Difference between revisions of "Relax 1.2.10"
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{{lowercase title}} | {{lowercase title}} | ||
| − | = Description = | + | {{infobox relax release |
| + | | version = 1.2.10 | ||
| + | | prev = 1.2.9 | ||
| + | | next = 1.2.11 | ||
| + | | keywords = Model-free automated protocol | ||
| + | | type = Minor bugfix | ||
| + | | date = 12 January 2007 | ||
| + | | manual = no | ||
| + | }} | ||
| + | |||
| + | == Description == | ||
<section begin=description/> | <section begin=description/> | ||
| − | This is a major bug fix release which includes a number of feature enhancements. Significant changes include the addition of convergence tests to the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, | + | This is a major bug fix release which includes a number of feature enhancements. Significant changes include the addition of convergence tests to the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b], the ability to compile the [[C|C modules]] on Mac OS X, more advanced spin system selection, the model-free and reduced spectral density mapping results files no longer being truncated, and improvements to the [http://www.nmr-relax.com/manual/Model_free_analysis.html model-free section of the user manual] by the addition of flow diagrams detailing the steps of different model-free analysis protocols. Significant bugfixes include more flexibility in the reading of XEasy text files, a number of fixes in the 'full_analysis.py' sample script, the proper setup of Monte Carlo simulation when reading results files, and a couple of MS Windows fixes. More details and additional features, changes, and bugfixes are detailed below. |
<section end=description/> | <section end=description/> | ||
| − | = Download = | + | == Download == |
<section begin=download/> | <section begin=download/> | ||
| Line 13: | Line 23: | ||
<section end=download/> | <section end=download/> | ||
| − | = CHANGES file = | + | == CHANGES file == |
<section begin=metadata/> | <section begin=metadata/> | ||
| − | Version 1.2.10 | + | Version 1.2.10 <br/> |
| − | (12 January 2007, from /1.2) | + | (12 January 2007, from /1.2) <br/> |
http://svn.gna.org/svn/relax/tags/1.2.10 | http://svn.gna.org/svn/relax/tags/1.2.10 | ||
<section end=metadata/> | <section end=metadata/> | ||
| − | == Features == | + | === Features === |
<section begin=features/> | <section begin=features/> | ||
| − | * Addition of tests to the 'full_analysis.py' script for the identification of convergence [d'Auvergne and Gooley, | + | * Addition of tests to the 'full_analysis.py' script for the identification of convergence [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b]. |
* Different columns can be specified for the residue number in the [http://www.nmr-relax.com/manual/select_read.html select.read] and [http://www.nmr-relax.com/manual/deselect_read.html unselect.read] user functions. | * Different columns can be specified for the residue number in the [http://www.nmr-relax.com/manual/select_read.html select.read] and [http://www.nmr-relax.com/manual/deselect_read.html unselect.read] user functions. | ||
* More advanced selection of spin systems or residues is possible through the use of the Boolean operators 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. | * More advanced selection of spin systems or residues is possible through the use of the Boolean operators 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. | ||
* Addition of a sample script for the creation a LaTeX longtable of the model-free results. | * Addition of a sample script for the creation a LaTeX longtable of the model-free results. | ||
| − | * The rows of the model-free and reduced spectral density results files are no longer truncated for deselected spin systems, hence all data is now stored in the results file. (see bug #8059) | + | * The rows of the model-free and reduced spectral density results files are no longer truncated for deselected spin systems, hence all data is now stored in the results file. ([https://gna.org/bugs/?8059 see bug #8059]) |
<section end=features/> | <section end=features/> | ||
| − | == Changes == | + | === Changes === |
<section begin=changes/> | <section begin=changes/> | ||
| − | * The relax core design diagram in the development chapter of the manual has been updated. | + | * The [http://www.nmr-relax.com/manual/The_divisions_of_relax_s_source_code.html relax core design diagram in the development chapter of the manual] has been updated. |
* Three flow diagrams have been added to the relax manual detailing the steps of different model-free analysis protocols. | * Three flow diagrams have been added to the relax manual detailing the steps of different model-free analysis protocols. | ||
| − | * Spin systems are now identified when deselected by the | + | * Spin systems are now identified when deselected by the [http://www.nmr-relax.com/manual/eliminate.html eliminate user function]. |
* The model-free Molmol cutoff for fast and slow motions has been changed from 100 to 200 ps. | * The model-free Molmol cutoff for fast and slow motions has been changed from 100 to 200 ps. | ||
| − | * For the clarification of bug #8059 a RelaxNoTensorError is raised instead of returning None when no diffusion tensor data is present. | + | * For the clarification of [https://gna.org/bugs/?8059 bug #8059] a [http://www.nmr-relax.com/api/1.2/errors.RelaxErrors.RelaxNoTensorError-class.html RelaxNoTensorError] is raised instead of returning None when no diffusion tensor data is present. |
| − | * The Scons target 'source_dist' now creates and GPG signs both the 'tar.bz2' and 'zip' source distribution packages. (see task #4087) | + | * The Scons target 'source_dist' now creates and GPG signs both the 'tar.bz2' and 'zip' source distribution packages. ({{gna task link|4087|text=see task #4087}}) |
<section end=changes/> | <section end=changes/> | ||
| − | == Bugfixes == | + | === Bugfixes === |
<section begin=bugfixes/> | <section begin=bugfixes/> | ||
| − | * The C modules can now be compiled on Mac OS X. (see bug #7670) | + | * The [[C|C modules]] can now be compiled on Mac OS X. ([https://gna.org/bugs/?7670 see bug #7670]) |
| − | * The order of the proton and heteronucleus dimensions and number of header lines in the XEasy text file is now automatically detected. (see bug #7676) | + | * The order of the proton and heteronucleus dimensions and number of header lines in the XEasy text file is now automatically detected. ([https://gna.org/bugs/?7676 see bug #7676]) |
| − | * The 'full_analysis.py' script now throws a RelaxError if only one round of optimisation of the global model has been executed. (see bug #7787) | + | * The 'full_analysis.py' script now throws a RelaxError if only one round of optimisation of the global model has been executed. ([https://gna.org/bugs/?7787 see bug #7787]) |
| − | * The model selection of the global model in the 'full_analysis.py' script has been fixed. (see bug #7863) | + | * The model selection of the global model in the 'full_analysis.py' script has been fixed. ([https://gna.org/bugs/?7863 see bug #7863]) |
| − | * Monte Carlo simulations no longer fail if the local | + | * Monte Carlo simulations no longer fail if the local τ<sub>m</sub> global model has been selected in the 'full_analysis.py' script. ([https://gna.org/bugs/?7875 see bug #7875]) |
| − | * The Monte Carlo simulation data in the model-free results file is now correctly read back into the program. (see bug #7755) | + | * The Monte Carlo simulation data in the model-free results file is now correctly read back into the program. ([https://gna.org/bugs/?7755 see bug #7755]) |
| − | * The Monte Carlo simulation state used to be turned on after reading a results file containing simulations. (see bug #7890) | + | * The Monte Carlo simulation state used to be turned on after reading a results file containing simulations. ([https://gna.org/bugs/?7890 see bug #7890]) |
| − | * After reading model-free results files, model selection would fail as the heteronucleus and proton data structures did not exist. (see bug #7891) | + | * After reading model-free results files, model selection would fail as the heteronucleus and proton data structures did not exist. ([https://gna.org/bugs/?7891 see bug #7891]) |
| − | * The model-free Molmol fast correlation time macro ( | + | * The model-free Molmol fast correlation time macro (τ<sub>e</sub> < 100 ps and τ<sub>f</sub>) no longer sets the bond length to zero when no parameter is present. |
| − | * The docstring fetching Scons target no longer fails. (see bug #8182) | + | * The docstring fetching Scons target no longer fails. ([https://gna.org/bugs/?8182 see bug #8182]) |
| − | * The model-free ' | + | * The model-free 'S<sup>2</sup> difference stored in a new run' test of the test suite now passes. ([https://gna.org/bugs/?8183 see bug #8183]) |
| − | * The 'source_dist' Scons target now works on MS Windows. (see bug #7678) | + | * The 'source_dist' Scons target now works on MS Windows. ([https://gna.org/bugs/?7678 see bug #7678]) |
| − | * The MS Windows BAT file execution failure "python: can't open file 'C:\Program': [Errno 2] No such file or directory" has been fixed. (see bug #8201) | + | * The MS Windows BAT file execution failure "python: can't open file 'C:\Program': [Errno 2] No such file or directory" has been fixed. ([https://gna.org/bugs/?8201 see bug #8201]) |
| − | * The reading in of the results files from relax versions 1.2.0 to 1.2.9 in which deselected spin system lines are truncated now works. (see bug #8248) | + | * The reading in of the results files from relax versions [[relax 1.2.0|1.2.0]] to [[relax 1.2.9|1.2.9]] in which deselected spin system lines are truncated now works. ([https://gna.org/bugs/?8248 see bug #8248]) |
<section end=bugfixes/> | <section end=bugfixes/> | ||
| − | = | + | == Links == |
| − | <section | + | <section begin=links/> |
| − | + | For reference, the following links are also part of the announcement for this release: | |
| − | * [ | + | * [http://wiki.nmr-relax.com/Relax_1.2.10 Official release notes] |
| − | <section end= | + | * {{gna link|url=gna.org/forum/forum.php?forum_id=1454|text=Gna! news item}} |
| − | + | * [http://article.gmane.org/gmane.science.nmr.relax.announce/15 Gmane] | |
| + | * [http://www.mail-archive.com/relax-announce%40gna.org/msg00007.html Mail archive] | ||
| + | * [https://mail.gna.org/public/relax-announce/2007-01/msg00000.html Local archives] | ||
| + | * [http://marc.info/?l=relax-announce&m=135070664524998&w=2 MARC] | ||
| + | <section end=links/> | ||
| − | = Announcements = | + | == Announcements == |
{{:relax release announcements}} | {{:relax release announcements}} | ||
| − | = See also = | + | == References == |
| + | |||
| + | * [*d'Auvergne and Gooley, 2007] {{#lst:Citations|dAuvergneGooley07}} | ||
| + | * [*d'Auvergne and Gooley, 2008b] {{#lst:Citations|dAuvergneGooley08b}} | ||
| + | <HarvardReferences /> | ||
| + | |||
| + | == 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 13:44, 16 October 2020
 | |||||
| relax version 1.2.10 | |||||
| |||||
| Keywords | Model-free automated protocol | ||||
|---|---|---|---|---|---|
| Release type | Minor bugfix | ||||
| Release date | 12 January 2007 | ||||
Contents
Description
This is a major bug fix release which includes a number of feature enhancements. Significant changes include the addition of convergence tests to the 'full_analysis.py' script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b], the ability to compile the C modules on Mac OS X, more advanced spin system selection, the model-free and reduced spectral density mapping results files no longer being truncated, and improvements to the model-free section of the user manual by the addition of flow diagrams detailing the steps of different model-free analysis protocols. Significant bugfixes include more flexibility in the reading of XEasy text files, a number of fixes in the 'full_analysis.py' sample script, the proper setup of Monte Carlo simulation when reading results files, and a couple of MS Windows fixes. More details and additional features, changes, and bugfixes are detailed 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 1.2.10
(12 January 2007, from /1.2)
http://svn.gna.org/svn/relax/tags/1.2.10
Features
- Addition of tests to the 'full_analysis.py' script for the identification of convergence [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b].
- Different columns can be specified for the residue number in the select.read and unselect.read user functions.
- More advanced selection of spin systems or residues is possible through the use of the Boolean operators 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'.
- Addition of a sample script for the creation a LaTeX longtable of the model-free results.
- The rows of the model-free and reduced spectral density results files are no longer truncated for deselected spin systems, hence all data is now stored in the results file. (see bug #8059)
Changes
- The relax core design diagram in the development chapter of the manual has been updated.
- Three flow diagrams have been added to the relax manual detailing the steps of different model-free analysis protocols.
- Spin systems are now identified when deselected by the eliminate user function.
- The model-free Molmol cutoff for fast and slow motions has been changed from 100 to 200 ps.
- For the clarification of bug #8059 a RelaxNoTensorError is raised instead of returning None when no diffusion tensor data is present.
- The Scons target 'source_dist' now creates and GPG signs both the 'tar.bz2' and 'zip' source distribution packages. (see task #4087)
Bugfixes
- The C modules can now be compiled on Mac OS X. (see bug #7670)
- The order of the proton and heteronucleus dimensions and number of header lines in the XEasy text file is now automatically detected. (see bug #7676)
- The 'full_analysis.py' script now throws a RelaxError if only one round of optimisation of the global model has been executed. (see bug #7787)
- The model selection of the global model in the 'full_analysis.py' script has been fixed. (see bug #7863)
- Monte Carlo simulations no longer fail if the local τm global model has been selected in the 'full_analysis.py' script. (see bug #7875)
- The Monte Carlo simulation data in the model-free results file is now correctly read back into the program. (see bug #7755)
- The Monte Carlo simulation state used to be turned on after reading a results file containing simulations. (see bug #7890)
- After reading model-free results files, model selection would fail as the heteronucleus and proton data structures did not exist. (see bug #7891)
- The model-free Molmol fast correlation time macro (τe < 100 ps and τf) no longer sets the bond length to zero when no parameter is present.
- The docstring fetching Scons target no longer fails. (see bug #8182)
- The model-free 'S2 difference stored in a new run' test of the test suite now passes. (see bug #8183)
- The 'source_dist' Scons target now works on MS Windows. (see bug #7678)
- The MS Windows BAT file execution failure "python: can't open file 'C:\Program': [Errno 2] No such file or directory" has been fixed. (see bug #8201)
- The reading in of the results files from relax versions 1.2.0 to 1.2.9 in which deselected spin system lines are truncated now works. (see bug #8248)
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.
