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<section start=references/>* [*d'Auvergne and Gooley, 20082007] {{#lst:Citations|dAuvergneGooley07}}* [*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: [http2008b] {{#lst://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).<section end=references/>Citations|dAuvergneGooley08b}}
Internal link to Modelfree4.
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{{infobox relax release| version = 1.3.1| prev = 1.3.0| next = 1.3.2| keywords = Complete redesign| type = Major feature| date = 28 September 2008| manual = yes}} == Description ==
<section begin=description/>
For for identifying and selecting spins, the spin identification string concept has been introduced. The string is composed of three components: the molecule id token beginning with the '#' character, the residue id token beginning with the ':' character, and the atom or spin system id token beginning with the '@' character. Each token can be composed of multiple elements separated by the ',' character and each individual element can either be a number, name, or range of numbers separated by the '-' character. Hence the full id string specification is "#<mol_name> :<res_id>[, <res_id>[, <res_id>, ...]] @<atom_id>[, <atom_id>[, <atom_id>, ...]],". Basic usage of the Boolean operators and ('&') and or ('|') is also supported.
Note that in this version, not all parts of relax are currently functional. Many, such as relaxation curve fitting, model-free analysis, reduced spectral density mapping, consistency testing, etc. are fully functional but if you do uncover a non-operational user function, please submit a bug report or use the stable [[relax 1.2.14|1.2.14]] version. Conversion of the last parts of relax to the new design will not be too hard, especially if all issues are reported. Note that this is a development line and that scripts written for version [[relax 1.3.1 |1.3.1]] may not work automatically in future 1.3 versions.
<section end=description/>
== Download ==
<section begin=download/>
<section end=download/>
== CHANGES file ==
<section begin=metadata/>
<section end=metadata/>
=== Features ===
<section begin=features/>
* All spins can be looped over simply by using the spin_loop() generator function.
* Molecules, residues, and spins are now selected by the new syntax of the spin identification string.
* Improvements and simplifications to the 'full_analysis.py' script [d'Auvergne and Gooley, 2882007][d'Auvergne and Gooley, 2008b] with all user modifiable variables shifted to the top of the script as global variables.* Automatic looping until convergence has been added to the 'full_analysis.py' [d'Auvergne and Gooley, 2882007][d'Auvergne and Gooley, 2008b] script to further simplify usage.
* Setting the type of nucleus is now done with the [http://www.nmr-relax.com/manual/value_set.html value.set user function] on a spin-by-spin basis. This is important for RNA, small molecules and protein analyses with Ca and N data.
* A new analysis type, the N-state model for interpreting domain motions using RDC and PCS data, is now supported.
<section end=features/>
=== Changes ===
<section begin=changes/>
* User scripts can now be used directly as system tests.
* All threading code has been eliminated in preparation for replacement by the multi_processor code.
* The precision of the <sup>15</sup>N gyromagnetic ratio input into Art Palmer's [[Modelfree4 ]] program has been increased.
* Scientific python is no longer an essential dependency.
* The 'unselect' user function class has been renamed to 'deselect'.
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>
* The unit test and system test frameworks are now functional.
* The failure of reduced spectral density mapping has been identified and fixed ([https://gna.org/bugs/?9238 bug #9238], [https://gna.org/bugs/?9562 bug #9562]).* The second set of extended model-free formulae were accessing undefined functions ([https://gna.org/bugs/?9189 bug #9189]).* Docstring fetching issues with Python 2.5 have been fixed ([https://gna.org/bugs/?9390 bug #9390]).* The sample script for placing model-free results into a LaTeX table now works ([https://gna.org/bugs/?10189 bug #10189]).
* The default parameter values for relaxation curve fitting were incorrectly set.
* Security: Replaced the insecure os.tempnam() with tempfile.mktemp().
* ZeroDivisionError fix for model elimination and Monte Carlo simulation elimination ([https://gna.org/bugs/?11004 bug #11004]).* The handling of spins with missing XH bond vectors has been fixed ([https://gna.org/bugs/?11378 bug #11378]).* The [http://www.nmr-relax.com/manual/relax_data_display.html relax_data.display() user function ] is now functional again ([https://gna.org/bugs/?11383 bug #11383]).
* MS Windows with Python 2.5 is now supported.
<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_1.3.1 Official release notes]* [https://gna.org/forum/forum.php?forum_id=1965 Gna! news item]* [http://article.gmane.org/gmane.science.nmr.relax.announce/21 Gmane]* [http://www.mail-archive.com/relax-announce%40gna.org/msg00013.html Mail archive]* [https://mail.gna.org/public/relax-announce/2008-09/msg00000.html Local archives]* [http://marc.info/?l=relax-announce&m=135070664625004&w=2 MARC]<section end=links/> == Announcements ==
{{:relax release announcements}}
== References ==
<HarvardReferences />
== See also ==
* [http://www.nmr-relax.com/api/1.3/ The relax 1.3 API documentation]
{{:relax release see also}}
