Trusted, Bureaucrats
4,228
edits
Changes
Jump to navigation
Jump to search
Changed the dauvergne_protocol LST tags.
* Added the document-close Oxygen icons.
* Added support for old save files in the Peak_intensity.sync_ds() method (for the GUI).
* Argument change_all for deselecting residues in the d'Auvergne protocol[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b] has to be boolean.
* The relax_fit overfit_deselect() method now skips deselected spins. This prevents unnecessary warnings about missing data for deselected spins.
* All of the overfit_deselect() methods now skip deselected spins, avoiding confusing warnings.
* The value.write user function now also adds to the cdp.result_files structure.
* Modified the execution lock to have a mode. This allows for greater control and avoid string comparison of names to determine if a script or auto-analysis acquired the lock.
* The dauvergne_protocol is now more robust if the program is interrupted and restarted later[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b]. The opt/results.bz2 file is now searched for, and if not the round is assumed incomplete.
* The pymol.tensor_pdb() user function now shows the diffusion tensor using PyMOL sticks.
* Creation of the new structure.read_xyz user function.
* Fix for the RelaxWarning system on Mac OS X, the base class __str__ method now returns a simple string. On a Mac, the warning message text was in unicode whereas the __str__() method must return a standard string. So now __str__() is using the str() method to convert.
* Fix for the structure.vectors user function. It no longer complains about a PDB already loaded when no PDB has been loaded.
* Fix for the resetting of the global optimisation round in the dauvergne_protocol auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b]. The value was being reset to None at every round.* Fix for the round determination in the dauvergne_protocol auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b]. The 'opt' directory was missing in the path.
* Fix for the saving/loading of a results file in GUI mode. The save files were containing the ds.relax_gui object and restoring it on loading. This caused the data storage of the GUI to change underneath the GUI resulting in a crash or race conditions.
* Fix for the resetting of the relax data store - the cdp structure is now set to None. Previously the data store would be cleared, but the __builtin__.cdp structure would point to the old current data pipe, keeping it in existence and causing problems in the GUI.
<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://dx.doi.org/10.1039/b702202f 10.1039/b702202f).
* [*d'Auvergne and Gooley, 20082008b] 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://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).
<section end=references/>
<HarvardReferences />
