. For some reason, a file named 'cite.tex' cannot be handled by latex2html.
* The latex2html compilation of the user manual now ignores the \bibitem{} commands. This is needed for the HTML version of the user manual.
* Removed the text '.eps.gz' from all of the LaTeX included graphics in the user manual. This allows latex2html to select and use the PNG images instead, producing much better graphics for the online manual (http://www.nmr-relax.com/manual/index.html).
* Fix for the graphics.fetch_icon() function for when no file format is specified.
* Elimination of all duplicated chapter, section and subsection titles in the user manual. This fixes bug #20185 ([https://gna.org/bugs/?20185)bug #20185].
* The HTML files for the user manual now have longer names - this is needed for removing the duplicates.
* Fix for the duplicate title finding script - the LaTeX and HTML mode alternatives are no longer mixed up.
* Fix for bug #20177 ([https://gna.org/bugs/?20177)bug #20177]. This was simply a lower precision OS/Python/numpy combination causing a test suite failure - there are no practical effects and only the precision of the system/GUI test has been lowered.
* Another bug fix for the sequence GUI editor window. This bug was being triggered by the User_functions.test_structure_pdb_read() GUI test which now passes.
* Small fix for the User_functions.test_structure_pdb_read() GUI test.
* Fix for bug #20184 ([https://gna.org/bugs/?20184)bug #20184]. The behaviour of the gui.string_conv.gui_to_int() and related functions has changed in the last few months and the Sequence_window() GUI element has not changed to match. This has been fixed and the User_functions.test_structure_pdb_read() GUI test now passes.
* Fixes for the User_functions.test_structure_pdb_read() GUI test.
* Fix for bug #20183 ([https://gna.org/bugs/?20183) bug #20183 - the failure of the sequence editor window]. The problem was that fields which could be either single values or lists (or tuples) of values were not properly handled.* Fix for bug #20182 ([https://gna.org/bugs/?20182) bug #20182 - the sequence element window ordering issue]. The sequence element window now has the parent wx.Window element set. This prevents the main relax window from being set as the parent and hence coming to the front after the sequence element window is launched from a user function window.* Fix for bug #20181 ([https://gna.org/bugs/?20181) bug #20181 - the GUI sequence editor window TypeError problem].
* Window ordering bug fix for the user function windows launched from the spin viewer window. The spin viewer window no longer hides behind the main relax window after the launch of the user function.
* Bug fix for the repetition of Monte Carlo simulations in the relaxation curve-fitting analyses. This is in the specific analysis API, so will allow all analysis types to repeat Monte Carlo simulations for error analysis.
* 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 bug #20173 ([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 bug #20152 ([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 bug #20152 ([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 {{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 {{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 bug #20133 ([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 bug #20120 ([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 reading of Sparky peak lists. Spin names with numbers at the end were not being correctly identified. This fix allows Trp indole NE1-HE1 data to be loaded.
* 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(wω) mapping chapter of the user manual.* Fixed some citations in the newly introduced model-free J(wω) paragraph.
* Fixed a bunch of links in the development chapter of the user manual.
* Small fix for the sample script in the relaxation curve-fitting chapter of the relax manual.
* Small fix for the sample script in the NOE chapter of the relax manual.
* Bug fix for the RDC Q factor calculations for when the dipolar constants are not all the same. Now instead of a RelaxError, a warning is given and the Q factor normalised by 2Da^2D<sub>a</sub><sup>2</sup>(4 + 3R)/5 is skipped. This allows long range and mixed nuclear pairs to be supported.
* Import additions to fix the epydoc import of the 'sconstruct' script for the API documentation.
* Epydoc docstring fixes for the API documentation.
* Import fix for the epydoc building of the API documentation.
<section end=bugfixes/> == Links == <section begin=bugfixeslinks/>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]* {{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]* [https://mail.gna.org/public/relax-announce/2012-09/msg00000.html Local archives]* [http://marc.info/?l=relax-announce&m=135070664825023&w=2 MARC]<section end=links/> == Announcements =={{:relax release announcements}} == References == * [*d'Auvergne and Gooley, 2007] {{#lst:Citations|dAuvergneGooley07}}* [*d'Auvergne and Gooley, 2008b] {{#lst:Citations|dAuvergneGooley08b}}<HarvardReferences />
== See also ==
* [http://www.nmr-relax.com/api/2.1/ The relax 2.1 API documentation]{{:relax release see also}}[[Category:Release_NotesDocumentation]]