Relax 3.1.0 - Revision history

Bugman: Convert to internal links for Tutorial for adding relaxation dispersion models to relax.

2020-10-16T13:30:19Z

Convert to internal links for Tutorial for adding relaxation dispersion models to relax.

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Bugman: Switch to the {{gna task url}} template to remove dead Gna! links.

2020-10-16T12:39:25Z

Switch to the {{gna task url}} template to remove dead Gna! links.

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Bugman: /* Changes */ Switch to the {{relax developer link}} template to remove dead Gna! links.

2020-10-15T12:04:32Z

Changes: Switch to the {{relax developer link}} template to remove dead Gna! links.

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Bugman: /* Changes */ Switch to the {{relax developer link}} template to remove dead Gna! links.

2020-10-15T11:50:41Z

Changes: Switch to the {{relax developer link}} template to remove dead Gna! links.

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

2020-10-14T11:23:13Z

Links: Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: Switch to the {{gna link}} template for avoiding dead links.

2020-10-05T22:22:41Z

Switch to the {{gna link}} template for avoiding dead links.

Bugman: Undo revision 6839 by Bugman (talk)

2016-11-18T07:22:20Z

Undo revision 6839 by Bugman (talk)

Bugman: /* References */ Fix for the Korzhnev et al., 2005 citation.

2016-11-18T07:21:14Z

References: Fix for the Korzhnev et al., 2005 citation.

Bugman: Internal link to Modelfree4.

2015-12-15T16:13:01Z

Internal link to Modelfree4.

Bugman: Spacing fix.

2015-11-03T17:52:49Z

Spacing fix.

@@ Line 626: / Line 626: @@
 *  Expanded the modelling of dispersion data section of the relax user manual.
 *  Expansion of the modelling of dispersion data section of the relax user manual.
-*  The relaxation dispersion auto-analysis now outputs text and Grace files for all parameters.  This is in response to [https://gna.org/bugs/?20917 bug #20917] submitted by [https://gna.org/users/tlinnet Troels Linnet].
+*  The relaxation dispersion auto-analysis now outputs text and Grace files for all parameters.  This is in response to [https://gna.org/bugs/?20917 bug #20917] submitted by {{relax developer link|username=tlinnet|text=Troels Linnet}}.
 *  The Monte Carlo simulations now generate parameter errors for the relaxation dispersion analysis.  The simulation index was being ignored, hence the input data was never the randomised data and all errors were zero.
 *  Removed many decimal points from the MHz value in the Grace plots from relax_disp.plot_disp_curves.
@@ Line 633: / Line 633: @@
 *  Fix for the dispersion auto-analysis - p<sub>A</sub> and p<sub>B</sub> parameters are no longer output for the [[IT99]] model.  These are not parameters of this model.
 *  Updated the relax results for Flemming Hansen's truncated CPMG data for all the recent changes.
-*  Fix for [https://gna.org/bugs/?20916 bug #2091 - Suggestion for Python script for PNG/EPS/SVG conversion of grace files].  [https://gna.org/users/tlinnet Troels Linnet] provided this patch, and was discovered during work on a Windows 7 system.  This patch will provide a grace2images.py file in each folder where a call to specific_analyses/relax_disp/disp_data.py is called.  It is called in plot_disp_curves(dir=None, force=None) and call the function lib.software.grace.script_grace2images().  The conversion script can be executed in Linux and Windows, if the PATH to xmgrace has been specified.  It will look in a folder for grace files of ending *.agr and by default convert to PNG.  One can also convert to EPS and SVG.  Probably more options could be added, as PDF.  The conversion depends on xmgrace compilation, and so PNG conversion is for fast inspection of graphs in folder, and EPS for further external conversion to PDF etc.  The patch, the output file, and small script to test is attached.  I miss to make the file executable in relax, so the script can be executed directly in Linux.
+*  Fix for [https://gna.org/bugs/?20916 bug #2091 - Suggestion for Python script for PNG/EPS/SVG conversion of grace files].  {{relax developer link|username=tlinnet|text=Troels Linnet}} provided this patch, and was discovered during work on a Windows 7 system.  This patch will provide a grace2images.py file in each folder where a call to specific_analyses/relax_disp/disp_data.py is called.  It is called in plot_disp_curves(dir=None, force=None) and call the function lib.software.grace.script_grace2images().  The conversion script can be executed in Linux and Windows, if the PATH to xmgrace has been specified.  It will look in a folder for grace files of ending *.agr and by default convert to PNG.  One can also convert to EPS and SVG.  Probably more options could be added, as PDF.  The conversion depends on xmgrace compilation, and so PNG conversion is for fast inspection of graphs in folder, and EPS for further external conversion to PDF etc.  The patch, the output file, and small script to test is attached.  I miss to make the file executable in relax, so the script can be executed directly in Linux.
 *  Mac OS X bug fix for the new analysis GUI wizard.  The blank button is now using the blank_150x150.png file instead of no image, preventing nasty wxPython bugs from appearing on that system.
 *  Fix for [https://gna.org/bugs/?20917 bug #20917].  The problem is that the Grace files for each spin system are not created by the [http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html relax_disp.plot_disp_curves user function] as the ':' character cannot be placed in a file name in MS Windows.  All of the file name from the ':' onwards is lost.  The solution is to replace each of the characters '#:@' in the spin ID string with '_'.
-*  Another update of the relax results for Flemming Hansen's truncated CPMG data.  This includes the grace2images.py script creation contributed by [https://gna.org/users/tlinnet Troels Linnet] and the change of the file name of the per-spin dispersion curves.
+*  Another update of the relax results for Flemming Hansen's truncated CPMG data.  This includes the grace2images.py script creation contributed by {{relax developer link|username=tlinnet|text=Troels Linnet}} and the change of the file name of the per-spin dispersion curves.
 *  The value checks in the Relax_disp.test_hansen_cpmg_data_auto_analysis system test are now less precise.  This is to allow the tests to pass on certain MS Windows systems.
 *  Fix for the setting of the execute permissions on the grace2images.py scripts.  The problem was identified in the post at http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000.  This is within the [http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html relax_disp.plot_disp_curves user function] after the grace2images.py script has been created.  The commit matches the changes from trunk for the [[Modelfree4]] batch script.
@@ Line 875: / Line 875: @@
 *  Implemented the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html relax_disp.spin_lock_offset user function].  This includes both the front end and the back end specific_analyses.relax_disp.disp_data.spin_lock_offset() function.
 *  The offset is now set for all spectra in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test.  Previously only the reference was set.
-*  Fixed a typo in the dispersion chapter of the user manual.  This was identified by [https://gna.org/users/tlinnet Troels Linnet] at http://thread.gmane.org/gmane.science.nmr.relax.devel/4410.
+*  Fixed a typo in the dispersion chapter of the user manual.  This was identified by {{relax developer link|username=tlinnet|text=Troels Linnet}} at http://thread.gmane.org/gmane.science.nmr.relax.devel/4410.
 *  Fix for the [http://www.nmr-relax.com/manual/relax_disp_spin_lock_offset.html relax_disp.spin_lock_offset user function].  The cdp.dispersion_points structure was being updated when it should not be touched - a remnant of the relax_disp.spin_lock_field backend which this code was copied from.
 *  Added some more arguments to the dispersion target function class for off-resonance R<sub>1&rho;</sub> models.  This is the structure for the spin-lock offsets and the tilt angles for each spin.
@@ Line 892: / Line 892: @@
 *  Turned off clustering in the Relax_disp.test_r1rho_off_res_fixed_time_tp02 system test.  This speeds the test up by more than half.
 *  Fix for the [[TP02]] dispersion model.  The rotating frame tilt angle for this model is calculated from the population averaged chemical shift and not the equal weighted average.
-*  Attempt at fixing [https://gna.org/bugs/?21080 bug #21080].  This was reported by [https://gna.org/users/tlinnet Troels Linnet].  The problem is a standard GUI problem.  The text from a wxPython GUI is a Unicode string.  But relax requires standard strings.  Therefore the gui.string_conv.gui_to_str() function needs to be used on the return value of the GUI element GetValue() method, but this call was forgotten.
+*  Attempt at fixing [https://gna.org/bugs/?21080 bug #21080].  This was reported by {{relax developer link|username=tlinnet|text=Troels Linnet}}.  The problem is a standard GUI problem.  The text from a wxPython GUI is a Unicode string.  But relax requires standard strings.  Therefore the gui.string_conv.gui_to_str() function needs to be used on the return value of the GUI element GetValue() method, but this call was forgotten.
 *  Fix for the synthetic data for the [[TP02]] dispersion model.  The chemical shift is being set to that of state A, the major species, rather than the non-weighted chemical shift average.  This could also have been set to the population weighted average.
 *  The [[TP02]] dispersion model now assumes the chemical shift is that of the major population A.  Previously the linear chemical shift average was assumed.
@@ Line 1,249: / Line 1,249: @@
 *  Fix for the [[NS CPMG 2-site expanded]] model equations in the manual.
 *  Better section spacing in the dispersion chapter of the manual.  Each model section is now on a new page.
-*  Fix for the display of the spin-lock &nu;<sub>1</sub> values in the dispersion GUI tab.  This was reported by [https://gna.org/users/tlinnet Troels] at http://thread.gmane.org/gmane.science.nmr.relax.devel/4708.  The GUI spectrum element at gui.components.spectrum was at fault, the add_disp_point() method was buggy.
+*  Fix for the display of the spin-lock &nu;<sub>1</sub> values in the dispersion GUI tab.  This was reported by {{relax developer link|username=tlinnet|text=Troels}} at http://thread.gmane.org/gmane.science.nmr.relax.devel/4708.  The GUI spectrum element at gui.components.spectrum was at fault, the add_disp_point() method was buggy.
 *  Fix for the right click pop up menu entry "Set the spin-lock field" in the dispersion GUI tab.  This is for the spectra list [http://www.nmr-relax.com/manual/relax_disp_spin_lock_field.html relax_disp.spin_lock_field user function] call.  The reference spectra are now detected and the field value set to None.  This fix has been propagated to the [http://www.nmr-relax.com/manual/relax_disp_cpmg_frq.html relax_disp.cpmg_frq user function] menu entry as well.
 *  Correcting the R<sub>1&rho;</sub> settings script for the right calculation of the spin-lock offset, omega_rf, in ppm when offset values are provided in Hz.

@@ Line 1,595: / Line 1,595: @@
 For reference, the following links are also part of the announcement for this release:
 * [http://wiki.nmr-relax.com/Relax_3.1.0 Official release notes]
-* [https://gna.org/forum/forum.php?forum_id=2421 Gna! news item]
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2421|text=Gna! news item}}
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/46 Gmane]
 * [https://mail.gna.org/public/relax-announce/2013-11/msg00001.html Local archives]

@@ Line 1,087: / Line 1,087: @@
 *  Modified headers for scripts producing analysis for data which is full or truncated.  Progress [https://gna.org/support/?3071 sr #3071 - Implementation of Tollinger/Kay dispersion model (2001)].  Following the guide at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
 *  Created the dispersion default_value_doc object.  This table is needed for the [http://www.nmr-relax.com/manual/value_set.html value.set user function].
-*  Huge speed win for the relaxation dispersion analysis - optimisation now uses the multi-processor.  The relaxation dispersion optimisation has been parallelised at the level of the spin clustering.  It uses [https://gna.org/users/varioustoxins Gary Thompson's] multi-processor framework.  This allows the code to run on multi-core, multi-processor systems, clusters, grids, and anywhere the OpenMPI protocol is available.  Because the parallelisation is at the cluster level there are some situations, whereby instead of optimisation being faster when running on multiple slaves, the optimisation will be slower.  This is the case when all spins being studied in clustered into a small number of clusters.  It is also likely to be slower for the [http://www.nmr-relax.com/manual/minimise.html minimise user function] when no clustering is defined, due to the overhead costs of data transfer (but for the numeric models, in this case there will be a clear win).  The two situations where there will be a huge performance win is the [http://www.nmr-relax.com/manual/grid_search.html grid_search user function] when no clustering is defined and the Monte Carlo simulations for error analysis.
+*  Huge speed win for the relaxation dispersion analysis - optimisation now uses the multi-processor.  The relaxation dispersion optimisation has been parallelised at the level of the spin clustering.  It uses {{gna link|url=gna.org/users/varioustoxins|text=Gary Thompson's}} multi-processor framework.  This allows the code to run on multi-core, multi-processor systems, clusters, grids, and anywhere the OpenMPI protocol is available.  Because the parallelisation is at the cluster level there are some situations, whereby instead of optimisation being faster when running on multiple slaves, the optimisation will be slower.  This is the case when all spins being studied in clustered into a small number of clusters.  It is also likely to be slower for the [http://www.nmr-relax.com/manual/minimise.html minimise user function] when no clustering is defined, due to the overhead costs of data transfer (but for the numeric models, in this case there will be a clear win).  The two situations where there will be a huge performance win is the [http://www.nmr-relax.com/manual/grid_search.html grid_search user function] when no clustering is defined and the Monte Carlo simulations for error analysis.
 *  Decreased the number of grid increments in the dispersion sample scripts from 21 to 11.  This is a much easier optimisation problem than the other analyses in relax, so 21 increments is an overkill.  It also takes far too long for some of the models due to the high number of parameters.
 *  Removed a tonne of unused imports from the modules of the specific_analyses.relax_disp package.

@@ Line 1,614: / Line 1,614: @@
 * [*Davis et al., 1994] {{#lst:Citations|Davis94}}
 * [*Ishima and Torchia 1999] {{#lst:Citations|IshimaTorchia99}}
-* [*Korzhnev et al., 2005] {{#lst:Citations|Korzhnev05}}
+* [*Korzhnev et al., 2005a] {{#lst:Citations|Korzhnev05a}}
 * [*Luz and Meiboom 1963] {{#lst:Citations|LuzMeiboom63}}
 * [*Meiboom 1961] {{#lst:Citations|Meiboom61}}

@@ Line 1,614: / Line 1,614: @@
 * [*Davis et al., 1994] {{#lst:Citations|Davis94}}
 * [*Ishima and Torchia 1999] {{#lst:Citations|IshimaTorchia99}}
-* [*Korzhnev et al., 2005a] {{#lst:Citations|Korzhnev05a}}
+* [*Korzhnev et al., 2005] {{#lst:Citations|Korzhnev05}}
 * [*Luz and Meiboom 1963] {{#lst:Citations|LuzMeiboom63}}
 * [*Meiboom 1961] {{#lst:Citations|Meiboom61}}

@@ Line 638: / Line 638: @@
 *  Another update of the relax results for Flemming Hansen's truncated CPMG data.  This includes the grace2images.py script creation contributed by [https://gna.org/users/tlinnet Troels Linnet] and the change of the file name of the per-spin dispersion curves.
 *  The value checks in the Relax_disp.test_hansen_cpmg_data_auto_analysis system test are now less precise.  This is to allow the tests to pass on certain MS Windows systems.
-*  Fix for the setting of the execute permissions on the grace2images.py scripts.  The problem was identified in the post at http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000.  This is within the [http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html relax_disp.plot_disp_curves user function] after the grace2images.py script has been created.  The commit matches the changes from trunk for the Modelfree4 batch script.
+*  Fix for the setting of the execute permissions on the grace2images.py scripts.  The problem was identified in the post at http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000.  This is within the [http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html relax_disp.plot_disp_curves user function] after the grace2images.py script has been created.  The commit matches the changes from trunk for the [[Modelfree4]] batch script.
 *  Shifted from argparse to optparse in the grace2images.py scripts from relax_disp.plot_disp_curves.  This is associated with [https://gna.org/bugs/?20916 bug #20916] and the change suggested in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000.  The argparse module is only available from for Python 2.7.3 (the version with many Python 3 features backported) and Python &ge; 3.2.  The module has been replaced with the similar optparse module as used by relax, and which available in all Python version supported by relax.
 *  Updated the grace2images.py scripts created by the [http://www.nmr-relax.com/manual/relax_disp_plot_disp_curves.html relax_disp.plot_disp_curves user function].  This was discussed in [https://gna.org/bugs/?20916 bug #20916] and the change suggested in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/3953/focus=4000.  Improved that both small and big letters for image types can be used on the command line.

@@ Line 1,434: / Line 1,434: @@
 *  Added support for <sup>1</sup>H SQ CPMG data for the [[:Category:MMQ CPMG data|MMQ-type]] dispersion models.  The key is to skip the protons in the spin cluster loops and to instead find the proton spin containers attached to the heteronuclei of the spins of the cluster.  The EXP_TYPE_PROTON_SQ_CPMG and EXP_TYPE_PROTON_MQ_CPMG experiment type variables have been created to aid this.  The MODEL_LIST_MMQ list variable has also been created to more consistently identify the [[:Category:MMQ CPMG data|MMQ-type]] dispersion models.  The has_disp_data() function has been created to simplify the finding of dispersion data for a given cluster, experiment type, spectrometer frequency and dispersion point.  The has_proton_sq_cpmg() and has_proton_mq_cpmg() are used to determine if there is proton dispersion data for the given heteronucleus.  The loop_exp() function has been modified to yield the proton SQ and MQ data if present.  Similarly the num_exp_types() and return_index_from_exp_type() functions exhibit different behaviour if this data is present.  The return_r2eff_arrays() function now assembles all of the proton data on top of the heteronuclear data by fetching the protons attached to the heteronuclei and aliasing the correct spin for the given experiment type.
 *  Updated the relaxation dispersion target functions.  The input data structures have changed type.
-*  Implemented the [[MMQ 2-site]] CPMG model equations[Korzhnev et al., 2005a].  The original code from Mathilde Lescanne and Dominique Marion has only slightly been modified for this change as the MQ data treatment in the Korzhnev et al., 2004 reference is the same as in the 2005 reference, but using a different notation.  This has been renamed to r2eff_mmq_2site_mq().  The new r2eff_mmq_2site_sq_dq_zq() function has been added to the lib.dispersion.mmq_2site module to allows the SQ, DQ, and ZQ R<sub>2eff</sub> data to be calculated.  This function follows the notation of the 2005 paper.  The populate_matrix() function has been modified to only accept one combined chemical shift difference value.  It can now also accept different values for R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup>, though the mmq_2site module defaults to R<sub>2A</sub><sup>0</sup>=R<sub>2B</sub><sup>0</sup>.
+*  Implemented the [[MMQ 2-site]] CPMG model equations [Korzhnev et al., 2005a].  The original code from Mathilde Lescanne and Dominique Marion has only slightly been modified for this change as the MQ data treatment in the Korzhnev et al., 2004 reference is the same as in the 2005 reference, but using a different notation.  This has been renamed to r2eff_mmq_2site_mq().  The new r2eff_mmq_2site_sq_dq_zq() function has been added to the lib.dispersion.mmq_2site module to allows the SQ, DQ, and ZQ R<sub>2eff</sub> data to be calculated.  This function follows the notation of the 2005 paper.  The populate_matrix() function has been modified to only accept one combined chemical shift difference value.  It can now also accept different values for R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup>, though the mmq_2site module defaults to R<sub>2A</sub><sup>0</sup>=R<sub>2B</sub><sup>0</sup>.
 *  The r2eff_mmq_*() functions of lib.dispersion.mmq_2site now accept different R<sub>2A</sub><sup>0</sup> and R<sub>2B</sub><sup>0</sup> arguments.  These are set to the same thing within the dispersion target function.
 *  Converted the spin specific 'r2', 'r2a', and 'r2b' dispersion parameters from lists to dictionaries.  The new parameter keys are based on the experiment type and the spectrometer frequency.  These keys are supported by the generate_r20_key() and decompose_r20_key() pair of functions in the specific_analyses.relax_disp.disp_data module.  This enables support for different R<sub>2</sub><sup>0</sup> parameters for each experiment type - a key piece of infrastructure for the [[:Category:MMQ CPMG data|MMQ]] models.  The [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] backend was modified so the parameter list only contains one instance for each of the 'r2', 'r2a', or 'r2b' strings.  The specific_analyses.relax_disp.parameters.loop_parameters() function was modified so that the R<sub>2</sub><sup>0</sup>key rather than frequency index is returned for the R<sub>2</sub><sup>0</sup> parameters.  Many other code changes were required.