Difference between revisions of "Relax 1.3.2"
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{{lowercase title}} | {{lowercase title}} | ||
| − | = | + | {{infobox relax release |
| + | | version = 1.3.2 | ||
| + | | prev = 1.3.1 | ||
| + | | next = 1.3.3 | ||
| + | | keywords = Model-free analysis, NOE analysis | ||
| + | | type = Major bugfix | ||
| + | | date = 8 October 2008 | ||
| + | | manual = yes | ||
| + | }} | ||
| − | + | == Description == | |
| − | |||
| − | |||
| − | = | + | <section begin=description/> |
| + | This release solves many major bugs in the final stages of model-free analysis, especially when using the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]. This version also marks the return of the NOE analysis. If you are using [[relax 1.3.1|relax version 1.3.1]], it is recommended that you upgrade to [[relax 1.3.2|1.3.2]]. Bugs which have been resolved include: problems reading PDB files; failure of the [http://www.nmr-relax.com/manual/value_set.html value.set], [http://www.nmr-relax.com/manual/fix.html fix] and [http://www.nmr-relax.com/manual/value_write.html value.write] user functions; non-functional [http://www.nmr-relax.com/manual/eliminate.html model elimination]; model selection issues in certain situations; and various Monte Carlo simulation issues. | ||
| + | <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 == | ||
| − | = | + | <section begin=metadata/> |
| − | + | Version 1.3.2 <br/> | |
| − | Version 1.3.2 | + | (8 October 2008, from /1.3) <br/> |
| − | (8 October 2008, from /1.3) | ||
http://svn.gna.org/svn/relax/tags/1.3.2 | http://svn.gna.org/svn/relax/tags/1.3.2 | ||
| + | <section end=metadata/> | ||
| − | == Features == | + | === Features === |
| + | <section begin=features/> | ||
* The NOE analysis has been converted to the new design and is fully functional again. | * The NOE analysis has been converted to the new design and is fully functional again. | ||
| + | <section end=features/> | ||
| − | == Changes == | + | === Changes === |
| + | <section begin=changes/> | ||
* Internal abstractions to the relax data store by using the generic_fns.pipes API. | * Internal abstractions to the relax data store by using the generic_fns.pipes API. | ||
* Added more literature references to the 'full_analysis.py' script. | * Added more literature references to the 'full_analysis.py' script. | ||
* Eliminated Monte Carlo simulations are better identified during user function execution. | * Eliminated Monte Carlo simulations are better identified during user function execution. | ||
| + | <section end=changes/> | ||
| − | == Bugfixes == | + | === Bugfixes === |
| + | <section begin=bugfixes/> | ||
* The generation of the cone geometric object for the N-state model is fixed. | * The generation of the cone geometric object for the N-state model is fixed. | ||
* Fixes for the relax_curve_diff.py and latex_mf_table.py sample scripts (identified by the relax data store abstraction). | * Fixes for the relax_curve_diff.py and latex_mf_table.py sample scripts (identified by the relax data store abstraction). | ||
* Fixed the reading of relax 1.2 model-free results files (identified by the relax data store abstraction). | * Fixed the reading of relax 1.2 model-free results files (identified by the relax data store abstraction). | ||
* Various PDB file loading issues fixed. | * Various PDB file loading issues fixed. | ||
| − | * value.set | + | * [http://www.nmr-relax.com/manual/value_set.html value.set] no longer fails when the parameter being set already exists ({{gna bug link|12406}}). |
| − | * Fix for the bug whereby model elimination does nothing for model-free models. This fix may solve other model-free related issues (bug | + | * Fix for the bug whereby model elimination does nothing for model-free models. This fix may solve other model-free related issues ({{gna bug link|12407}}). |
| − | * Model elimination no longer fails when no diffusion tensor is loaded (bug | + | * Model elimination no longer fails when no diffusion tensor is loaded ({{gna bug link|12408}}). |
| − | * The error when loading the PDB file through the reading of the results file in the 'final' stage of the 'full_analysis.py' sample script is fixed (bug | + | * The error when loading the PDB file through the reading of the results file in the 'final' stage of the 'full_analysis.py' sample script is fixed ({{gna bug link|12409}}). |
* Model elimination is fixed in the 'full_analysis.py' script. | * Model elimination is fixed in the 'full_analysis.py' script. | ||
| − | * The fix | + | * The [http://www.nmr-relax.com/manual/fix.html fix user function] works again when the element argument is set to 'all'. |
* Fix for the duplication of sequence data during model selection. | * Fix for the duplication of sequence data during model selection. | ||
| − | * Monte Carlo simulations were failing due to a missing sequence error (bug | + | * Monte Carlo simulations were failing due to a missing sequence error ({{gna bug link|12410}}). |
| − | * The model elimination error "AttributeError: 'SpinContainer' object has no attribute 'params'." has been fixed (bug | + | * The model elimination error "AttributeError: 'SpinContainer' object has no attribute 'params'." has been fixed ({{gna bug link|12411}}). |
| − | * A missing global chi-squared value was causing failure of global model selection (bug | + | * A missing global chi-squared value was causing failure of global model selection ({{gna bug link|12412}}). |
| − | * Monte Carlo simulation elimination was removing the simulation not from the affected spin but from all spins (bug | + | * Monte Carlo simulation elimination was removing the simulation not from the affected spin but from all spins ({{gna bug link|12416}}). |
| − | * Fix for the failure of the value.write | + | * Fix for the failure of the [http://www.nmr-relax.com/manual/value_write.html value.write user function] in all analysis types ({{gna bug link|12418}}). |
| + | <section end=bugfixes/> | ||
| + | |||
| + | == Links == | ||
| + | |||
| + | <section begin=links/> | ||
| + | For reference, the following links are also part of the announcement for this release: | ||
| + | * [http://wiki.nmr-relax.com/Relax_1.3.2 Official release notes] | ||
| + | * {{gna link|url=gna.org/forum/forum.php?forum_id=1973|text=Gna! news item}} | ||
| + | * [http://article.gmane.org/gmane.science.nmr.relax.announce/22 Gmane] | ||
| + | * [http://www.mail-archive.com/relax-announce%40gna.org/msg00014.html Mail archive] | ||
| + | * [https://mail.gna.org/public/relax-announce/2008-10/msg00000.html Local archives] | ||
| + | * [http://marc.info/?l=relax-announce&m=135070664625005&w=2 MARC] | ||
| + | <section end=links/> | ||
| + | == Announcements == | ||
| + | {{:relax release announcements}} | ||
| − | |||
| − | * [*d'Auvergne and Gooley, | + | == References == |
| + | |||
| + | * [*d'Auvergne and Gooley, 2007] {{#lst:Citations|dAuvergneGooley07}} | ||
| + | * [*d'Auvergne and Gooley, 2008b] {{#lst:Citations|dAuvergneGooley08b}} | ||
<HarvardReferences /> | <HarvardReferences /> | ||
| + | == See also == | ||
| − | + | * [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation] | |
| − | + | {{:relax release see also}} | |
| − | [[Category: | + | [[Category:Model-free analysis]] |
Latest revision as of 12:49, 14 October 2020
 | |||||
| relax version 1.3.2 | |||||
| |||||
| Keywords | Model-free analysis, NOE analysis | ||||
|---|---|---|---|---|---|
| Release type | Major bugfix | ||||
| Release date | 8 October 2008 | ||||
|
| |||||
 The relax 1.3.2 user manual | |||||
Contents
Description
This release solves many major bugs in the final stages of model-free analysis, especially when using the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]. This version also marks the return of the NOE analysis. If you are using relax version 1.3.1, it is recommended that you upgrade to 1.3.2. Bugs which have been resolved include: problems reading PDB files; failure of the value.set, fix and value.write user functions; non-functional model elimination; model selection issues in certain situations; and various Monte Carlo simulation issues.
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 1.3.2
(8 October 2008, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.2
Features
- The NOE analysis has been converted to the new design and is fully functional again.
Changes
- Internal abstractions to the relax data store by using the generic_fns.pipes API.
- Added more literature references to the 'full_analysis.py' script.
- Eliminated Monte Carlo simulations are better identified during user function execution.
Bugfixes
- The generation of the cone geometric object for the N-state model is fixed.
- Fixes for the relax_curve_diff.py and latex_mf_table.py sample scripts (identified by the relax data store abstraction).
- Fixed the reading of relax 1.2 model-free results files (identified by the relax data store abstraction).
- Various PDB file loading issues fixed.
- value.set no longer fails when the parameter being set already exists (Bug #12406).
- Fix for the bug whereby model elimination does nothing for model-free models. This fix may solve other model-free related issues (Bug #12407).
- Model elimination no longer fails when no diffusion tensor is loaded (Bug #12408).
- The error when loading the PDB file through the reading of the results file in the 'final' stage of the 'full_analysis.py' sample script is fixed (Bug #12409).
- Model elimination is fixed in the 'full_analysis.py' script.
- The fix user function works again when the element argument is set to 'all'.
- Fix for the duplication of sequence data during model selection.
- Monte Carlo simulations were failing due to a missing sequence error (Bug #12410).
- The model elimination error "AttributeError: 'SpinContainer' object has no attribute 'params'." has been fixed (Bug #12411).
- A missing global chi-squared value was causing failure of global model selection (Bug #12412).
- Monte Carlo simulation elimination was removing the simulation not from the affected spin but from all spins (Bug #12416).
- Fix for the failure of the value.write user function in all analysis types (Bug #12418).
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
- The combined release notes for all relax versions (warning, this is very large).
- The combined release descriptions for all relax versions.
- The combined release metadata for all relax versions.
- The combined release features for all relax versions.
- The combined release changes for all relax versions (warning, this is very large).
- The combined release bugfixes for all relax versions.
- The combined release announcement links for all relax versions.
