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{{infobox relax release| version = 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/>
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== Download ==
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== CHANGES file ==
<section begin=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.
<section end=features/>
=== Changes ===
<section begin=changes/>
* 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 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 orderanalysis]][[Category:N-state modelanalysis]]