Relax 1.3.5 - Revision history

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

2020-10-14T12:46:50Z

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

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

2015-11-03T17:16:31Z

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

Bugman: Added an infobox.

2015-10-22T14:09:36Z

Added an infobox.

Bugman: Increased the sectioning depth.

2015-10-22T14:06:41Z

Increased the sectioning depth.

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

2014-11-26T10:23:38Z

See also: Added a link to the API documentation.

Bugman: Created a links section.

2014-09-20T17:38:27Z

Created a links section.

Bugman: Formatting of all symbols/parameters.

2014-09-20T17:36:45Z

Formatting of all symbols/parameters.

Bugman: User function HTML manual links.

2014-09-20T17:34:01Z

User function HTML manual links.

Bugman: Tracker links with full descriptions.

2014-09-20T17:29:57Z

Tracker links with full descriptions.

Bugman: /* References */ Link fix.

2014-09-13T21:12:59Z

References: Link fix.

@@ Line 184: / Line 184: @@
 For reference, the following links are also part of the announcement for this release:
 * [http://wiki.nmr-relax.com/Relax_1.3.5 Official release notes]
-* [https://gna.org/forum/forum.php?forum_id=2205 Gna! news item]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2205|text=Gna! news item}}
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/26 Gmane]
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00018.html Mail archive]

@@ Line 197: / Line 197: @@
 == 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 />

← Older revision		Revision as of 14:09, 22 October 2015
Line 1:		Line 1:
	{{lowercase title}}		{{lowercase title}}
		+
		+	{{infobox relax release
		+	\| version = 1.3.5
		+	\| prev = 1.3.4
		+	\| next = 1.3.6
		+	\| keywords = frame order theory, N-state model, plotting, rotations, stereochemistry
		+	\| type = Major feature
		+	\| date = 21 May 2010
		+	\| manual = yes
		+	}}

	== Description ==		== Description ==

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 {{lowercase title}}
-= Description =
+== Description ==
 <section begin=description/>
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 <section end=description/>
-= Download =
+== Download ==
 <section begin=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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 <section end=changes/>
-== 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 193: / Line 193: @@
 <HarvardReferences />
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation]

@@ Line 195: / Line 195: @@
 = See also =
 {{:relax release see also}}
 [[Category:Frame order analysis]]
 [[Category:N-state model analysis]]

@@ Line 25: / Line 25: @@
 <section begin=features/>
 *  Addition of the [http://www.nmr-relax.com/manual/frame_order_ref_domain.html frame_order.ref_domain user function] to specify the alignment of different domains.
-*  Converted the reduced J(w) mapping sample script to the relax 1.3 design to make it functional.
+*  Converted the reduced J(&omega;) mapping sample script to the relax 1.3 design to make it functional.
 *  Created the 'rigid' frame order model.
 *  Made the profile module optional, removing the dependency on the Python development packages.

@@ Line 59: / Line 59: @@
 *  Epydoc docstring improvements/fixes for the API documentation.
 *  Many updates using 2to3 preparing for a transition to Python 3.x.
-*  Renamed the pipe.list() user function to pipe.display().
+*  Renamed the [http://www.nmr-relax.com/manual/pipe_list.html pipe.list user function] to [http://www.nmr-relax.com/manual/pipe_display.html pipe.display].
 *  Created a base class for the user function classes.  More user function back end simplifications.
 *  Addition of many new RelaxError classes for the user function interface.
@@ Line 75: / Line 75: @@
 *  Added a very basic, and completely empty module and class for SRLS analysis.
 *  Redesign of the relax state loading for adding support for a XML formatted state file.
-*  Shifted the results.write() force arg to the end.
+*  Shifted the [http://www.nmr-relax.com/manual/results_write.html results.write] force arg to the end.
 *  Created the relax data store is_empty() method.
-*  Renamed the state.load() and state.save() directory argument from dir_name to dir for consistency with the rest of relax.
+*  Renamed the [http://www.nmr-relax.com/manual/state_load.html state.load] and [http://www.nmr-relax.com/manual/state_save.html state.save] directory argument from dir_name to dir for consistency with the rest of relax.
 *  Redesigned the relaxation curve fitting grid search for the new design of the minfx grid search.
 *  Redesigned the N-state model grid search setup around the new minfx interface.
 *  Redesigned the model-free grid search setup around the new minfx interface.
 *  Renamed the 'grace.py' sample script to 'mf_grace_S2_vs_te.py'.
-*  Added the spin_id_col arg to the rdc.read() user function.
+*  Added the spin_id_col arg to the [http://www.nmr-relax.com/manual/rdc_read.html rdc.read user function].
-*  Changes to the pcs.read() and rdc.read() user function interfaces.
+*  Changes to the [http://www.nmr-relax.com/manual/pcs_read.html pcs.read] and [http://www.nmr-relax.com/manual/rdc_read.html rdc.read] user function interfaces.
 *  Column numbering now starts at 1 rather than 0 within the user functions.
 *  The relax_io.read_spin_data_file() function has been created to handle all columnar text files where each row corresponds to a spin.
@@ Line 93: / Line 93: @@
 *  Added user variable checking to the full_analysis.py script.
 *  Added functions for determining the element name and isotope number from an isotope name.
-*  Added frame order methods necessary for the dx.map() user function.
+*  Added frame order methods necessary for the [http://www.nmr-relax.com/manual/dx_map.html dx.map user function].
 *  Huge clean up / redesign of the specific analysis internal API.
 *  Better layout of the user functions in the relax manual significantly dropping the page count.
@@ Line 100: / Line 100: @@
 *  Modified the alignment tensor print out to be more compact.
 *  The PCS centre can now be forcefully overwritten.
-*  Added the back end to the rdc.back_calc() user function (making it functional).
+*  Added the back end to the [http://www.nmr-relax.com/manual/rdc_back_calc.html rdc.back_calc user function] (making it functional).
 *  Modified all the specific analysis overfit_deselect() methods to warn when spins are deselected.
-*  align_tensor.display() now prints the magnetic susceptibility tensor.
+*  [http://www.nmr-relax.com/manual/align_tensor_display.html align_tensor.display] now prints the magnetic susceptibility tensor.
 *  The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
 *  Simplifications and clean up of the prompt and script UI code.
@@ Line 116: / Line 116: @@
 *  Partially removed the need for downstream Fink specific modifications.
 *  Creation of the NOE auto-analysis module.
-*  Fixes for the structure.load_spins() user function docstring for RNA/DNA work.
+*  Fixes for the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins user function] docstring for RNA/DNA work.
-*  The n_state_model.select_model() user function can now change the model.
+*  The [http://www.nmr-relax.com/manual/n_state_model_select_model.html n_state_model.select_model user function] can now change the model.
 *  Added a maximum global iteration arg and check into the dauvergne_protocol.py module[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b].
 <section end=changes/>
@@ Line 131: / Line 131: @@
 *  Fix for the calls to transpose_14().
 *  Bug fix for the relaxation curve-fitting difference plot script.
-*  Fix for the spin.number() user function, the number can be None to reset the values.
+*  Fix for the [http://www.nmr-relax.com/manual/spin_number.html spin.number user function], the number can be None to reset the values.
-*  Fix for the script() user function, the function intro flag at the end of executing an external script was not being restored.
+*  Fix for the [http://www.nmr-relax.com/manual/script.html script user function], the function intro flag at the end of executing an external script was not being restored.
 *  Improvements to the optimisation tests ([https://gna.org/bugs/?14173 bug #14173], [https://gna.org/bugs/?14174 bug #14174], [https://gna.org/bugs/?14175 bug #14175], [https://gna.org/bugs/?14176 bug #14176], [https://gna.org/bugs/?14177 bug #14177], [https://gna.org/bugs/?14182 bug #14182]).
 *  Fix for the R_euler_zyz() rotation matrix function.
@@ Line 147: / Line 147: @@
 *  Fixed the PDF manual compilation ([https://gna.org/bugs/?14464 bug #14464]).
 *  Fix for the retrieval of bond vectors for the N-state model.
-*  Fixes for the dx.map() user function interface.
+*  Fixes for the [http://www.nmr-relax.com/manual/dx_map.html dx.map user function] interface.
 *  Epydoc docstring fixes.
 *  Fix for when [https://gna.org/bugs/?14872 the selection string (i.e. spin_id) is unicode (bug #14872)].

@@ Line 133: / Line 133: @@
 *  Fix for the spin.number() user function, the number can be None to reset the values.
 *  Fix for the script() user function, the function intro flag at the end of executing an external script was not being restored.
-*  Improvements to the optimisation tests (bug #14173, bug #14174, bug #14175, bug #14176, bug #14177, bug #14182).
+*  Improvements to the optimisation tests ([https://gna.org/bugs/?14173 bug #14173], [https://gna.org/bugs/?14174 bug #14174], [https://gna.org/bugs/?14175 bug #14175], [https://gna.org/bugs/?14176 bug #14176], [https://gna.org/bugs/?14177 bug #14177], [https://gna.org/bugs/?14182 bug #14182]).
 *  Fix for the R_euler_zyz() rotation matrix function.
 *  Fix for the R_to_axis_angle() rotation matrix function.
@@ Line 143: / Line 143: @@
 *  Fix for the test suite, the temporary files were not always deleted if a .bz2 extension was added.
 *  Fix for the reading of Xplor NOE data when a line starts with '#'.
-*  Fix for the Dasha and Modelfree interfaces for when spins have too little data (bug #14428).
+*  Fix for [https://gna.org/bugs/?14428 the Dasha and Modelfree interfaces for when spins have too little data (bug #14428)].
 *  Fixes for the RDC and PCS read() functions, the alignment tensor ID had the same variable name as the spin ID.
-*  Fixed the PDF manual compilation (bug #14464).
+*  Fixed the PDF manual compilation ([https://gna.org/bugs/?14464 bug #14464]).
 *  Fix for the retrieval of bond vectors for the N-state model.
 *  Fixes for the dx.map() user function interface.
 *  Epydoc docstring fixes.
-*  Fix for when the selection string (i.e. spin_id) is unicode (bug #14872).
+*  Fix for when [https://gna.org/bugs/?14872 the selection string (i.e. spin_id) is unicode (bug #14872)].
 *  Fix for the PCS back calculation for when no weights are given.
 *  The last weight in the'fixed' and 'population' N-state models, if supplied, was being converted to zero (1 - sum(weights)) hence the last state/structure was not being included.
-*  Added the missing user functions in the mf_multimodel.py sample script (bug #14885).
+*  Added the missing user functions in the mf_multimodel.py sample script ([https://gna.org/bugs/?14885 bug #14885]).
-*  Fix for the Monte Carlo simulations in the full_analysis.py script (bug #14941).
+*  Fix for the Monte Carlo simulations in the full_analysis.py script ([https://gna.org/bugs/?14941 bug #14941]).
-*  Fix for optimisation of models tm4 to tm8 in the mf_multimodel sample script when over-fitting occurs (bug #15050).
+*  Fix for optimisation of models tm4 to tm8 in the mf_multimodel sample script when over-fitting occurs ([https://gna.org/bugs/?15050 bug #15050]).
 *  Removed the beta angle folding from the frame order module as it was failing.
 *  Fix and updates to the generic_fns.angles.wrap_angles() function.
 *  Fix for the internal structural object PDB writing - the TER records are between the ATOM and HETATM records.
-*  Fixed a final model-free analysis failure in the d'Auvergne protocol, the auto-analysis behind the full_analysis.py script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] (bug #15874).
+*  Fixed a final model-free analysis failure in the d'Auvergne protocol, the auto-analysis behind the full_analysis.py script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] ([https://gna.org/bugs/?15874 bug #15874]).
 *  Fixes for the N-state model when RDC or PCS data is missing.
 *  Fixed the Q-factor calculating functions to handle missing RDC or PCS lists.

@@ Line 176: / Line 176: @@
 <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/>