Difference between revisions of "Relax 1.3.3"

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(Addition of labelled section transclusion tags.)
(Converted Dasha, OpenDX, Modelfree, NMRView, XEasy to be internal links.)
(14 intermediate revisions by the same user not shown)
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{{lowercase title}}
 
{{lowercase title}}
  
= Description =
+
{{infobox relax release
 +
| version  = 1.3.3
 +
| prev    = 1.3.2
 +
| next    = 1.3.4
 +
| keywords = [[DASHA]], [[OpenDX]], [[Modelfree4]], [[NMRView]], [[XEasy]]
 +
| type    = Major feature and bugfix
 +
| date    = 10 December 2013
 +
| manual  = yes
 +
}}
 +
 
 +
== Description ==
  
 
<section begin=description/>
 
<section begin=description/>
This is a major bugfix and feature release.  Support for the programs Dasha, Modelfree and OpenDX has returned and XEasy and NMRView peak lists can now be read.  Upgrading to this version is highly recommended as it fixes a number of very important bugs.  Some of these are include faulty error analysis when performing relaxation curve-fitting, [http://www.nmr-relax.com/manual/results_write.html results.write] failure, model selection failure if spins were deselected, diffusion tensor optimisation failure, and internal PDB reader problems.
+
This is a major bugfix and feature release.  Support for the programs [[Dasha]], [[Modelfree4]] and [[OpenDX]] has returned and [[XEasy]] and [[NMRView]] peak lists can now be read.  Upgrading to this version is highly recommended as it fixes a number of very important bugs.  Some of these are include faulty error analysis when performing relaxation curve-fitting, [http://www.nmr-relax.com/manual/results_write.html results.write] failure, model selection failure if spins were deselected, diffusion tensor optimisation failure, and internal PDB reader problems.
 
<section end=description/>
 
<section end=description/>
  
= Download =
+
== Download ==
  
 
<section begin=download/>
 
<section begin=download/>
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<section end=download/>
 
<section end=download/>
  
= CHANGES file =
+
== CHANGES file ==
  
 
<section begin=metadata/>
 
<section begin=metadata/>
Version 1.3.3
+
Version 1.3.3 <br/>
(29 November 2008, from /1.3)
+
(29 November 2008, from /1.3) <br/>
 
http://svn.gna.org/svn/relax/tags/1.3.3
 
http://svn.gna.org/svn/relax/tags/1.3.3
 
<section end=metadata/>
 
<section end=metadata/>
  
== Features ==
+
=== Features ===
  
 
<section begin=features/>
 
<section begin=features/>
*  Dasha can be run from within relax again.
+
[http://www.nmr-relax.com/manual/dasha_execute.html Dasha can be run] from within relax again.
*  Art Palmer's Modelfree can be run from within relax again.
+
[http://www.nmr-relax.com/manual/palmer_execute.html Art Palmer's Modelfree can be run] from within relax again.
*  OpenDX execution and control is once again supported.
+
[http://www.nmr-relax.com/manual/dx_execute.html OpenDX execution and control] is once again supported.
*  NMRView peak lists are now supported.
+
[http://www.nmr-relax.com/manual/spectrum_read_intensities.html NMRView peak lists] are now supported.
*  XEasy peak lists are again supported.
+
[http://www.nmr-relax.com/manual/spectrum_read_intensities.html XEasy peak lists] are again supported.
 
<section end=features/>
 
<section end=features/>
  
== Changes ==
+
=== Changes ===
  
 
<section begin=changes/>
 
<section begin=changes/>
 
*  Internal relax cleanups by the addition of the specific model_loop() method - this should eliminate a series of potential hidden bugs.
 
*  Internal relax cleanups by the addition of the specific model_loop() method - this should eliminate a series of potential hidden bugs.
*  The results.write() and results.display() now only support XML output.
+
*  The [http://www.nmr-relax.com/manual/results_write.html results.write] and [http://www.nmr-relax.com/manual/results_display.html results.display] now only support XML output.
 
*  More information is now extracted from the Modelfree mfout files.
 
*  More information is now extracted from the Modelfree mfout files.
 
*  The version of the Modelfree program is checked and if it is an old, buggy version, relax will refuse to execute it.
 
*  The version of the Modelfree program is checked and if it is an old, buggy version, relax will refuse to execute it.
Line 42: Line 52:
 
<section end=changes/>
 
<section end=changes/>
  
== Bugfixes ==
+
=== Bugfixes ===
  
 
<section begin=bugfixes/>
 
<section begin=bugfixes/>
 
*  A failure of the minimisation set() function has been fixed.
 
*  A failure of the minimisation set() function has been fixed.
*  The reset() user function now works again.
+
*  The [http://www.nmr-relax.com/manual/reset.html reset user function] now works again.
 
*  Fixes to the relax data store methods add(), to_xml() and from_xml().
 
*  Fixes to the relax data store methods add(), to_xml() and from_xml().
 
*  Many fixes for the support of Art Palmer's Modelfree program.
 
*  Many fixes for the support of Art Palmer's Modelfree program.
 
*  The mapping of the global parameter space (diffusion tensor, etc.) for visualisation in OpenDX has been fixed.
 
*  The mapping of the global parameter space (diffusion tensor, etc.) for visualisation in OpenDX has been fixed.
*  state.save() no longer fails after running state.load() (bug #12437).
+
[http://www.nmr-relax.com/manual/state_save.html state.save] no longer fails after running [http://www.nmr-relax.com/manual/state_load.html state.load] ([https://gna.org/bugs/?12437 bug #12437]).
*  Sparky peak lists with the assignment '?-?' are now handled properly (bug #11913).
+
*  Sparky peak lists with the assignment '?-?' are now handled properly ([https://gna.org/bugs/?11913 bug #11913]).
*  Error analysis in relaxation curve-fitting was incorrectly implemented with standard deviation rather than variance averaging (bug #12456).
+
*  Error analysis in relaxation curve-fitting was incorrectly implemented with standard deviation rather than variance averaging ([https://gna.org/bugs/?12456 bug #12456]).
 
*  A number of fixes for the LaTeX table generating sample script.
 
*  A number of fixes for the LaTeX table generating sample script.
*  Fixes for the teeing and logging via the -l and -t command line arguments (bug #12489).
+
*  Fixes for the teeing and logging via the -l and -t command line arguments ([https://gna.org/bugs/?12489 bug #12489]).
*  Fix for when XH bond vector data from a PDB file is missing for a spin system (bug #12487).
+
*  Fix for when XH bond vector data from a PDB file is missing for a spin system ([https://gna.org/bugs/?12487 bug #12487]).
 
*  Many fixes for when structural data is missing.
 
*  Many fixes for when structural data is missing.
*  The relax script is no longer overwritten if the log or tee file is not specified on the command line (bug #12498).
+
*  The relax script is no longer overwritten if the log or tee file is not specified on the command line ([https://gna.org/bugs/?12498 bug #12498]).
*  Missing RelaxError failure in the sequence handling code (found when trying to solve bug #12582).
+
*  Missing RelaxError failure in the sequence handling code (found when trying to solve [https://gna.org/bugs/?12582 bug #12582]).
*  A failure in the results.write() user function has been fixed (bug #12582).
+
*  A failure in the [http://www.nmr-relax.com/manual/results_write.html results.write user function] has been fixed ([https://gna.org/bugs/?12582 bug #12582]).
 
*  Model selection no longer fails if no model is ever selected.
 
*  Model selection no longer fails if no model is ever selected.
*  Model selection was failing if spins were deselected (bug #12591).
+
*  Model selection was failing if spins were deselected ([https://gna.org/bugs/?12591 bug #12591]).
*  The directory name can now be part of the file name argument to results.read() (bug #12588).
+
*  The directory name can now be part of the file name argument to [http://www.nmr-relax.com/manual/results_read.html results.read] ([https://gna.org/bugs/?12588 bug #12588]).
*  Optimisation of only the diffusion tensor after calling fix() was failing if some spins were deselected (bug #12607).
+
*  Optimisation of only the diffusion tensor after calling [http://www.nmr-relax.com/manual/fix.html fix] was failing if some spins were deselected ([https://gna.org/bugs/?12607 bug #12607]).
*  The internal PDB reader was failing when the PDB file contained CONECT records (bug #12637).
+
*  The internal PDB reader was failing when the PDB file contained CONECT records ([https://gna.org/bugs/?12637 bug #12637]).
 
<section end=bugfixes/>
 
<section end=bugfixes/>
  
= See also =
+
== Links ==
 +
 
 +
<section begin=links/>
 +
For reference, the following links are also part of the announcement for this release:
 +
* [http://wiki.nmr-relax.com/Relax_1.3.3 Official release notes]
 +
* [https://gna.org/forum/forum.php?forum_id=2003 Gna! news item]
 +
* [http://article.gmane.org/gmane.science.nmr.relax.announce/23 Gmane]
 +
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00015.html Mail archive]
 +
* [https://mail.gna.org/public/relax-announce/2008-11/msg00000.html Local archives]
 +
* [http://marc.info/?l=relax-announce&m=135070664625006&w=2 MARC]
 +
<section end=links/>
 +
 
 +
== Announcements ==
 +
{{:relax release announcements}}
 +
 
 +
 
 +
== See also ==
  
[[Category:Release_Notes]]
+
* [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation]
 +
{{:relax release see also}}
 +
[[Category:Model-free analysis]]

Revision as of 15:18, 15 December 2015


Official relax releases
relax logo
relax version 1.3.3
Previous version Next version
← relax 1.3.2 relax 1.3.4 →

Keywords DASHA, OpenDX, Modelfree4, NMRView, XEasy
Release type Major feature and bugfix
Release date 10 December 2013

The PDF version of the relax 1.3.3 user manual The relax 1.3.3 user manual

Description

This is a major bugfix and feature release. Support for the programs Dasha, Modelfree4 and OpenDX has returned and XEasy and NMRView peak lists can now be read. Upgrading to this version is highly recommended as it fixes a number of very important bugs. Some of these are include faulty error analysis when performing relaxation curve-fitting, results.write failure, model selection failure if spins were deselected, diffusion tensor optimisation failure, and internal PDB reader problems.


Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).


CHANGES file

Version 1.3.3
(29 November 2008, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.3


Features


Changes

  • Internal relax cleanups by the addition of the specific model_loop() method - this should eliminate a series of potential hidden bugs.
  • The results.write and results.display now only support XML output.
  • More information is now extracted from the Modelfree mfout files.
  • The version of the Modelfree program is checked and if it is an old, buggy version, relax will refuse to execute it.
  • The system tests can now handle the sometimes large differences in Modelfree results between the GNU gcc and Portland C compiler versions.
  • Fixes and improvements to much of the API documentation.


Bugfixes

  • A failure of the minimisation set() function has been fixed.
  • The reset user function now works again.
  • Fixes to the relax data store methods add(), to_xml() and from_xml().
  • Many fixes for the support of Art Palmer's Modelfree program.
  • The mapping of the global parameter space (diffusion tensor, etc.) for visualisation in OpenDX has been fixed.
  • state.save no longer fails after running state.load (bug #12437).
  • Sparky peak lists with the assignment '?-?' are now handled properly (bug #11913).
  • Error analysis in relaxation curve-fitting was incorrectly implemented with standard deviation rather than variance averaging (bug #12456).
  • A number of fixes for the LaTeX table generating sample script.
  • Fixes for the teeing and logging via the -l and -t command line arguments (bug #12489).
  • Fix for when XH bond vector data from a PDB file is missing for a spin system (bug #12487).
  • Many fixes for when structural data is missing.
  • The relax script is no longer overwritten if the log or tee file is not specified on the command line (bug #12498).
  • Missing RelaxError failure in the sequence handling code (found when trying to solve bug #12582).
  • A failure in the results.write user function has been fixed (bug #12582).
  • Model selection no longer fails if no model is ever selected.
  • Model selection was failing if spins were deselected (bug #12591).
  • The directory name can now be part of the file name argument to results.read (bug #12588).
  • Optimisation of only the diffusion tensor after calling fix was failing if some spins were deselected (bug #12607).
  • The internal PDB reader was failing when the PDB file contained CONECT records (bug #12637).


Links

For reference, the following links are also part of the announcement for this release:


Announcements

If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.


See also