Difference between revisions of "Relax 1.2.11"

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{{lowercase title}}
 
{{lowercase title}}
  
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= Description =
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{{infobox relax release
 +
| version  = 1.2.11
 +
| prev    = 1.2.10
 +
| next    = 1.2.12
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| keywords = Reduced spectral density mapping
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| type    = Major bugfix
 +
| date    = 21 October 2007
 +
| manual  = no
 +
}}
 +
 
 +
== Description ==
  
 
<section begin=description/>
 
<section begin=description/>
−
This is another major bug fix release.  Please upgrade to this version if you wish to use relax for reduced spectral density mapping as significant bugs in that part of relax have been identified and fixed.  Other significant changes include this being the only version of relax which will run with Python 2.5, the addition of [http://www.nmr-relax.com/manual/grace_write.html Grace plotting abilities] improving the analysis of relaxation exponential curve-fitting, large simplifications for the user and automatic looping over iterations in the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008], and improvements to the reading and writing of model-free results files.  See below for additional improvements.
+
This is another major bug fix release.  Please upgrade to this version if you wish to use relax for reduced spectral density mapping as significant bugs in that part of relax have been identified and fixed.  Other significant changes include this being the only version of relax which will run with Python 2.5, the addition of [http://www.nmr-relax.com/manual/grace_write.html Grace plotting abilities] improving the analysis of relaxation exponential curve-fitting, large simplifications for the user and automatic looping over iterations in the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b], and improvements to the reading and writing of model-free results files.  See below for additional improvements.
 
<section end=description/>
 
<section end=description/>
  
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= Download =
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== Download ==
  
 
<section begin=download/>
 
<section begin=download/>
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<section end=download/>
 
<section end=download/>
  
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= CHANGES file =
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== CHANGES file ==
  
 
<section begin=metadata/>
 
<section begin=metadata/>
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<section end=metadata/>
 
<section end=metadata/>
  
−
== Features ==
+
=== Features ===
  
 
<section begin=features/>
 
<section begin=features/>
 
*  The Grace plotting abilities have been extended, especially concerning relaxation exponential curve-fitting.
 
*  The Grace plotting abilities have been extended, especially concerning relaxation exponential curve-fitting.
 
*  A sample script has been added to plot the difference between the measured and back calculated peak intensities.
 
*  A sample script has been added to plot the difference between the measured and back calculated peak intensities.
−
*  Automatic looping over iterations in the 'full_analysis.py' sample script is now possible.
+
*  Automatic looping over iterations in the 'full_analysis.py' sample script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] is now possible.
 
<section end=features/>
 
<section end=features/>
  
−
== Changes ==
+
=== Changes ===
  
 
<section begin=changes/>
 
<section begin=changes/>
−
*  The 'full_analysis.py' sample script has been significantly improved with all user modifiable options shifted to the top of the script.
+
*  The 'full_analysis.py' sample script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] has been significantly improved with all user modifiable options shifted to the top of the script.
 
*  The default CSA value is now -172 ppm.
 
*  The default CSA value is now -172 ppm.
 
<section end=changes/>
 
<section end=changes/>
  
−
== Bugfixes ==
+
=== Bugfixes ===
  
 
<section begin=bugfixes/>
 
<section begin=bugfixes/>
−
*  The previous release had problems reading results files from relax versions 1.2.0 to 1.2.9, but now results files from all versions can be read (see bug #8248).
+
*  The previous release had problems reading results files from relax versions [[relax 1.2.0|1.2.0]] to [[relax 1.2.9|1.2.9]], but now results files from all versions can be read ({{gna bug link|8248|text=see bug #8248}}).
−
*  The synopsis of the system/functional tests now says '[ Failed ]' if one the tests fails (see bug #8682).
+
*  The synopsis of the system/functional tests now says '''[ Failed ]''' if one the tests fails ({{gna bug link|8682 see bug #8682]).
−
*  relax now works with Python 2.5 (see bug #9093).
+
*  relax now works with Python 2.5 ({{gna bug link|9093|text=see bug #9093}}).
−
*  The writing of the model-free results file, which failed under certain circumstances because of the 'heteronuc' and 'proton' attributes, has been fixed (see bug #8996).
+
*  The writing of the model-free results file, which failed under certain circumstances because of the 'heteronuc' and 'proton' attributes, has been fixed ({{gna bug link|8996|text=see bug #8996}}).
−
*  The problem whereby there is data loss for deselected residues when using 'results.write()' followed by 'results.read()' has been resolved (see bug #8953).
+
*  The problem whereby there is data loss for deselected residues when using [http://www.nmr-relax.com/manual/results_write.html results.write] followed by [http://www.nmr-relax.com/manual/results_read.html results.read] has been resolved ({{gna bug link|8953|text=see bug #8953}}).
−
*  Relaxation data can now be read if deselected spin systems have a relaxation data value or error value set to 'None' (see bug #9101).
+
*  Relaxation data can now be read if deselected spin systems have a relaxation data value or error value set to 'None' ([https://gna.org/bugs/?9101|text=see bug #9101}}).
−
*  The fatal bug of the reduced spectral density mapping values being incorrectly calculated has been fixed (see bug #9238).
+
*  The fatal bug of the reduced spectral density mapping values being incorrectly calculated has been fixed ({{gna bug link|9238|text=see bug #9238}}).
−
*  When using the alternate model-free parameter set {S2f, tf, S2s, ts}, the incorrect functions were being called (see bug #9189).
+
*  When using the alternate model-free parameter set {S<sub>f</sub><sup>2</sup>, &tau;<sub>f</sub>, S<sub>s</sub><sup>2</sup>, &tau;<sub>s</sub>}, the incorrect functions were being called ({{gna bug link|9189|text=see bug #9189}}).
−
*  A second fatal problem in the reduced spectral density mapping code, the heteronuclear frequency being overwritten by that of the proton, has been fixed (see bug #9259).
+
*  A second fatal problem in the reduced spectral density mapping code, the heteronuclear frequency being overwritten by that of the proton, has been fixed ({{gna bug link|9259|text=see bug #9259}}).
−
*  Another problem with relax and Python 2.5, because of the Scientific package, has been resolved (see bug #9390).
+
*  Another problem with relax and Python 2.5, because of the Scientific package, has been resolved ({{gna bug link|9390|text=see bug #9390}}).
−
*  The XH bond length is now correctly set in the reduced spectral density mapping analysis (see bug #9562).
+
*  The XH bond length is now correctly set in the reduced spectral density mapping analysis ({{gna bug link|9562|text=see bug #9562}}).
−
*  The convergence test in the 'full_analysis.py' sample script was failing if spin systems were deselected (see bug #9892 and bug #10022).
+
*  The convergence test in the 'full_analysis.py' sample script was failing if spin systems were deselected (see {{gna bug link|9892}} and {{gna bug link|10022}}).
 
<section end=bugfixes/>
 
<section end=bugfixes/>
  
−
= Announcements =
+
== Links ==
 +
 
 +
<section begin=links/>
 +
For reference, the following links are also part of the announcement for this release:
 +
* [http://wiki.nmr-relax.com/Relax_1.2.11 Official release notes]
 +
* {{gna link|url=gna.org/forum/forum.php?forum_id=1736|text=Gna! news item}}
 +
* [http://article.gmane.org/gmane.science.nmr.relax.announce/17 Gmane]
 +
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00009.html Mail archive]
 +
* [https://mail.gna.org/public/relax-announce/2007-10/msg00000.html Local archives]
 +
* [http://marc.info/?l=relax-announce&m=135070664525000&w=2 MARC]
 +
<section end=links/>
 +
 
 +
== Announcements ==
 
{{:relax release announcements}}
 
{{:relax release announcements}}
  
  
−
= References =
+
== 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}}
−
* [*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]).
 
−
<section end=references/>
 
 
<HarvardReferences />
 
<HarvardReferences />
  
−
= See also =
+
== See also ==
  
 +
* [http://www.nmr-relax.com/api/1.2/ The relax 1.2 API documentation]
 
{{:relax release see also}}
 
{{:relax release see also}}
−
[[Category:Model-free]]
+
[[Category:Model-free analysis]]

Latest revision as of 22:04, 13 October 2020


Official relax releases
relax logo
relax version 1.2.11
Previous version Next version
← relax 1.2.10 relax 1.2.12 →
Keywords Reduced spectral density mapping
Release type Major bugfix
Release date 21 October 2007

Description

This is another major bug fix release. Please upgrade to this version if you wish to use relax for reduced spectral density mapping as significant bugs in that part of relax have been identified and fixed. Other significant changes include this being the only version of relax which will run with Python 2.5, the addition of Grace plotting abilities improving the analysis of relaxation exponential curve-fitting, large simplifications for the user and automatic looping over iterations in the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b], and improvements to the reading and writing of model-free results files. See below for additional improvements.


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 1.2.11
(21 October 2007, from /1.2)
http://svn.gna.org/svn/relax/tags/1.2.11


Features

  • The Grace plotting abilities have been extended, especially concerning relaxation exponential curve-fitting.
  • A sample script has been added to plot the difference between the measured and back calculated peak intensities.
  • Automatic looping over iterations in the 'full_analysis.py' sample script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] is now possible.


Changes

  • The 'full_analysis.py' sample script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] has been significantly improved with all user modifiable options shifted to the top of the script.
  • The default CSA value is now -172 ppm.


Bugfixes

  • The previous release had problems reading results files from relax versions 1.2.0 to 1.2.9, but now results files from all versions can be read (see bug #8248).
  • The synopsis of the system/functional tests now says [ Failed ] if one the tests fails (see bug #8682).
  • relax now works with Python 2.5 (see bug #9093).
  • The writing of the model-free results file, which failed under certain circumstances because of the 'heteronuc' and 'proton' attributes, has been fixed (see bug #8996).
  • The problem whereby there is data loss for deselected residues when using results.write followed by results.read has been resolved (see bug #8953).
  • Relaxation data can now be read if deselected spin systems have a relaxation data value or error value set to 'None' (see bug #9101).
  • The fatal bug of the reduced spectral density mapping values being incorrectly calculated has been fixed (see bug #9238).
  • When using the alternate model-free parameter set {Sf2, τf, Ss2, τs}, the incorrect functions were being called (see bug #9189).
  • A second fatal problem in the reduced spectral density mapping code, the heteronuclear frequency being overwritten by that of the proton, has been fixed (see bug #9259).
  • Another problem with relax and Python 2.5, because of the Scientific package, has been resolved (see bug #9390).
  • The XH bond length is now correctly set in the reduced spectral density mapping analysis (see bug #9562).
  • The convergence test in the 'full_analysis.py' sample script was failing if spin systems were deselected (see Bug #9892 and Bug #10022).


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)

<HarvardReferences />

See also


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