Relax 2.2.3 - Revision history

Bugman: Switch to the {{gna link}} template for avoiding dead links.

2020-10-15T21:28:14Z

Switch to the {{gna link}} template for avoiding dead links.

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

2020-10-13T22:29:23Z

Links: Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: Internal link to Modelfree4.

2015-12-15T16:14:15Z

Internal link to Modelfree4.

Bugman: /* References */ Switched to a labelled section transclusion for the citations.

2015-11-03T17:04:55Z

References: Switched to a labelled section transclusion for the citations.

Bugman: Added the 'manual' parameter to {{infobox relax release}}.

2015-10-22T18:18:25Z

Added the 'manual' parameter to {{infobox relax release}}.

Bugman: Added an infobox.

2015-10-22T09:38:49Z

Added an infobox.

Bugman: Increased the sectioning depth.

2015-10-22T09:37:12Z

Increased the sectioning depth.

Bugman: /* See also */ Added a link to the API documentation.

2014-11-26T10:28:55Z

See also: Added a link to the API documentation.

Bugman: /* References */ Link fix.

2014-09-13T21:11:03Z

References: Link fix.

Bugman: Changed the dauvergne_protocol LST tags.

2014-09-13T19:07:55Z

Changed the dauvergne_protocol LST tags.

@@ Line 208: / Line 208: @@
 *  Bug fix for the XYZ 3D structure file reader.  The atom name is now correctly set up for each atom in the file.  The element type setting has also been simplified.
 *  Fix for [https://gna.org/bugs/?20603 bug #20603, the relaxation data right click menu failure].  The problem was that there was that the last menu item specified had no contents.  This item has been removed.
-*  Fix for [https://gna.org/bugs/?20563 bug #20563, the end failure of the model-free auto-analysis].  This was reported by [https://gna.org/users/stacy Stanislava Panova].  The problem was related to the Monte Carlo simulations.  The generic_fns.monte_carlo.create_data() function is now asking for the errors associated with a certain data point, even if that data point does not exist.  The solution was to check if the relaxation data ID string is present in spin.ri_data_err before accessing the key-value pair (in the specific API _return_error_relax_data() common method).
+*  Fix for [https://gna.org/bugs/?20563 bug #20563, the end failure of the model-free auto-analysis].  This was reported by {{gna link|url=gna.org/users/stacy|text=Stanislava Panova}}.  The problem was related to the Monte Carlo simulations.  The generic_fns.monte_carlo.create_data() function is now asking for the errors associated with a certain data point, even if that data point does not exist.  The solution was to check if the relaxation data ID string is present in spin.ri_data_err before accessing the key-value pair (in the specific API _return_error_relax_data() common method).
 *  Bug fix for the maintenance of the spin ID lookup table metadata.  This is important for small molecules.  Non-unique IDs were being placed into the lookup table,resulting in incorrect spin containers being sometimes used.  Now the molecule container has the _res_name_count and _res_num_count metadata and the residue container the _spin_name_count and _spin_num_count structures.  These are updated via metadata_update() and are used by the spin_id_variants() function to create a list of purely unique spin IDs.
 *  The spin_id argument to the [http://www.nmr-relax.com/manual/residue_delete.html residue.delete user function] is no longer read-only.  This allows spin ranges or other complicated IDs to be specified.  This is needed for the Bmrb GUI tests to pass.

@@ Line 220: / Line 220: @@
 For reference, the following links are also part of the announcement for this release:
 * [http://wiki.nmr-relax.com/Relax_2.2.3 Official release notes]
-* [https://gna.org/forum/forum.php?forum_id=2383 Gna! news item]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2383|text=Gna! news item}}
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/40 Gmane]
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00036.html Mail Archive]

@@ Line 117: / Line 117: @@
 *  The [http://www.nmr-relax.com/manual/rdc_back_calc.html rdc.back_calc] and [http://www.nmr-relax.com/manual/pcs_back_calc.html pcs.back_calc] user functions now warn if no data was calculated.  This is to inform the user about problems at the place that they occur instead of later on with, for example, the creation of empty data files.
 *  Updated the float module to handle numpy floats.  This makes the floatToBinaryString() function compatible with the numpy.float16 type.
-*  Removed the prune parameter from the backend of the [http://www.nmr-relax.com/manual/monte_carlo_error_analysis.html monte_carlo.error_analysis user function].  This was a dangerous parameter used to mimic the 'Trim' parameter from the Modelfree4 program.  The result is bad statistics.  The probable reason for the 'Trim' parameter was the failure of model-free models in the simulations, but this issue was solved using model elimination (see http://www.nmr-relax.com/refs.html#dAuvergneGooley06).
+*  Removed the prune parameter from the backend of the [http://www.nmr-relax.com/manual/monte_carlo_error_analysis.html monte_carlo.error_analysis user function].  This was a dangerous parameter used to mimic the 'Trim' parameter from the [[Modelfree4]] program.  The result is bad statistics.  The probable reason for the 'Trim' parameter was the failure of model-free models in the simulations, but this issue was solved using model elimination (see http://www.nmr-relax.com/refs.html#dAuvergneGooley06).
 *  Created the Structure.test_read_xyz_strychnine system test to demonstrate a bug in the XYZ parser.  This is for the reading of XYZ structure files.
 *  Created the lib.text package for text manipulation.  The first module will be the text formatting of tables.

@@ Line 233: / Line 233: @@
 == References ==
-<section start=references/>
+* [*d'Auvergne and Gooley, 2007] {{#lst:Citations|dAuvergneGooley07}}
-* [*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://dx.doi.org/10.1039/b702202f 10.1039/b702202f]).
+* [*d'Auvergne and Gooley, 2008b] {{#lst:Citations|dAuvergneGooley08b}}
 <HarvardReferences />

@@ Line 8: / Line 8: @@
 | type     = Major feature and bugfix
 | date     = 11 March 2013
 }}

← Older revision		Revision as of 09:38, 22 October 2015
Line 1:		Line 1:
	{{lowercase title}}		{{lowercase title}}
		+
		+	{{infobox relax release
		+	\| version = 2.2.3
		+	\| prev = 2.2.2
		+	\| next = 2.2.4
		+	\| keywords = relax library, structure
		+	\| type = Major feature and bugfix
		+	\| date = 11 March 2013
		+	}}

	== Description ==		== Description ==

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 {{lowercase title}}
-= Description =
+== Description ==
 <section begin=description/>
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 <section end=description/>
-= Download =
+== Download ==
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 <section end=download/>
-= CHANGES file =
+== CHANGES file ==
 <section begin=metadata/>
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 <section end=metadata/>
-== Features ==
+=== Features ===
 <section begin=features/>
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 <section end=features/>
-== Changes ==
+=== Changes ===
 <section begin=changes/>
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-== Bugfixes ==
+=== Bugfixes ===
 <section begin=bugfixes/>
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 <section end=bugfixes/>
-= Links =
+== Links ==
 <section begin=links/>
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 <section end=links/>
-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= References =
+== References ==
 <section start=references/>
@@ Line 229: / Line 229: @@
 <HarvardReferences />
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/2.2/ The relax 2.2 API documentation]

@@ Line 231: / Line 231: @@
 = See also =
 {{:relax release see also}}
 [[Category:GUI]]
 [[Category:relax library]]
 [[Category:Structure]]

@@ Line 224: / Line 224: @@
 <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://dx.doi.org/10.1039/b702202f 10.1039/b702202f).
+* [*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://dx.doi.org/10.1039/b702202f 10.1039/b702202f]).
 * [*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://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).
 <section end=references/>

@@ Line 68: / Line 68: @@
 *  Completed the unit test of the generic_fns.structure.pdb_read.helix() function.
 *  Implemented the generic_fns.structure.pdb_read.helix() function.
-*  Created the Mf.test_bug_20531_molmol_macro_write_relaxfault system test.  This is an attempt at catching bug #20531.  It creates all of the m0-m9 and tm0-tm9 models, sets some parameter values, and then attempts to create all of the Molmol macros, PyMOL macros, Grace plots and parameter text files as present in the auto_analysis.dauvergne_protocol module[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008].
+*  Created the Mf.test_bug_20531_molmol_macro_write_relaxfault system test.  This is an attempt at catching bug #20531.  It creates all of the m0-m9 and tm0-tm9 models, sets some parameter values, and then attempts to create all of the Molmol macros, PyMOL macros, Grace plots and parameter text files as present in the auto_analysis.dauvergne_protocol module[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b].
 *  The spectrometer frequency is now set in the Mf.test_bug_20531_molmol_macro_write_relaxfault system test.  This is needed for the Rex scaling.
 *  The spin name, element and isotope is now set in Mf.test_bug_20531_molmol_macro_write_relaxfault.  This is required in this system test so that the marco creation is not skipped.
@@ Line 175: / Line 175: @@
 *  Converted many calls to generic_fns.mol_res_spin.generate_spin_id() to generate_spin_id_unique().  This will allow many future bugs to be avoided, as the spin ID string is most often used to retrieve spin containers.  By using the generate_spin_id_unique() function, the returning of spin containers will always be correct.
 *  Created the Mf.test_bug_20563_missing_ri_error system test to catch [https://gna.org/bugs/?20563 bug #20563].  The data added to the test suite is a highly truncated data set of a analysis completed using the data attached to the bug report.
-*  Modified the dauvergne_protocol model-free auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008] to aid in debugging.  The write_results_dir argument has been added to allow the test suite to read from one directory in test suite shared data directories and redirect output to a temporary directory.
+*  Modified the dauvergne_protocol model-free auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] to aid in debugging.  The write_results_dir argument has been added to allow the test suite to read from one directory in test suite shared data directories and redirect output to a temporary directory.
 *  The files from the Mf.test_bug_20563_missing_ri_error system test are now placed in a temporary directory.  This is essential for the test suite to prevent files from going everywhere.
 *  The [http://www.nmr-relax.com/manual/frq_set.html frq.set user function] units argument is no longer read-only.  This is needed for some of the GUI tests in the frame_order_testing branch.
@@ Line 225: / Line 225: @@
 <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://dx.doi.org/10.1039/b702202f 10.1039/b702202f).
-* [*d'Auvergne and Gooley, 2008] 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://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).
+* [*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://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).
 <section end=references/>
 <HarvardReferences />