Relax 2.1.1 - Revision history

Bugman: Switch to the {{relax developer link}} template to remove dead Gna! links.

2020-10-16T09:13:07Z

Switch to the {{relax developer link}} template to remove dead Gna! links.

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

2020-10-14T11:41:14Z

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

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

2015-11-03T17:11:13Z

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

Bugman: Added an infobox.

2015-10-22T14:16:04Z

Added an infobox.

Bugman: Increased the sectioning depth.

2015-10-22T14:14:35Z

Increased the sectioning depth.

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

2014-11-26T10:26:44Z

See also: Added a link to the API documentation.

Bugman: /* References */ Link fix.

2014-09-13T21:11:13Z

References: Link fix.

Bugman: Fixes for the user function links.

2014-09-13T20:55:07Z

Fixes for the user function links.

Bugman: Created a links section.

2014-09-13T20:25:00Z

Created a links section.

Bugman: Formatting of all symbols/parameters.

2014-09-13T20:22:05Z

Formatting of all symbols/parameters.

@@ Line 79: / Line 79: @@
 *  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>&eta;</sub>.  This was suggested by [https://gna.org/users/bugman Edward d'Auvergne] in a post at:https://mail.gna.org/public/relax-devel/2012-09/msg00044.html.
+*  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>&eta;</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.
@@ Line 85: / Line 85: @@
 *  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/bugman 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 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 [https://gna.org/users/bugman 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/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.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 {{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 [https://gna.org/users/bugman 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 [https://gna.org/users/bugman 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 [https://gna.org/users/bugman 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 [https://gna.org/users/bugman Edward d'Auvergne] in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00025.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 [https://gna.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00022.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 [https://gna.org/users/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
+*  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 [https://gna.org/users/bugman 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 R<sub>x</sub> curve-fitting chapter of the manual.
 *  Some editing of the NOE chapter of the relax user manual.
@@ Line 225: / Line 225: @@
 *  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/bugman Edward d'Auvergne] in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00039.html.
+*  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 [https://gna.org/users/bugman Edward d'Auvergne] in a post at:https://mail.gna.org/public/relax-devel/2012-09/msg00040.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 [https://gna.org/bugs/?20133 bug #20133] - this was simply a missing import.

@@ Line 253: / Line 253: @@
 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.org/forum/forum.php?forum_id=2362 Gna! news item]
+* {{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]

@@ Line 266: / Line 266: @@
 == 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 14:16, 22 October 2015
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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 ==		== Description ==

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 {{lowercase title}}
-= Description =
+== Description ==
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-= Download =
+== Download ==
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-= CHANGES file =
+== CHANGES file ==
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-== Features ==
+=== Features ===
 <section begin=features/>
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-== Changes ==
+=== Changes ===
 <section begin=changes/>
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-== Bugfixes ==
+=== Bugfixes ===
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-= Links =
+== Links ==
 <section begin=links/>
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-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= References =
+== References ==
 <section start=references/>
@@ Line 262: / Line 262: @@
 <HarvardReferences />
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/2.1/ The relax 2.1 API documentation]
 {{:relax release see also}}
 [[Category:Documentation]]

@@ Line 257: / Line 257: @@
 <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 43: / Line 43: @@
 *  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 user function].
+*  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.
@@ Line 57: / Line 57: @@
 *  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 user function] arguments.
+*  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 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 user function].  This is only seen in the GUI.
+*  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 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".
+*  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.
@@ Line 114: / Line 114: @@
 *  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 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.
+*  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.
@@ Line 131: / Line 131: @@
 *  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 user function].
+*  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(&omega;) equation forms.
@@ Line 182: / Line 182: @@
 *  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.
+*  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/>
@@ Line 210: / Line 210: @@
 *  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 user function] should have been checking that the diffusion tensor had been initialised.  This is now being performed.
+*  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 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].
+*  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/bugman Edward d'Auvergne] in a post at https://mail.gna.org/public/relax-devel/2012-09/msg00039.html.
@@ Line 219: / Line 219: @@
 *  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 user function] documentation - the prompt examples were wrong.
+*  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.
@@ Line 225: / Line 225: @@
 *  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 user function] 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 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(&omega;) mapping chapter of the user manual.
 *  Fixed some citations in the newly introduced model-free J(&omega;) paragraph.

@@ Line 24: / Line 24: @@
 <section begin=features/>
-*  Creation of extensive tutorials for both the script and GUI modes for the NOE, R1 and R2, model-free chapters with screenshots in of the GUI in operation.
+*  Creation of extensive tutorials for both the script and GUI modes for the NOE, R<sub>1</sub> and R<sub>2</sub>, model-free chapters with screenshots in of the GUI in operation.
-*  Restored support for multiple spin types in the NOE, R1 and R2 analyses allowing, for example, tryptophan sidechain indole NE1 data to be analysed.
+*  Restored support for multiple spin types in the NOE, R<sub>1</sub> and 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.
@@ Line 38: / Line 38: @@
 <section begin=changes/>
-*  Modified the model-free optimisation final printout to be more multi-processor friendly.  The message saying that the optimised chi2 is an improvement or not now includes the spin ID string if present.  This is more informative for the multi-processor mpi4py printouts.
+*  Modified the model-free optimisation final printout to be more multi-processor friendly.  The message saying that the optimised &chi;<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.
@@ Line 69: / Line 69: @@
 *  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 and F_eta.  This was suggested by [https://gna.org/users/bugman Edward d'Auvergne] in a post at:https://mail.gna.org/public/relax-devel/2012-09/msg00044.html.
+*  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>&eta;</sub>.  This was suggested by [https://gna.org/users/bugman 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.
@@ Line 85: / Line 85: @@
 *  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/bugman 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/bugman Edward d'Auvergne] at https://mail.gna.org/public/relax-devel/2012-09/msg00019.html.
-*  Editing of the nmrPipe script in the Rx curve-fitting chapter of the manual.
+*  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.
-*  The old R1 and R2 analysis screenshots have been shifted to the intro chapter.
+*  The old R<sub>1</sub> and 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 analysis.  These will be used in the relaxation curve-fitting chapter of the user manual.
+*  Added a tonne of GUI screenshots of an 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.
@@ Line 97: / Line 97: @@
 *  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(w) mapping chapter.
+*  Added a LaTeX label to the J(&omega;) 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 curve-fitting and NOE chapters in the relax manual.  This is because the NOE chapter references passages from the Rx curve-fitting chapter, so it's more logical to have the Rx curve-fitting chapter first.
+*  Changed the order of the R<sub>x</sub> curve-fitting and NOE chapters in the relax manual.  This is because the NOE chapter references passages from the R<sub>x</sub> curve-fitting chapter, so it's more logical to have the 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.
@@ Line 125: / Line 125: @@
 *  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 curve-fitting chapter of the user manual.
+*  Added some Sparky info to the 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 fitting chapter.
+*  The NOE chapter now points to the recommendations in the R<sub>x</sub> fitting chapter.
-*  Added a new section called 'From spectra to peak intensities' to the Rx fitting chapter of the manual.  This adds a number of recommendations for high quality relaxation rates.
+*  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 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(w) equation forms.
+*  Added a paragraph to the model-free chapter of the user manual explaining the J(&omega;) 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.
@@ Line 227: / Line 227: @@
 *  Fix for the incomplete [http://www.nmr-relax.com/manual/relax_data.temp_control user function] description.
 *  Spell fix for the [http://www.nmr-relax.com/manual/relax_data.temp_calibration user function] description.
-*  Fixes for the referencing in the J(w) mapping chapter of the user manual.
+*  Fixes for the referencing in the J(&omega;) mapping chapter of the user manual.
-*  Fixed some citations in the newly introduced model-free J(w) paragraph.
+*  Fixed some citations in the newly introduced model-free J(&omega;) 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^2(4 + 3R)/5 is skipped.  This allows long range and mixed nuclear pairs to be supported.
+*  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 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.