Difference between revisions of "Relax 1.2.13"

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m (→‎Links: Fix the broken Gna! forum link by switching to {{gna link}}.)
 
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{{lowercase title}}
 
{{lowercase title}}
  
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= Description =
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{{infobox relax release
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| version  = 1.2.13
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| prev    = 1.2.12
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| next    = 1.2.14
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| keywords = Consistency testing of relaxation data
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| type    = Features and major bugfix
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| date    = 19 April 2008
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| manual  = no
 +
}}
  
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<onlyinclude>
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== Description ==
−
This release introduces new features and fixes a number of important bugs.  The most significant feature is the consistency testing of relaxation data from different field strengths using the J(0), F_eta and F_R2 values [Morin and Gagne, 2009][Fushman et al., 1998].  Important bugs which have been fixed include the failure of Monte Carlo simulations when model-free model 'm0' is encountered causing the parameter errors for all subsequent residues to be zero, the failure of reading of Art Palmer's Modelfree 4 'mfout' file, and the handling of missing structural data.  For a full description of the additions and fixes, please see below.
 
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</onlyinclude>
 
  
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= Download =
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<section begin=description/>
 +
This release introduces new features and fixes a number of important bugs.  The most significant feature is the [http://www.nmr-relax.com/manual/Consistency_testing.html consistency testing of relaxation data from different field strengths] using the J(0), F<sub>&eta;</sub> and F<sub>R<sub>2</sub></sub> values [Morin and Gagné, 2009][Fushman et al., 1998].  Important bugs which have been fixed include the failure of Monte Carlo simulations when model-free model [[m0]] is encountered causing the parameter errors for all subsequent residues to be zero, the failure of reading of Art Palmer's [[Modelfree4]] 'mfout' file, and the handling of missing structural data.  For a full description of the additions and fixes, please see below.
 +
<section end=description/>
  
 +
== Download ==
 +
 +
<section begin=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).  
 
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).  
 +
<section end=download/>
  
 +
== CHANGES file ==
  
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= CHANGES file =
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<section begin=metadata/>
−
 
+
Version 1.2.13 <br/>
−
Version 1.2.13
+
(19 April 2008, from /1.2) <br/>
−
(19 April 2008, from /1.2)
 
 
http://svn.gna.org/svn/relax/tags/1.2.13
 
http://svn.gna.org/svn/relax/tags/1.2.13
 +
<section end=metadata/>
  
−
== Features ==
+
=== Features ===
−
 
 
−
*  Consistency testing has been added allowing datasets recorded at different magnetic fields to be checked using the consistency function values J(0), Feta, and FR2.
 
−
*  The 'full_analysis.py' script [d'Auvergne and Gooley, 2008] can now perform a model-free analysis in the absence of structural data.
 
  
 +
<section begin=features/>
 +
*  [http://www.nmr-relax.com/manual/Consistency_testing.html Consistency testing] has been added allowing datasets recorded at different magnetic fields to be checked using the consistency function values J(0), F<sub>&eta;</sub> and F<sub>R<sub>2</sub></sub>.
 +
*  The 'full_analysis.py' script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] can now perform a model-free analysis in the absence of structural data.
 +
<section end=features/>
  
−
== Changes ==
+
=== Changes ===
  
 +
<section begin=changes/>
 
*  Better support for MS Windows Vista in the scons build system and the relax introduction.
 
*  Better support for MS Windows Vista in the scons build system and the relax introduction.
 
*  A file listing the unresolved residues is no longer necessary for running the 'full_analysis.py' script.
 
*  A file listing the unresolved residues is no longer necessary for running the 'full_analysis.py' script.
 
*  A few small documentation additions and fixes.
 
*  A few small documentation additions and fixes.
 +
<section end=changes/>
  
 +
=== Bugfixes ===
  
−
== Bugfixes ==
+
<section begin=bugfixes/>
−
 
+
*  The parameters D<sub>&#8741;</sub> and D<sub>&#8869;</sub> are now properly checked upon initialisation of this spheroidal diffusion tensor.
−
*  The parameters Dpar and Dper are now properly checked upon initialisation of this spheroidal diffusion tensor.
 
 
*  Initialisation of an empty diffusion tensor to the default values of zero now works.
 
*  Initialisation of an empty diffusion tensor to the default values of zero now works.
−
*  The default value of the Iinf relaxation curve fitting parameter can now be set.
+
*  The default value of the I<sub>&infin;</sub> relaxation curve fitting parameter can now be set.
−
*  Fix for the complete failure of the reading in of Art Palmer's Modelfree 4 'mfout' results file (see bug #8997).
+
*  Fix for the complete failure of the reading in of Art Palmer's [[Modelfree4]] 'mfout' results file ([https://gna.org/bugs/?8997 see bug #8997]).
−
*  Fix for a rare ZeroDivisionError during Monte Carlo simulations (see bug #11004).
+
*  Fix for a rare ZeroDivisionError during Monte Carlo simulations ([https://gna.org/bugs/?11004 see bug #11004]).
−
*  relax no longer fails if XH bond vectors cannot be extracted from a PDB file (see bug #11378).
+
*  relax no longer fails if XH bond vectors cannot be extracted from a PDB file ([https://gna.org/bugs/?11378 see bug #11378]).
−
*  The relax_data.display() user function no longer fails (see bug #11383).
+
*  The [http://www.nmr-relax.com/manual/relax_data_display.html relax_data.display user function] no longer fails ([https://gna.org/bugs/?11383 see bug #11383]).
−
*  The selection of model-free model 'm0' causes Monte Carlo simulations to fail resulting in zero errors from that residue onwards (see bug #11476).
+
*  The selection of model-free model [[m0]] causes Monte Carlo simulations to fail resulting in zero errors from that residue onwards ([https://gna.org/bugs/?11476 see bug #11476]).
−
*  Another column fusion bug in Modelfree 4's 'mfout' results file can be handled (see bug #11483).
+
*  Another column fusion bug in [[Modelfree4]]'s 'mfout' results file can be handled ([https://gna.org/bugs/?11483 see bug #11483]).
 
*  Optimisation fix - the steady-state NOE value, gradient, and Hessian is now properly calculated when an order parameter of exactly 0.0 is encountered.
 
*  Optimisation fix - the steady-state NOE value, gradient, and Hessian is now properly calculated when an order parameter of exactly 0.0 is encountered.
 +
<section end=bugfixes/>
  
 +
== Links ==
  
−
= References =
+
<section begin=links/>
 +
For reference, the following links are also part of the announcement for this release:
 +
* [http://wiki.nmr-relax.com/Relax_1.2.13 Official release notes]
 +
* {{gna link|url=gna.org/forum/forum.php?forum_id=1872|text=Gna! news item}}
 +
* [http://article.gmane.org/gmane.science.nmr.relax.announce/19 Gmane]
 +
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00011.html Mail archive]
 +
* [https://mail.gna.org/public/relax-announce/2008-04/msg00000.html Local archives]
 +
* [http://marc.info/?l=relax-announce&m=135070664625002&w=2 MARC]
 +
<section end=links/>
  
−
* [*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]).
+
== Announcements ==
−
* [*Fushman et al., 1998] Fushman, D., Tjandra, N., and Cowburn, D. (1998).  Direct measurement of 15N chemical shift anisotropy in solution.  ''J. Am. Chem. Soc.'', '''120'''(42), 10947-10952. (DOI: [http://dx.doi.org/10.1021/ja981686m 10.1021/ja981686m]).
+
{{:relax release announcements}}
−
* [*Morin and Gange, 2009] Morin, S. and Gagné, S. (2009).  Simple tests for the validation of multiple field spin relaxation data.  ''J. Biomol. NMR'', '''45''', 361-372. (DOI: [http://dx.doi.org/10.1007/s10858-009-9381-4 10.1007/s10858-009-9381-4]).
 
  
 +
 +
== References ==
 +
 +
* [*d'Auvergne and Gooley, 2007] {{#lst:Citations|dAuvergneGooley07}}
 +
* [*d'Auvergne and Gooley, 2008b] {{#lst:Citations|dAuvergneGooley08b}}
 +
* [*Fushman et al., 1998] {{#lst:Citations|Fushman98}}
 +
* [*Morin and Gagné, 2009] {{#lst:Citations|MorinGagné09}}
 
<HarvardReferences />
 
<HarvardReferences />
  
 +
== See also ==
  
−
= See also =
+
* [http://www.nmr-relax.com/api/1.2/ The relax 1.2 API documentation]
−
 
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{{:relax release see also}}
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[[Category:Release_Notes]]
+
[[Category:Consistency testing analysis]]
 +
[[Category:Model-free analysis]]

Latest revision as of 22:08, 13 October 2020


Official relax releases
relax logo
relax version 1.2.13
Previous version Next version
← relax 1.2.12 relax 1.2.14 →
Keywords Consistency testing of relaxation data
Release type Features and major bugfix
Release date 19 April 2008

Description

This release introduces new features and fixes a number of important bugs. The most significant feature is the consistency testing of relaxation data from different field strengths using the J(0), Fη and FR2 values [Morin and Gagné, 2009][Fushman et al., 1998]. Important bugs which have been fixed include the failure of Monte Carlo simulations when model-free model m0 is encountered causing the parameter errors for all subsequent residues to be zero, the failure of reading of Art Palmer's Modelfree4 'mfout' file, and the handling of missing structural data. For a full description of the additions and fixes, please see below.


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 1.2.13
(19 April 2008, from /1.2)
http://svn.gna.org/svn/relax/tags/1.2.13


Features

  • Consistency testing has been added allowing datasets recorded at different magnetic fields to be checked using the consistency function values J(0), Fη and FR2.
  • The 'full_analysis.py' script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] can now perform a model-free analysis in the absence of structural data.


Changes

  • Better support for MS Windows Vista in the scons build system and the relax introduction.
  • A file listing the unresolved residues is no longer necessary for running the 'full_analysis.py' script.
  • A few small documentation additions and fixes.


Bugfixes

  • The parameters D∥ and D⊥ are now properly checked upon initialisation of this spheroidal diffusion tensor.
  • Initialisation of an empty diffusion tensor to the default values of zero now works.
  • The default value of the I∞ relaxation curve fitting parameter can now be set.
  • Fix for the complete failure of the reading in of Art Palmer's Modelfree4 'mfout' results file (see bug #8997).
  • Fix for a rare ZeroDivisionError during Monte Carlo simulations (see bug #11004).
  • relax no longer fails if XH bond vectors cannot be extracted from a PDB file (see bug #11378).
  • The relax_data.display user function no longer fails (see bug #11383).
  • The selection of model-free model m0 causes Monte Carlo simulations to fail resulting in zero errors from that residue onwards (see bug #11476).
  • Another column fusion bug in Modelfree4's 'mfout' results file can be handled (see bug #11483).
  • Optimisation fix - the steady-state NOE value, gradient, and Hessian is now properly calculated when an order parameter of exactly 0.0 is encountered.


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.


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: 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: 10.1007/s10858-007-9213-3)
  • [*Fushman et al., 1998] Fushman, D., Tjandra, N., and Cowburn, D. (1998). Direct measurement of 15N chemical shift anisotropy in solution. J. Am. Chem. Soc., 120(42), 10947-10952. (DOI: 10.1021/ja981686m)
  • [*Morin and Gagné, 2009] Morin, S. and Gagné, S. (2009). Simple tests for the validation of multiple field spin relaxation data. J. Biomol. NMR, 45, 361-372. (DOI: 10.1007/s10858-009-9381-4)

<HarvardReferences />

See also


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