Difference between revisions of "Relax 1.2.4"
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= Description = | = Description = | ||
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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. 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. | ||
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= Download = | = Download = | ||
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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). | ||
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= CHANGES file = | = CHANGES file = | ||
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Version 1.2.4 | Version 1.2.4 | ||
(2 May 2006, from /1.2) | (2 May 2006, from /1.2) | ||
http://svn.gna.org/svn/relax/tags/1.2.4 | http://svn.gna.org/svn/relax/tags/1.2.4 | ||
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== Features == | == Features == | ||
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* 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 relax test suite 'relax --test-suite'. | ||
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* Added support for arbitrary colour gradients in the Molmol macros. ([https://gna.org/task/?3146 task #3146]) | * Added support for arbitrary colour gradients in the Molmol macros. ([https://gna.org/task/?3146 task #3146]) | ||
* Addition of a file for colour operations. All X11 colours and all Molmol colours can be selected by name. ([https://gna.org/task/?3146 task #3146]) | * Addition of a file for colour operations. All X11 colours and all Molmol colours can be selected by name. ([https://gna.org/task/?3146 task #3146]) | ||
| − | + | <section end=features/> | |
== Changes == | == Changes == | ||
| + | <section begin=changes/> | ||
* The 'full_analysis.py' sample script now only searches over 6^6 rather than 11^6 grid points for the ellipsoid diffusion tensor to speed up the analysis. | * The 'full_analysis.py' sample script now only searches over 6^6 rather than 11^6 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'. | ||
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* 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'. | ||
* Removed the bugs file 'docs/BUGS'. | * Removed the bugs file 'docs/BUGS'. | ||
| − | + | <section end=changes/> | |
== Bugfixes == | == Bugfixes == | ||
| + | <section begin=bugfixes/> | ||
* Small bugs in the sconstruct script have been removed. | * Small bugs in the 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. | ||
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* Fix of the failure of [http://www.nmr-relax.com/manual/molmol_view.html molmol.view] when the PDB is missing. ([https://gna.org/bugs/?5753 bug #5753]) | * Fix of the failure of [http://www.nmr-relax.com/manual/molmol_view.html molmol.view] when the PDB is missing. ([https://gna.org/bugs/?5753 bug #5753]) | ||
* Fix to the failure of [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read] when relaxation data is missing. ([https://gna.org/bugs/?5805 bug #5805]) | * Fix to the failure of [http://www.nmr-relax.com/manual/relax_data_read.html relax_data.read] when relaxation data is missing. ([https://gna.org/bugs/?5805 bug #5805]) | ||
| − | + | <section end=bugfixes/> | |
= See also = | = See also = | ||
[[Category:Release_Notes]] | [[Category:Release_Notes]] | ||
Revision as of 19:14, 10 September 2014
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 6^6 rather than 11^6 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 tm grid search which was between 6-12 ns to be between 1-12ns.
- 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', 'Dper', 'Dpar', '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)
