Difference between revisions of "Relax 1.2.4"
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{{lowercase title}} | {{lowercase title}} | ||
| − | = Description = | + | {{infobox relax release |
| + | | version = 1.2.4 | ||
| + | | prev = 1.2.3 | ||
| + | | next = 1.2.5 | ||
| + | | keywords = Manual, model-free analysis, MOLMOL, test suite | ||
| + | | type = Major feature and bugfix | ||
| + | | date = 2 May 2006 | ||
| + | | manual = yes | ||
| + | }} | ||
| + | |||
| + | == Description == | ||
<section begin=description/> | <section begin=description/> | ||
| − | This is a long overdue release which includes many new features, changes, and bugfixes. Molmol macros which plot parameter values onto the structure using arbitrary colour gradients through the X11 colours, Molmol colours, or RGB vectors can now be created by the program. A test suite has been added to aid in debugging and checking that new code does not break the functionality of the program. The [http://www.nmr-relax.com/manual/index.html relax manual] has been significantly updated. Hyperlinks are now present. The chapter [http://www.nmr-relax.com/manual/Open_source_infrastructure.html Open source infrastructure] has been added and the [http://www.nmr-relax.com/manual/relax_development.html development chapter] has been rewritten. Hybrid runs are now supported. Half the protein can be analysed in one run, the other half in another, and then the two combined into one hybrid run. | + | This is a long overdue release which includes many new features, changes, and bugfixes. [http://www.nmr-relax.com/manual/molmol_macro_write.html Molmol macros which plot parameter values onto the structure using arbitrary colour gradients through the X11 colours, Molmol colours, or RGB vectors can now be created by the program]. A test suite has been added to aid in debugging and checking that new code does not break the functionality of the program. The [http://www.nmr-relax.com/manual/index.html relax manual] has been significantly updated. Hyperlinks are now present. The chapter [http://www.nmr-relax.com/manual/Open_source_infrastructure.html Open source infrastructure] has been added and the [http://www.nmr-relax.com/manual/relax_development.html development chapter] has been rewritten. Hybrid runs are now supported. Half the protein can be analysed in one run, the other half in another, and then the two combined into one hybrid run. |
<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 1.2.4 | + | Version 1.2.4 <br/> |
| − | (2 May 2006, from /1.2) | + | (2 May 2006, from /1.2) <br/> |
http://svn.gna.org/svn/relax/tags/1.2.4 | http://svn.gna.org/svn/relax/tags/1.2.4 | ||
<section end=metadata/> | <section end=metadata/> | ||
| − | == Features == | + | === Features === |
<section begin=features/> | <section begin=features/> | ||
* Added elimination of Monte Carlo simulations to the sample scripts. | * Added elimination of Monte Carlo simulations to the sample scripts. | ||
| − | * Creation of the relax test suite 'relax --test-suite'. | + | * Creation of the [http://www.nmr-relax.com/api/1.2/test_suite-module.html relax test suite] 'relax --test-suite'. |
* Creation of the committers file. | * Creation of the committers file. | ||
* The hyperref LaTeX package is now used in the relax manual. | * The hyperref LaTeX package is now used in the relax manual. | ||
* Addition of a chapter called [http://www.nmr-relax.com/manual/Open_source_infrastructure.html Open source infrastructure]. | * Addition of a chapter called [http://www.nmr-relax.com/manual/Open_source_infrastructure.html Open source infrastructure]. | ||
* Rewrite of the [http://www.nmr-relax.com/manual/relax_development.html Development of relax] chapter. | * Rewrite of the [http://www.nmr-relax.com/manual/relax_development.html Development of relax] chapter. | ||
| − | * Addition of the user function [http://www.nmr-relax.com/manual/pipe_hybridise.html run.hybridise]. ( | + | * Addition of the user function [http://www.nmr-relax.com/manual/pipe_hybridise.html run.hybridise]. ({{gna task link|3122}}) |
| − | * The user function | + | * The [http://www.nmr-relax.com/manual/relax_data_read.html user function relax_data.read] no longer deselects residues when no data is encountered. ([https://gna.org/bugs/?5501 bug #5501]) |
| − | * Residues are deselected by the user functions | + | * Residues are deselected by the user functions [http://www.nmr-relax.com/manual/grid_search.html grid_search], [http://www.nmr-relax.com/manual/calc.html calc], and [http://www.nmr-relax.com/manual/minimise.html minimise] if k > n or if there is less than 3 data sets. ([https://gna.org/bugs/?5501 bug #5501]) |
| − | * Mapping parameter values onto the structure through Molmol macros. ( | + | * Mapping parameter values onto the structure through Molmol macros. ({{gna task link|3146}}) |
| − | * Added support for arbitrary colour gradients in the Molmol macros. ( | + | * Added support for arbitrary colour gradients in the Molmol macros. ({{gna task link|3146}}) |
| − | * Addition of a file for colour operations. All X11 colours and all Molmol colours can be selected by name. ( | + | * Addition of a [http://www.nmr-relax.com/api/1.2/colour-module.html file for colour operations]. All X11 colours and all Molmol colours can be selected by name. ({{gna task link|3146}}) |
<section end=features/> | <section end=features/> | ||
| − | == Changes == | + | === Changes === |
<section begin=changes/> | <section begin=changes/> | ||
| − | * The 'full_analysis.py' sample script now only searches over 6 | + | * The 'full_analysis.py' sample script now only searches over 6<sup>6</sup> rather than 11<sup>6</sup> grid points for the ellipsoid diffusion tensor to speed up the analysis. |
* Updated the manual to replace the references to 'make' with 'sconstruct'. | * Updated the manual to replace the references to 'make' with 'sconstruct'. | ||
| − | * Extension of the installation chapter. | + | * Extension of the [http://www.nmr-relax.com/manual/Installation_instructions.html installation chapter]. |
* Changed the square and round brackets to curly brackets and replaced ':' with '=' in the user function docstrings. | * Changed the square and round brackets to curly brackets and replaced ':' with '=' in the user function docstrings. | ||
| − | * All the model-free Molmol functions have been moved into their own class Molmol. | + | * All the model-free Molmol functions have been moved into their own class [http://www.nmr-relax.com/api/1.2/specific_fns.model_free.Molmol-class.html Molmol]. |
* The null device can now be opened instead of a file for writing by passing 'devnull' as the name. | * The null device can now be opened instead of a file for writing by passing 'devnull' as the name. | ||
* Updated the release checklist so that the directory 'relax-x.x.x' is included in the distributions rather than just 'relax'. | * Updated the release checklist so that the directory 'relax-x.x.x' is included in the distributions rather than just 'relax'. | ||
| Line 51: | Line 61: | ||
<section end=changes/> | <section end=changes/> | ||
| − | == Bugfixes == | + | === Bugfixes === |
<section begin=bugfixes/> | <section begin=bugfixes/> | ||
| − | * Small bugs in the sconstruct script have been removed. | + | * Small bugs in the [http://www.nmr-relax.com/api/1.2/script-sconstruct-module.html sconstruct script] have been removed. |
* The value reading function can now handle rows which contain no data. | * The value reading function can now handle rows which contain no data. | ||
* The ellipsoid diffusion tensor was being incorrectly initialised in the 'full_analysis.py' script. | * The ellipsoid diffusion tensor was being incorrectly initialised in the 'full_analysis.py' script. | ||
| − | * Another Numeric version issue. The model m0 with no parameters which used to be handled okay by the grid search and minimisation code was failing due to changes in Numeric. | + | * Another Numeric version issue. The [[m0|model m0]] with no parameters which used to be handled okay by the grid search and minimisation code was failing due to changes in Numeric. |
* In certain situations, the angle folding function which is called after model-free minimisation used the wrong run name. | * In certain situations, the angle folding function which is called after model-free minimisation used the wrong run name. | ||
* Fixed the -fPIC option segfault problem on some Linux systems. ([https://gna.org/bugs/?5473 bug #5473]) | * Fixed the -fPIC option segfault problem on some Linux systems. ([https://gna.org/bugs/?5473 bug #5473]) | ||
| − | * Changed the | + | * Changed the τ<sub>m</sub> grid search which was between 6-12 ns to be between 1-12 ns. |
| − | * Fixed some grammar in the intro chapter of the manual. | + | * Fixed some grammar in the [http://www.nmr-relax.com/manual/Introduction.html intro chapter of the manual]. |
* Fixed a bug in the model-free sample script in the spheroid diffusion tensor function. | * Fixed a bug in the model-free sample script in the spheroid diffusion tensor function. | ||
* Removed the spaces in front of the \index{} commands from the manual LaTeX source files. | * Removed the spaces in front of the \index{} commands from the manual LaTeX source files. | ||
| − | * The diffusion parameters | + | * The diffusion parameters D<sub>iso</sub>, D<sub>⊥</sub>, D<sub>∥</sub>, D<sub>ratio</sub>, D<sub>x</sub>, D<sub>y</sub>, and D<sub>z</sub> are generated on the fly. ([https://gna.org/bugs/?5559 bug #5559]) |
* Fixed the spacing after 'Gna!' in the manual. | * Fixed the spacing after 'Gna!' in the manual. | ||
| − | * The | + | * The [http://www.nmr-relax.com/manual/grace_write.html grace.write user function] now plots the associated errors. ([https://gna.org/bugs/?5659 bug #5659]) |
| − | * Fix to the parameter errors not being scaled in the value.read | + | * Fix to the parameter errors not being scaled in the [http://www.nmr-relax.com/manual/value_read.html value.read user function]. ([https://gna.org/bugs/?5670 bug #5670]) |
* Parameter errors were not always included in the results file. ([https://gna.org/bugs/?5660 bug #5660]) | * Parameter errors were not always included in the results file. ([https://gna.org/bugs/?5660 bug #5660]) | ||
* Removed the memory leak in the relaxation curve-fitting [[C|C modules]]. ([https://gna.org/bugs/?5602 bug #5602]) | * Removed the memory leak in the relaxation curve-fitting [[C|C modules]]. ([https://gna.org/bugs/?5602 bug #5602]) | ||
| Line 76: | Line 86: | ||
<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_1.2.4 Official release notes] | ||
| + | * {{gna link|url=gna.org/forum/forum.php?forum_id=1163|text=Gna! news item}} | ||
| + | * [http://article.gmane.org/gmane.science.nmr.relax.announce/8 Gmane] | ||
| + | * [http://www.mail-archive.com/relax-announce%40gna.org/msg00000.html Mail archive] | ||
| + | * [https://mail.gna.org/public/relax-announce/2006-05/msg00000.html Local archives] | ||
| + | * [http://marc.info/?l=relax-announce&m=135070664424991&w=2 MARC] | ||
| + | <section end=links/> | ||
| + | |||
| + | == Announcements == | ||
{{:relax release announcements}} | {{:relax release announcements}} | ||
| − | = See also = | + | == See also == |
| − | [ | + | * [http://www.nmr-relax.com/api/1.2/ The relax 1.2 API documentation] |
| + | {{:relax release see also}} | ||
Latest revision as of 12:25, 16 October 2020
 | |||||
| relax version 1.2.4 | |||||
| |||||
| Keywords | Manual, model-free analysis, MOLMOL, test suite | ||||
|---|---|---|---|---|---|
| Release type | Major feature and bugfix | ||||
| Release date | 2 May 2006 | ||||
|
| |||||
 The relax 1.2.4 user manual | |||||
Contents
Description
This is a long overdue release which includes many new features, changes, and bugfixes. Molmol macros which plot parameter values onto the structure using arbitrary colour gradients through the X11 colours, Molmol colours, or RGB vectors can now be created by the program. A test suite has been added to aid in debugging and checking that new code does not break the functionality of the program. The relax manual has been significantly updated. Hyperlinks are now present. The chapter Open source infrastructure has been added and the development chapter has been rewritten. Hybrid runs are now supported. Half the protein can be analysed in one run, the other half in another, and then the two combined into one hybrid run.
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 1.2.4
(2 May 2006, from /1.2)
http://svn.gna.org/svn/relax/tags/1.2.4
Features
- Added elimination of Monte Carlo simulations to the sample scripts.
- Creation of the relax test suite 'relax --test-suite'.
- Creation of the committers file.
- The hyperref LaTeX package is now used in the relax manual.
- Addition of a chapter called Open source infrastructure.
- Rewrite of the Development of relax chapter.
- Addition of the user function run.hybridise. (Task #3122)
- The user function relax_data.read no longer deselects residues when no data is encountered. (bug #5501)
- Residues are deselected by the user functions grid_search, calc, and minimise if k > n or if there is less than 3 data sets. (bug #5501)
- Mapping parameter values onto the structure through Molmol macros. (Task #3146)
- Added support for arbitrary colour gradients in the Molmol macros. (Task #3146)
- Addition of a file for colour operations. All X11 colours and all Molmol colours can be selected by name. (Task #3146)
Changes
- The 'full_analysis.py' sample script now only searches over 66 rather than 116 grid points for the ellipsoid diffusion tensor to speed up the analysis.
- Updated the manual to replace the references to 'make' with 'sconstruct'.
- Extension of the installation chapter.
- Changed the square and round brackets to curly brackets and replaced ':' with '=' in the user function docstrings.
- All the model-free Molmol functions have been moved into their own class Molmol.
- The null device can now be opened instead of a file for writing by passing 'devnull' as the name.
- Updated the release checklist so that the directory 'relax-x.x.x' is included in the distributions rather than just 'relax'.
- Removed the bugs file 'docs/BUGS'.
Bugfixes
- Small bugs in the sconstruct script have been removed.
- The value reading function can now handle rows which contain no data.
- The ellipsoid diffusion tensor was being incorrectly initialised in the 'full_analysis.py' script.
- Another Numeric version issue. The model m0 with no parameters which used to be handled okay by the grid search and minimisation code was failing due to changes in Numeric.
- In certain situations, the angle folding function which is called after model-free minimisation used the wrong run name.
- Fixed the -fPIC option segfault problem on some Linux systems. (bug #5473)
- Changed the τm grid search which was between 6-12 ns to be between 1-12 ns.
- Fixed some grammar in the intro chapter of the manual.
- Fixed a bug in the model-free sample script in the spheroid diffusion tensor function.
- Removed the spaces in front of the \index{} commands from the manual LaTeX source files.
- The diffusion parameters Diso, D⊥, D∥, Dratio, Dx, Dy, and Dz are generated on the fly. (bug #5559)
- Fixed the spacing after 'Gna!' in the manual.
- The grace.write user function now plots the associated errors. (bug #5659)
- Fix to the parameter errors not being scaled in the value.read user function. (bug #5670)
- Parameter errors were not always included in the results file. (bug #5660)
- Removed the memory leak in the relaxation curve-fitting C modules. (bug #5602)
- The user function value.set no longer raises RelaxError in spectral density mapping runs. (bug #5698)
- Fix to the broken Molmol pipe. (bug #5752)
- Fix of the failure of molmol.view when the PDB is missing. (bug #5753)
- Fix to the failure of relax_data.read when relaxation data is missing. (bug #5805)
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
- 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.
