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<section start=references/>* [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. ''Mol. BioSyst.'', '''3'''(7), 483–494. (DOI: [http{{#lst://dx.doi.org/10.1039/b702202f 10.1039/b702202f]).Citations|dAuvergneGooley07}}* [*d'Auvergne and Gooley, 2008b] 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: [http{{#lst://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).<section end=references/>Citations|dAuvergneGooley08b}}
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{{infobox relax release| version = 1.3.6| prev = 1.3.5| next = 1.3.7| type = Major feature| date = 31 December 2010| manual = yes}} == Description ==
<section begin=description/>
<section end=description/>
== Download ==
<section begin=download/>
<section end=download/>
== CHANGES file ==
<section begin=metadata/>
<section end=metadata/>
=== Features ===
<section begin=features/>
* Addition of [https://{{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 <sup>15</sup>N gyromagnetic ratio.
* 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/>
* 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.
* 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.
<section end=changes/>
=== Bugfixes ===
<section begin=bugfixes/>
* 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.
* 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.
* 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.
<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 ==
<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:N-state model analysis]]