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{{infobox relax release| version = Description 1.3.5| prev =1.3.4| next = 1.3.6| keywords = frame order theory, N-state model, plotting, rotations, stereochemistry| type = Major feature| date = 21 May 2010| manual = yes}}
== Description ==
<section begin=description/>
This is a major feature release consisting of over a year's worth of improvements and bug fixes, with close to 2000 code changes. All users are recommended to upgrade to this newest version. New features include the ability to determine the stereochemistry of flexible organic molecules, expansion of the frame order theory, better support for RDCs and PCSs, 2D Grace plot improvements, and many new rotation_matrix module conversion functions.
<section end=description/>
== Download ==
<section begin= Download =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).
<section end=download/>
== CHANGES file ==
<section begin= CHANGES file =metadata/>Version 1.3.5<br/>(21 May 2010, from /1.3)<br/>
http://svn.gna.org/svn/relax/tags/1.3.5
<section end=metadata/>
=== Features ===
<section begin=features/>
* Addition of the [http://www.nmr-relax.com/manual/frame_order_ref_domain.html frame_order.ref_domain user function] to specify the alignment of different domains.
* Converted the reduced J(wω) mapping sample script to the relax 1.3 design to make it functional.
* Created the 'rigid' frame order model.
* Made the profile module optional, removing the dependency on the Python development packages.
* Creation of the [http://www.nmr-relax.com/manual/rdc_corr_plot.html rdc.corr_plot] and [http://www.nmr-relax.com/manual/pcs_corr_plot.html pcs.corr_plot] user functions for creating correlation plots of measured vs. back-calculated RDCs and PCSs.
* Added the -i or --info option to relax.
<section end=features/>
=== Changes ===
<section begin=changes/>
* Test suite fixes for Python 2.5.
* Epydoc docstring improvements/fixes for the API documentation.
* Many updates using 2to3 preparing for a transition to Python 3.x.
* Renamed the [http://www.nmr-relax.com/manual/pipe_list.html pipe.list() user function ] to [http://www.nmr-relax.com/manual/pipe_display.html pipe.display()].
* Created a base class for the user function classes. More user function back end simplifications.
* Addition of many new RelaxError classes for the user function interface.
* Added a very basic, and completely empty module and class for SRLS analysis.
* Redesign of the relax state loading for adding support for a XML formatted state file.
* Shifted the [http://www.nmr-relax.com/manual/results_write.html results.write() ] force arg to the end.
* Created the relax data store is_empty() method.
* Renamed the [http://www.nmr-relax.com/manual/state_load.html state.load() ] and [http://www.nmr-relax.com/manual/state_save.html state.save() ] directory argument from dir_name to dir for consistency with the rest of relax.
* Redesigned the relaxation curve fitting grid search for the new design of the minfx grid search.
* Redesigned the N-state model grid search setup around the new minfx interface.
* Redesigned the model-free grid search setup around the new minfx interface.
* Renamed the 'grace.py' sample script to 'mf_grace_S2_vs_te.py'.
* Added the spin_id_col arg to the [http://www.nmr-relax.com/manual/rdc_read.html rdc.read() user function].* Changes to the [http://www.nmr-relax.com/manual/pcs_read.html pcs.read() ] and [http://www.nmr-relax.com/manual/rdc_read.html rdc.read() ] user function interfaces.
* Column numbering now starts at 1 rather than 0 within the user functions.
* The relax_io.read_spin_data_file() function has been created to handle all columnar text files where each row corresponds to a spin.
* Added user variable checking to the full_analysis.py script.
* Added functions for determining the element name and isotope number from an isotope name.
* Added frame order methods necessary for the [http://www.nmr-relax.com/manual/dx_map.html dx.map() user function].
* Huge clean up / redesign of the specific analysis internal API.
* Better layout of the user functions in the relax manual significantly dropping the page count.
* Modified the alignment tensor print out to be more compact.
* The PCS centre can now be forcefully overwritten.
* Added the back end to the [http://www.nmr-relax.com/manual/rdc_back_calc.html rdc.back_calc() user function ] (making it functional).
* Modified all the specific analysis overfit_deselect() methods to warn when spins are deselected.
* [http://www.nmr-relax.com/manual/align_tensor_display.html align_tensor.display() ] now prints the magnetic susceptibility tensor.
* The rotation matrix to Euler angle algorithms have been converted to the general one of Ken Shoemake.
* Simplifications and clean up of the prompt and script UI code.
* Partially removed the need for downstream Fink specific modifications.
* Creation of the NOE auto-analysis module.
* Fixes for the [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins() user function ] docstring for RNA/DNA work.* The [http://www.nmr-relax.com/manual/n_state_model_select_model.html n_state_model.select_model() user function ] can now change the model.* Added a maximum global iteration arg and check into the dauvergne_protocol.py module[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b].<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>
* Fix for the quaternion_to_R() function (due to incorrect information in Wikipedia).
* Character encoding fix - cannot use umlauts.
* Fix for the calls to transpose_14().
* Bug fix for the relaxation curve-fitting difference plot script.
* Fix for the [http://www.nmr-relax.com/manual/spin_number.html spin.number() user function], the number can be None to reset the values.* Fix for the [http://www.nmr-relax.com/manual/script.html script() user function], the function intro flag at the end of executing an external script was not being restored.* Improvements to the optimisation tests ([https://gna.org/bugs/?14173 bug #14173], [https://gna.org/bugs/?14174 bug #14174], [https://gna.org/bugs/?14175 bug #14175], [https://gna.org/bugs/?14176 bug #14176], [https://gna.org/bugs/?14177 bug #14177], [https://gna.org/bugs/?14182 bug #14182]).
* Fix for the R_euler_zyz() rotation matrix function.
* Fix for the R_to_axis_angle() rotation matrix function.
* Fix for the test suite, the temporary files were not always deleted if a .bz2 extension was added.
* Fix for the reading of Xplor NOE data when a line starts with '#'.
* Fix for [https://gna.org/bugs/?14428 the Dasha and Modelfree interfaces for when spins have too little data (bug #14428)].
* Fixes for the RDC and PCS read() functions, the alignment tensor ID had the same variable name as the spin ID.
* Fixed the PDF manual compilation ([https://gna.org/bugs/?14464 bug #14464]).
* Fix for the retrieval of bond vectors for the N-state model.
* Fixes for the [http://www.nmr-relax.com/manual/dx_map.html dx.map() user function ] interface.
* Epydoc docstring fixes.
* Fix for when [https://gna.org/bugs/?14872 the selection string (i.e. spin_id) is unicode (bug #14872)].
* Fix for the PCS back calculation for when no weights are given.
* The last weight in the'fixed' and 'population' N-state models, if supplied, was being converted to zero (1 - sum(weights)) hence the last state/structure was not being included.
* Added the missing user functions in the mf_multimodel.py sample script ([https://gna.org/bugs/?14885 bug #14885]).* Fix for the Monte Carlo simulations in the full_analysis.py script ([https://gna.org/bugs/?14941 bug #14941]).* Fix for optimisation of models tm4 to tm8 in the mf_multimodel sample script when over-fitting occurs ([https://gna.org/bugs/?15050 bug #15050]).
* Removed the beta angle folding from the frame order module as it was failing.
* Fix and updates to the generic_fns.angles.wrap_angles() function.
* Fix for the internal structural object PDB writing - the TER records are between the ATOM and HETATM records.
* Fixed a final model-free analysis failure in the d'Auvergne protocol, the auto-analysis behind the full_analysis.py script [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] ([https://gna.org/bugs/?15874 bug #15874]).
* Fixes for the N-state model when RDC or PCS data is missing.
* Fixed the Q-factor calculating functions to handle missing RDC or PCS lists.
* Fix for when structural models are loaded out of order.
* Fix for the 'population' N-state model whereby the last probability can have a negative value.
* The infinite looping around the universal solution in the dauvergne_protocol module [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] is now being caught (for the full_analysis.py script).<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_1.3.5 Official release notes]* {{gna link|url=gna.org/forum/forum.php?forum_id=2205|text=Gna! news item}}* [http://article.gmane.org/gmane.science.nmr.relax.announce/26 Gmane]* [http://www.mail-archive.com/relax-announce%40gna.org/msg00018.html Mail archive]* [https://mail.gna.org/public/relax-announce/2010-06/msg00000.html Local archives]* [http://marc.info/?l=relax-announce&m=135070664625009&w=2 MARC]<section end=links/> == Announcements =={{:relax release announcements}} == 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/1.3/ The relax 1.3 API documentation]{{:relax release see also}}[[Category:Frame order analysis]][[Category:Release_NotesN-state model analysis]]