Difference between revisions of "Relax 3.1.6"

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(Formatting of all symbols/parameters.)
(User function HTML manual links.)
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*  Added the time point to be sent into the return function of cpmg frequencies.  Regarding [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].
 
*  Added the time point to be sent into the return function of cpmg frequencies.  Regarding [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].
 
*  Improved unit test for cathing both time and dispersion point when looping over experiment and time points.  Regarding [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].
 
*  Improved unit test for cathing both time and dispersion point when looping over experiment and time points.  Regarding [https://gna.org/bugs/?21665 bug #21665 - Running a CPMG analysis with two fields at two delay times].
*  Modified the spectrum.read_intensities user function frontend to load multiple files.  This follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5057/focus=5062.
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*  Modified the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function] frontend to load multiple files.  This follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5057/focus=5062.
*  Implemented the GUI element for loading multiple files.  This follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5057/focus=5062.  This is via the new user function argument type "file sel multi", now used by the spectrum.read_intensities user function.  The file selection element consists of two parts.  The GUI element embedded in the user function wizard page is similar to the "file sel" element, except that the preview button is not present.  The file selection button behaviour is also different in that it launches the new multiple file selection window.  The multiple file selection window is based on the 'sequence' data window, as used in the spectrum ID argument for the spectrum.read_intensities user function.  However the ListCtrl element has been replaced by a custom scrolled panel.  The 'Add' button adds a new file selection GUI element consisting of a TextCtrl for displaying and manual editing of the file name, the file selection button for launching the relax file selection dialog, and the preview button lost in the parent GUI element.  The scrolled panel allows more elements in the panel than can fit in the window.  The 'Delete all' and 'OK' buttons from the 'sequence' data window are also present and function as expected.
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*  Implemented the GUI element for loading multiple files.  This follows from the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/5057/focus=5062.  This is via the new user function argument type "file sel multi", now used by the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function].  The file selection element consists of two parts.  The GUI element embedded in the user function wizard page is similar to the "file sel" element, except that the preview button is not present.  The file selection button behaviour is also different in that it launches the new multiple file selection window.  The multiple file selection window is based on the 'sequence' data window, as used in the spectrum ID argument for the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function].  However the ListCtrl element has been replaced by a custom scrolled panel.  The 'Add' button adds a new file selection GUI element consisting of a TextCtrl for displaying and manual editing of the file name, the file selection button for launching the relax file selection dialog, and the preview button lost in the parent GUI element.  The scrolled panel allows more elements in the panel than can fit in the window.  The 'Delete all' and 'OK' buttons from the 'sequence' data window are also present and function as expected.
 
*  Modification of the new multiple file selection GUI element.  The multiple file selection window now shows the index (plus one) of each file selection element at the front of that element.  This way the user can easily see how many file elements there are and can match file names to numbers.  This will help in making sure that the file names and spectrum ID elements correspond to each other.
 
*  Modification of the new multiple file selection GUI element.  The multiple file selection window now shows the index (plus one) of each file selection element at the front of that element.  This way the user can easily see how many file elements there are and can match file names to numbers.  This will help in making sure that the file names and spectrum ID elements correspond to each other.
 
*  Added a 'Delete' button to the new multiple file selection GUI window.  This simply deletes the last item in the list.  This will be useful if the user clicks on the 'Add' button too many times - instead of clicking 'Delete all' and having to re-select all files, now the last element can be removed.
 
*  Added a 'Delete' button to the new multiple file selection GUI window.  This simply deletes the last item in the list.  This will be useful if the user clicks on the 'Add' button too many times - instead of clicking 'Delete all' and having to re-select all files, now the last element can be removed.
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*  Renamed the test_loop_exp_time() dispersion unit test to test_loop_exp_frq_offset_point_time().  This is for the specific_analyses.relax_disp.disp_data.Test_disp_data.test_loop_exp_frq_offset_point_time() unit test.  The name better reflects the function being tested.
 
*  Renamed the test_loop_exp_time() dispersion unit test to test_loop_exp_frq_offset_point_time().  This is for the specific_analyses.relax_disp.disp_data.Test_disp_data.test_loop_exp_frq_offset_point_time() unit test.  The name better reflects the function being tested.
 
*  Created the test_loop_exp_frq() dispersion unit test.  This checks the operation of the loop_exp_frq() function from the module specific_analyses.relax_disp.disp_data.  It uses the data attached to the bug report at https://gna.org/bugs/?21665.
 
*  Created the test_loop_exp_frq() dispersion unit test.  This checks the operation of the loop_exp_frq() function from the module specific_analyses.relax_disp.disp_data.  It uses the data attached to the bug report at https://gna.org/bugs/?21665.
*  Fixes for the unit tests of the spectrum.read_intensities user function.  A number of checks were not correctly set up, and the recent changes caused others to now fail.
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*  Fixes for the unit tests of the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function].  A number of checks were not correctly set up, and the recent changes caused others to now fail.
*  Modified the GUI window for inputting sequence data to include item numbers.  An non-editable initial column with the number of each item has been added.  This is to help the user when, for example, the items of one sequence element should match another (for example in the spectrum.read_intensities user function where multiple file names should match multiple spectrum IDs).
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*  Modified the GUI window for inputting sequence data to include item numbers.  An non-editable initial column with the number of each item has been added.  This is to help the user when, for example, the items of one sequence element should match another (for example in the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function] where multiple file names should match multiple spectrum IDs).
 
*  Added a 'Delete' button to the sequence input GUI window.  This is to match the multiple file selection GUI window.  The button allows the user to delete the last item from the list.  So if 'Add' has been clicked too many times, the user does not have to start again from scratch by clicking on 'Delete all'.
 
*  Added a 'Delete' button to the sequence input GUI window.  This is to match the multiple file selection GUI window.  The button allows the user to delete the last item from the list.  So if 'Add' has been clicked too many times, the user does not have to start again from scratch by clicking on 'Delete all'.
 
*  More modifications to the sequence input GUI window to match the multiple file selection element.  The window now starts with a single element rather than nothing.
 
*  More modifications to the sequence input GUI window to match the multiple file selection element.  The window now starts with a single element rather than nothing.
 
*  Continued expanding the tutorial for performing a relaxation dispersion analysis in the GUI.  This is for the dispersion chapter of the manual.
 
*  Continued expanding the tutorial for performing a relaxation dispersion analysis in the GUI.  This is for the dispersion chapter of the manual.
*  Created the Peak_lists.test_read_peak_list_sparky_double system test.  This is used to test the loading of multiple files simultaneously by the spectrum.read_intensities user function.
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*  Created the Peak_lists.test_read_peak_list_sparky_double system test.  This is used to test the loading of multiple files simultaneously by the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function].
*  Expanded the Peak_lists.test_read_peak_list_sparky_double system test to check all intensities.  This now checks all of the peak heights read by the spectrum.read_intensities user function.
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*  Expanded the Peak_lists.test_read_peak_list_sparky_double system test to check all intensities.  This now checks all of the peak heights read by the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function].
*  Expanded the capabilities of the spectrum.read_intensities user function.  Now multiple files can be loaded simultaneously.
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*  Expanded the capabilities of the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function].  Now multiple files can be loaded simultaneously.
*  Fix for the multiple file selection GUI element.  The GUI element now returns single values rather than lists from the GetValue() function when only a single file is selected.  This allows the spectrum.read_intensities user function to operate normally again in the GUI.
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*  Fix for the multiple file selection GUI element.  The GUI element now returns single values rather than lists from the GetValue() function when only a single file is selected.  This allows the [http://www.nmr-relax.com/manual/spectrum.read_intensities.html spectrum.read_intensities user function] to operate normally again in the GUI.
 
*  Minor fix for the Relax_disp.test_bug_21076_multi_col_peak_list system test.  The spectrum ID argument ['auto'] has been changed to the single value of 'auto'.  This argument should not be a list.
 
*  Minor fix for the Relax_disp.test_bug_21076_multi_col_peak_list system test.  The spectrum ID argument ['auto'] has been changed to the single value of 'auto'.  This argument should not be a list.
 
*  Expansion of the tutorial for running the relaxation dispersion analysis in the GUI.  The tutorial is now close to complete.  The peak intensity loading wizard section is complete as well the model selection window and optimisation settings sections and the relax execution.
 
*  Expansion of the tutorial for running the relaxation dispersion analysis in the GUI.  The tutorial is now close to complete.  The peak intensity loading wizard section is complete as well the model selection window and optimisation settings sections and the relax execution.
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*  Added save state for bug 21344.  Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R<sub>1&rho;</sub> dataset with missing combinations of time and spin-lock field strengths].
 
*  Added save state for bug 21344.  Regarding [https://gna.org/bugs/?21344 bug #21344 - Handling of in sparse acquired R<sub>1&rho;</sub> dataset with missing combinations of time and spin-lock field strengths].
 
*  Completed the tutorial for using the dispersion analysis in the GUI.  This is for the relaxation dispersion chapter of the manual.
 
*  Completed the tutorial for using the dispersion analysis in the GUI.  This is for the relaxation dispersion chapter of the manual.
*  Some edits for the tutorial on using the dispersion GUI analysis.  The results of the relax_disp.insignificance user function are now shown to demonstrate what this does.
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*  Some edits for the tutorial on using the dispersion GUI analysis.  The results of the [http://www.nmr-relax.com/manual/relax_disp.insignificance.html relax_disp.insignificance user function] are now shown to demonstrate what this does.
 
*  Fixes for some incorrectly reported results in the dispersion GUI tutorial in the manual.  The non-clustered results had been incorrectly copied from the log messages.
 
*  Fixes for some incorrectly reported results in the dispersion GUI tutorial in the manual.  The non-clustered results had been incorrectly copied from the log messages.
 
*  More incorrect value fixes for the dispersion GUI tutorial in the manual.  The pA and kex values were also somehow incorrect.
 
*  More incorrect value fixes for the dispersion GUI tutorial in the manual.  The pA and kex values were also somehow incorrect.
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*  A concluding statement has been added to the dispersion GUI analysis tutorial in the manual.
 
*  A concluding statement has been added to the dispersion GUI analysis tutorial in the manual.
 
*  Added spacing in front of all lstlisting environments in the relaxation dispersion chapter of the manual.
 
*  Added spacing in front of all lstlisting environments in the relaxation dispersion chapter of the manual.
*  Spelling fix for the spectrometer frequency checks of the spectrometer.frequency user function.
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*  Spelling fix for the spectrometer frequency checks of the [http://www.nmr-relax.com/manual/spectrometer.frequency.html spectrometer.frequency user function].
 
*  Spell checking of the entire relaxation dispersion chapter of the manual.
 
*  Spell checking of the entire relaxation dispersion chapter of the manual.
 
*  Correction for some text in the dispersion chapter of the manual.  The text 'are differentially defined' has been changed to 'are dually defined', as the word differentially was incorrect.
 
*  Correction for some text in the dispersion chapter of the manual.  The text 'are differentially defined' has been changed to 'are dually defined', as the word differentially was incorrect.

Revision as of 08:16, 10 September 2014


Description

This is a major feature and bugfix release. A comprehensive tutorial has been added to the relaxation dispersion chapter of the manual which shows, step-by-step, the dispersion analysis in the GUI using screenshots. Other changes include improved PDB chain ID support, a new mode for running a relax script and then entering the prompt UI mode, multiple file reading by the spectrum.read_intensities user function, and improvements to the relaxation dispersion analysis. A number of major bugs in the dispersion analysis concerning different relaxation delay times for different experiments and for improved handling of the offset have also been fixed. A number of important GUI bugs have also been fixed. All users are recommended to upgrade to this version of relax.


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).


CHANGES file

Version 3.1.6 (28 February 2014, from /trunk) http://svn.gna.org/svn/relax/tags/3.1.6

Features

  • Full support for PDB chain IDs in the internal structural object.
  • Improvements for the devel_scripts/python_seek.py for finding all installed Python versions and modules. Individual modules can now be specified on the command line.
  • The pedantic command line option -p, --pedantic has been renamed to -e, --escalate.
  • The new prompt command line option -p, --prompt causes the relax prompt mode to launch after running a script to allow relax to be inspected interactively.
  • Better organisation of the relax command line options into groups, as shown by running 'relax -h'.
  • A tutorial for using the relaxation dispersion analysis in the GUI has been added to the manual. This includes step-by-step instructions with many screenshots.
  • Improvements to the manual including better and consistent line breaking for the GUI menu item text, user functions, file and directory paths, and Python module paths.
  • The spectrum.read_intensities user function can now load multiple files simultaneously, allowing for simplified use in the GUI.
  • Addition of a new GUI window element for loading multiple files.
  • Improvements to the sequence data input GUI window including the item count being displayed and a 'Delete' button to remove the last element.
  • Improvement for the relaxation dispersion auto-analysis - the names of the automatically created data pipes are now unique by appending the name of the data pipe bundle to the end. This allows multiple dispersion auto-analyses to exist simultaneously in the GUI or within one relax state file.
  • The relaxation dispersion analysis now handles deselected spins.
  • Improved colour coding of relax log messages in the relax manual.
  • The relaxation dispersion auto-analysis now creates the chi2.out text file. This is for more easily comparing the chi-squared values between analyses.


Changes


Bugfixes


See also