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{{infobox relax release| version = Description 1.3.6| prev =1.3.5| next = 1.3.7| type = Major feature| date = 31 December 2010| manual = yes}}
== Description == <onlyincludesection begin=description/>
This is a major feature release which includes many bug fixes and a security fix. Major additions include the addition of 9 new frame order models, execution locking, support for CCPN Analysis 2.1 peak lists, Monte Carlo simulations for the N-state model, optimisation of the Ln<sup>3+</sup> position in the N-state model, weighting of RDCs and PCSs during optimisation, and no longer using execfile() closing a security hole.
<section end=description/onlyinclude>
== Download ==
<section begin=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 1.3.6<br/>(31 December 2010, from /1.3)<br/>
http://svn.gna.org/svn/relax/tags/1.3.6
<section end=metadata/>
=== Features ===
<section begin=features/>* Addition of {{gna link|url=gna.org/users/michaelbieri|text=Michael Bieri's }} model-free data extraction script.
* Added support for CCPN Analysis 2.1 peak lists (exported in Sparky format).
* Execution locking has been implemented to prevent threaded execution from killing relax. This will be useful for the relax GUI.
* Scripts are now run as modules rather than using execfile(), closing a security hole.
* Created the [http://www.nmr-relax.com/manual/frame_order_domain_to_pdb.html frame_order.domain_to_pdb user function ] to associate PDB files with domains in the current data pipe.
* Rewrote [http://www.nmr-relax.com/manual/frame_order_pdb_model.html frame_order.cone_pdb] to handle all of the frame order models.
* The sign of the RDC can be inverted to correct for the negative 15N <sup>15</sup>N gyromagnetic ratio.
* Better identification of the molecule end in the internal PDB reader.
* Implemented Monte Carlo simulations for the N-state model.
* The RDC and PCS back-calculation user functions now add the alignment ID to the RDC and PCS if absent to allow both data types to be back-calculated in the absence of measured data.
* The N-state model calculate() method now stores the back-calculated RDCs and PCSs and Q factors.
* The PyMOL module pymol.cmd is now available within the pymol user function class, accessible as [http://www.nmr-relax.com/manual/pymol_command.html pymol.cmd] is now available within the pymol user function class, accessible as pymol.cmd from the prompt/script interface.<section end=features/>
=== Changes ===
<section begin=changes/>
* API documentation improvements with epydoc docstring fixes.
* Numerous new system tests to catch bugs and prevent bugs appearing in the future.
* The molecule type can now be specified.
* Improved the diffusion tensor print out.
* [http://www.nmr-relax.com/manual/pipe_delete.html pipe.delete() ] without args will now delete all data pipes.* Added some checks to the dauvergne_protocol model-free analysis [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] for the required previously optimised results.
* Shifted the steady-state NOE specific analysis code into its own package.
* Shifted the debug and pedantic flags into the __main__ namespace for better access from other modules.
* Citations now include the status if not 'published'.
* Created a new directory 'graphics' for all relax artwork.
* The [http://www.nmr-relax.com/manual/structure_load_spins.html structure.load_spins() user function ] now gives a RelaxWarning if no data could be found.* The negative cones and z-axes are now not created for the pseudo-ellipses in [http://www.nmr-relax.com/manual/frame_order_cone_pdb.html frame_order.cone_pdb()].* Added some transparency to the cone in [http://www.nmr-relax.com/manual/pymol_cone_pdb.html pymol.cone_pdb()].* Modified the [http://www.nmr-relax.com/manual/pymol_cone_pdb.html pymol.cone_pdb() user function ] to handle x, y, and z-axes.
* Modified create_cone_pdb() to accept a pre-made structural object and to create a file only when asked.
* Switched the names of the Pseudo_elliptic and Pseudo_elliptic2 classes.
* Parameters can be fixed to the original values during the frame order grid search.
* The user function argument checker arg_check.is_int_or_int_list() can now allow for None list elements.
* The frame order model can be overwritten by [http://www.nmr-relax.com/manual/frame_order_select_model.html frame_order.select_model()].
* Shifted to using numpy.sinc() for the frame order equations.
* Switched the theta and phi angles in cartesian_to_spherical() to match the rest of relax.
* Created a new module for performing coordinate transformations (maths_fns.coord_transform).
* The [http://www.nmr-relax.com/manual/pipe_display.html pipe.display() user function ] now places quotation marks around the pipe names and shows which is the current data pipe.* The [http://www.nmr-relax.com/manual/align_tensor_display.html align_tensor.display() user function ] now prints out the generalized degree of order (GDO) value.
* The back-calculated alignments tensors are now being stored in the current data pipe.
* Removed the docstring length check from the code validator script.
* The loading of RDCs and PCSs for non-existent spins now only throws a RelaxWarning.
* The [http://www.nmr-relax.com/manual/select_read.html select.read() ] and [http://www.nmr-relax.com/manual/deselect_read.html deselect.read() ] user functions can now accept file handles or dummy file objects.
* Limit arrays are now sent into the minfx generic interface for limiting simulated annealing.
* The [http://www.nmr-relax.com/manual/align_tensor_delete.html align_tensor.delete() user function ] can now be used to remove all tensors simultaneously.
* Made a RelaxError less stringent so that the paramagnetic centre can be unfixed.
* Initialising an alignment tensor now adds the ID to the alignment ID list.
* Changes to the NOE auto-analysis for the GUI: The output filename can be specified; The folder, where results files will be placed, can be specified; The label of heteronucleus and proton of peak lists and PDB file can be selected; The sequence is read either by sequence file or PDB file; Removed white spaces and progress output.
* Changed the alignment tensor parameter scaling back to 1 as this was slowing down the optimisation.
* The [http://www.nmr-relax.com/manual/rdc_back_calc.html rdc.back_calc() user function ] without an ID arg will back-calculate RDCs for all alignments.* Renamed the [http://www.nmr-relax.com/manual/pcs_centre.html pcs.centre() user function ] to [http://www.nmr-relax.com/manual/paramag_centre.html paramag.centre() ] to abstract for the PRE.
* Better support for RDC and PCS correlation plots with and without errors.
* Inverted the x and y axes in the RDC and PCS correlation plots.
* Better support for tensor-less N-state model optimisation.
* The [http://www.nmr-relax.com/manual/align_tensor_copy.html align_tensor.copy() ] tensor_to arg can now be None, this is useful for copying between data pipes.
* Added a function for the pseudo-elliptical cosine function, this is a numerical approximation generated by series expansion.
* Added a method for translating pymol.cmd.do() commands into specific pymol.cmd functions. This prevents problems with commands being executed asynchronously. For example images were being saved before ray-tracing was complete.
* The RDC and PCS correlation plots now only show selected spins.
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>* The loading of Monte Carlo simulation data from relax 1.2 version results files has been fixed ([https://gna.org/bugs/?17361 bug #17361]).
* Bug fix for the relaxation data add_data_to_spin() function - missing data for individual spins was not properly eliminated.
* For the 1.2 results files, the data is being extracted even if the spin is not selected.
* Sparky peak lists from CCPN Analysis 2.1 can now be read ([https://gna.org/bugs/?17341 bug #17341]).* Fix for the broken [http://www.nmr-relax.com/manual/grace_view.html grace.view() user function ] ([https://gna.org/bugs/?17344 bug #17344]).* Added 'CH' and 'OT' as carbon and oxygen atoms to the internal PDB reader ([https://gna.org/bugs/?17343 bug #17343]).
* The script path is now being removed from sys.path as this was causing incorrect scripts to be loaded if multiple scripts are executed sequentially or nested.
* Fix for [https://gna.org/bugs/?17276 the 'list index is out of range' error when differently sorted peak lists, or lists with missing data are loaded (bug #17276)].* Fix for the input of (DxxD<sub>xx</sub>, DyyD<sub>yy</sub>, DzzD<sub>zz</sub>, DxyD<sub>xy</sub>, DxzD<sub>xz</sub>, DyzD<sub>yz</sub>) ellipsoidal diffusion parameters.
* Fixes for some currently unused, but useful, diffusion tensor internal API functions.
* Fix for the NOE auto-analysis - the spins are now named to the value of the 'heteronuc' arg.
* Fix for the [http://www.nmr-relax.com/manual/frame_order_cone_pdb.html frame_order.cone_pdb() user function ] - the cone is already in the PDB frame, no rotation required.* Fix for the average domain rotation in [http://www.nmr-relax.com/manual/pymol_cone_pdb.html pymol.cone_pdb()].* Bug fix for the [http://www.nmr-relax.com/manual/frame_order_pivot.html frame_order.pivot() user function ] - it is now functional.* The base contents of the relax data store are no longer saved with a call to [http://www.nmr-relax.com/manual/results_write.html results.write()].* Fix for the [http://www.nmr-relax.com/manual/pcs_back_calc.html pcs.back_calc() user function ] for when multiple structures are loaded.* Fix for [http://www.nmr-relax.com/manual/rdc_read.html rdc.read() ] when neg_g_corr is set to True and the RDC list contains entries with None.* Fix for [https://gna.org/bugs/?13259 the failure of model elimination in the full analysis script (bug #13259)].
* Added a catch in iso_cone_S_to_theta() for bad order parameters > 1.
* The attached proton PDB name is no longer hardcoded to 'H' in the dauvergne_protocol auto analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b].
* When loading save states, data pipe names are always converted to a string to avoid unicode problems.
* Hardcoded the factorial() function to return support for Python 2.4 and 2.5.
* Small fixes and improvements to the [http://www.nmr-relax.com/manual/rdc_back_calc.html rdc.back_calc() user function ] - align IDs are being used instead of RDC IDs so RDCs can be back-calculated even if measured RDCs are not present. And spin info is also being checked for better error reporting to the user.
* Fix for the alignment tensor rotation matrix - it is now always in the right handed universe.
* Bug fix for the RDC back_calc() function - the align_id arg was being ignored.
* Bug fix for the control of PyMOL (as a module).
* Small fix for the grace.write_xy_header() function, the symbol numbers now range only between the legal values of 1 to 10.
<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_1.3.6 Official release notes]
* {{gna link|url=gna.org/forum/forum.php?forum_id=2251|text=Gna! news item}}
* [http://article.gmane.org/gmane.science.nmr.relax.announce/27 Gmane]
* [http://www.mail-archive.com/relax-announce%40gna.org/msg00019.html Mail archive]
* [https://mail.gna.org/public/relax-announce/2011-01/msg00000.html Local archives]
* [http://marc.info/?l=relax-announce&m=135070664625010&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]]