Relax 1.3.4 - Revision history

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

2020-10-14T12:47:27Z

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

Bugman: Typo fix.

2020-10-05T20:49:08Z

Typo fix.

Bugman: Increased the sectioning depth.

2015-10-22T17:20:29Z

Increased the sectioning depth.

Bugman: Added an infobox.

2015-10-22T14:11:59Z

Added an infobox.

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

2014-11-26T10:23:37Z

See also: Added a link to the API documentation.

Bugman: Created a links section.

2014-09-20T17:53:49Z

Created a links section.

Bugman: Formatting of all symbols/parameters.

2014-09-20T17:51:53Z

Formatting of all symbols/parameters.

Bugman: User function HTML manual links.

2014-09-20T17:48:24Z

User function HTML manual links.

Show changes

Bugman: Tracker links with full descriptions.

2014-09-20T17:40:38Z

Tracker links with full descriptions.

Bugman: Category link updates for the specific analyses.

2014-09-11T07:50:17Z

Category link updates for the specific analyses.

@@ Line 163: / Line 163: @@
 For reference, the following links are also part of the announcement for this release:
 * [http://wiki.nmr-relax.com/Relax_1.3.4 Official release notes]
-* [https://gna.org/forum/forum.php?forum_id=2108 Gna! news item]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2108|text=Gna! news item}}
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/24 Gmane]
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00016.html Mail archive]

@@ Line 14: / Line 14: @@
 <section begin=description/>
-This is a major feature release featuring innumerous changes and bugfixes.  New features include support for spin containers for psueedo atoms, NOE distance restraints, improved structure handling with multiple molecules and multiple models, the N-state model with equal and fixed probabilities, handling of the Bruker ncproc parameter, return of hybridisation, return of MOLMOL macros for illustrating model-free parameters, and initial support for the new Frame Order theories.
+This is a major feature release featuring innumerous changes and bugfixes.  New features include support for spin containers for psuedo atoms, NOE distance restraints, improved structure handling with multiple molecules and multiple models, the N-state model with equal and fixed probabilities, handling of the Bruker ncproc parameter, return of hybridisation, return of MOLMOL macros for illustrating model-free parameters, and initial support for the new Frame Order theories.
 <section end=description/>

@@ Line 11: / Line 11: @@
 }}
-= Description =
+== Description ==
 <section begin=description/>
@@ Line 17: / Line 17: @@
 <section end=description/>
-= Download =
+== Download ==
 <section begin=download/>
@@ Line 23: / Line 23: @@
 <section end=download/>
-= CHANGES file =
+== CHANGES file ==
 <section begin=metadata/>
@@ Line 31: / Line 31: @@
 <section end=metadata/>
-== Features ==
+=== Features ===
 <section begin=features/>
@@ Line 52: / Line 52: @@
 <section end=features/>
-== Changes ==
+=== Changes ===
 <section begin=changes/>
@@ Line 102: / Line 102: @@
 <section end=changes/>
-== Bugfixes ==
+=== Bugfixes ===
 <section begin=bugfixes/>
@@ Line 158: / Line 158: @@
 <section end=bugfixes/>
-= Links =
+== Links ==
 <section begin=links/>
@@ Line 170: / Line 170: @@
 <section end=links/>
-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation]

← Older revision		Revision as of 14:11, 22 October 2015
Line 1:		Line 1:
	{{lowercase title}}		{{lowercase title}}
		+
		+	{{infobox relax release
		+	\| version = 1.3.4
		+	\| prev = 1.3.3
		+	\| next = 1.3.5
		+	\| keywords = Bruker ncproc parameter, hybridisation, N-state model, MOLMOL, NOE distance restraints, pseudo-atoms, structure
		+	\| type = Major feature
		+	\| date = 12 August 2009
		+	\| manual = yes
		+	}}

	= Description =		= Description =

@@ Line 166: / Line 166: @@
 = See also =
 {{:relax release see also}}
 [[Category:Frame order analysis]]
 [[Category:Model-free analysis]]
 [[Category:N-state model analysis]]

@@ Line 52: / Line 52: @@
 *  The [http://www.nmr-relax.com/manual/noe_error.html noe.error user function] is now called [http://www.nmr-relax.com/manual/spectrum_baseplane_rmsd.html spectrum.baseplane_rmsd].
 *  The new [http://www.nmr-relax.com/manual/spectrum_integration_points.html spectrum.integration_points user function] is used to specify the number of points used in a volume integration.
-*  The R1 and R2 relaxation time period is now specified using [http://www.nmr-relax.com/manual/relax_fit_relax_time.html relax_fit.relax_time].
+*  The R<sub>1</sub> and R<sub>2</sub> relaxation time period is now specified using [http://www.nmr-relax.com/manual/relax_fit_relax_time.html relax_fit.relax_time].
 *  [http://www.nmr-relax.com/manual/grace_write.html grace.write] will now show a warning when an empty file is being created.
 *  Replicated spectra are now specified explicitly via [http://www.nmr-relax.com/manual/spectrum_replicated.html spectrum.replicated].
@@ Line 62: / Line 62: @@
 *  The RDC and PCS data is now checked before being loaded into relax.
 *  The N-state model grid search now handles alignment tensor parameters.
-*  For better optimisation, the grid search lower bound for alignment tensor elements has changed from 0 to -1e-3.
+*  For better optimisation, the grid search lower bound for alignment tensor elements has changed from 0 to -1e<sup>-3</sup>.
 *  Improvement to the algorithm for determining attached atoms in the internal PDB reader - a 2 rather than 1 Angstrom radius sphere is now being searched.
 *  The [http://www.nmr-relax.com/manual/molecule_name.html molecule.name user function] can now name unnamed molecules.
@@ Line 120: / Line 120: @@
 *  Bug fix for the [http://www.nmr-relax.com/manual/spin_copy.html spin.copy user function], non-empty spin containers are no longer overwritten if the name and num are set to None.
 *  Fix for the latex_mf_table.py sample script ([https://gna.org/bugs/?13163 bug #13163]).
-*  Rex values in XML results file not in s-1 ([https://gna.org/bugs/?13162 bug #13162]).
+*  Rex values in XML results file not in s<sup>-1</sup> ([https://gna.org/bugs/?13162 bug #13162]).
-*  Fix for the [http://www.nmr-relax.com/manual/structure_create_diff_tensor_pdb.html structure.create_diff_tensor_pdb user function] which was creating weird shaped ellipsoid diffusion tensor representations when 'alpha' and 'beta' were unequal ([https://gna.org/bugs/?13032 bug #13032]).
+*  Fix for the [http://www.nmr-relax.com/manual/structure_create_diff_tensor_pdb.html structure.create_diff_tensor_pdb user function] which was creating weird shaped ellipsoid diffusion tensor representations when &alpha; and &beta; were unequal ([https://gna.org/bugs/?13032 bug #13032]).
 *  Sparky assignments such as '004N-H' are now handled.
 *  Fixed a bad apostrophe character causing the 'full_analysis.py' script to fail.

@@ Line 95: / Line 95: @@
 <section begin=bugfixes/>
-*  A bug in the Monte Carlo simulations for relaxation curve-fitting has been fixed (bug #12670).
+*  A bug in the Monte Carlo simulations for relaxation curve-fitting has been fixed ([https://gna.org/bugs/?12670 bug #12670]).
 *  Fixes for the Pymol PDB file opening and pymol.cartoon() user function.
 *  The molecular centre of mass is now correctly calculated.
-*  Grace plots (http://plasma-gate.weizmann.ac.il/Grace/) were sometimes corrupted due to data being stored in numpy arrays and not Python lists (bug #12679).
+*  Grace plots (http://plasma-gate.weizmann.ac.il/Grace/) were sometimes corrupted due to data being stored in numpy arrays and not Python lists ([https://gna.org/bugs/?12679 bug #12679]).
 *  Fix for the value.read() user function, the directory and 'sep' arguments were being ignored.
-*  Multiple failures of structure.load_spins() for different PDB file layouts have been fixed (bug #12735).
+*  Multiple failures of structure.load_spins() for different PDB file layouts have been fixed ([https://gna.org/bugs/?12735 bug #12735]).
-*  Model-free optimisation failures on Mac OS X for PowerPC (bug #12573).
+*  Model-free optimisation failures on Mac OS X for PowerPC ([https://gna.org/bugs/?12573 bug #12573]).
 *  Many PDB file reading fixes for different multi-molecule/multi-model formats.
 *  The '-' character is now allowed in molecule, residue, and spin names (was a bug if the file name contains a '-' character).
@@ Line 119: / Line 119: @@
 *  All the relax_data.*() user functions have now been converted to the relax 1.3 design.
 *  Bug fix for the spin.copy() user function, non-empty spin containers are no longer overwritten if the name and num are set to None.
-*  Fix for the latex_mf_table.py sample script (bug #13163).
+*  Fix for the latex_mf_table.py sample script ([https://gna.org/bugs/?13163 bug #13163]).
-*  Rex values in XML results file not in s-1 (bug #13162).
+*  Rex values in XML results file not in s-1 ([https://gna.org/bugs/?13162 bug #13162]).
-*  Fix for the structure.create_diff_tensor_pdb() user function which was creating weird shaped ellipsoid diffusion tensor representations when 'alpha' and 'beta' were unequal (bug #13032).
+*  Fix for the structure.create_diff_tensor_pdb() user function which was creating weird shaped ellipsoid diffusion tensor representations when 'alpha' and 'beta' were unequal ([https://gna.org/bugs/?13032 bug #13032]).
 *  Sparky assignments such as '004N-H' are now handled.
 *  Fixed a bad apostrophe character causing the 'full_analysis.py' script to fail.
@@ Line 127: / Line 127: @@
 *  Bug fix for the results reading from_xml() method, the molecule name was being evaluated causing results.read() to fail.
 *  Fixes for the model-free Monte Carlo simulation methods for deselected spins.
-*  Models with high te values (>200 ns) were not being eliminated in the full_analysis.py sample script (bug #13259).
+*  Models with high te values (>200 ns) were not being eliminated in the full_analysis.py sample script ([https://gna.org/bugs/?13259 bug #13259]).
-*  Monte Carlo simulations were failing in the model-free.py sample script (bug #13442).
+*  Monte Carlo simulations were failing in the model-free.py sample script ([https://gna.org/bugs/?13442 bug #13442]).
 *  The model-free minimisation statistics are no longer reset by the Monte Carlo simulation setup.
 *  A number of bug fixes for Python 2.6 support.