Trusted, Bureaucrats
4,228
edits
Changes
Formatting of all symbols/parameters.
<section begin=description/>
This is a minor feature release. Improvements include the creation of ''R<sub>ex</sub>'' value files scaled to all spectrometer frequencies for the model-free auto-analysis [d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008] and some new capabilities in the structural API. Feel free to upgrade if you wish to use these new features.
<section end=description/>
* Helix and sheet information from PDB files are now stored in the internal structural object as metadata. The [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb] and [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb] user functions will preserve this information.
* The numbers output by the [http://www.nmr-relax.com/manual/value_display.html value.display] and [http://www.nmr-relax.com/manual/value_write.html value.write] user functions can now be scaled.
* The model-free auto-analysis now generates field strength dependent Rex R<sub>ex</sub> files for each field present.
<section end=features/>
<section begin=changes/>
* Added a comment to the output from value.display and value.write to describe the parameter. This idea is discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428. The idea is to take the parameter description from the specific analysis API and add it to the top of the file or output. This is to help understand what the Rex R<sub>ex</sub> value are. For example for the Rex R<sub>ex</sub> parameter the first line would be: "# Parameter description: Chemical exchange relaxation (sigma_ex = Rex / omega**2)."
* Created the Structure.test_read_merge system test to test a new concept - merging of structures. The idea is to add the merge argument to the structure.read_pdb user function to allow two different structures in two PDB files to be merged. This is useful if structures of individual domains have have been solved separately and are located in two PDB files. Then with the merge flag, you will not need to use and external program or hand edit PDB files to join them.
* Added the merge flag to the structure.read_pdb user function. This currently does nothing.
* Created the Structure.test_metadata_xml system test. This is used to check that the structural metadata (currently helices and sheets) are stored in the relax XML save files and then can be read back into relax again.
* The helix and sheet metadata is now stored in and read from relax XML state files.
* Added the scaling argument to the value.display and value.write user functions. The idea comes from a suggestion by Angelo Figueiredo <am dott figueiredo att fct dott unl dott pt> and was discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428/focus=1430. This allows the user to scale parameters to any value, for example scaling the Rex R<sub>ex</sub> value to the field strength dependent value.* The model-free auto-analysis (the dauvergne_protocol) now generates field strength dependent Rex R<sub>ex</sub> files. The idea comes from a suggestion by Angelo Figueiredo <am dott figueiredo att fct dott unl dott pt> and was discussed at http://thread.gmane.org/gmane.science.nmr.relax.user/1428/focus=1430. One file per field strength is generated and named 'rex_600' for 600 MHz, for example. The new scaling argument of the value.write user function is being used to scale the tiny field strength independent value used internally in relax to the Rex R<sub>ex</sub> value in rad.s^-1 that you would see in an R2 data set.
* Added the new 'comment' argument to the value.write user function. This is used to add user comments to the top of the file.
* The model-free auto-analysis (the dauvergne_protocol module) now adds comments to the Rex R<sub>ex</sub> files. This is through the new comment argument of the value.write user function. These comments explain that the Rex R<sub>ex</sub> values are scaled to the stated field strength.
* Modified the Mf.test_dauvergne_protocol system test to check for all the files and directories created.
* Created the new lib.text.sectioning module for formatting titles, subtitles and other sectioning text. The two functions title() and subtitle() have been implemented.