Relax 3.1.1

Description

This is a major feature and bugfix release which adds support for reading 3D structures of organic molecules from Gaussian log files, the new lib.periodic_table and lib.nmr modules, the NS MMQ 3-site linear, NS MMQ 3-site, NS R1rho 3-site linear, and NS R1rho 3-site relaxation dispersion models, R_1ρ dispersion data sets where multiple offsets and multiple spin-lock fields have been collected for each spin, the loading of spins directly from peak lists, and the reading of NMRPipe seriesTab files. Due to the improvements and the bugs fixed in the relaxation dispersion analysis, all users are recommended to upgrade to this version.

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 3.1.1 (10 December 2013, from /trunk) http://svn.gna.org/svn/relax/tags/3.1.1

Features

• Support for reading 3D structures of organic molecules from Gaussian log files using the new structure.read_gaussian user function.
• Addition of the lib.periodic_table module for storing information about the periodic table.
• Addition of the lib.nmr module for basic NMR related functions. It currently has functions for converting between ppm, Hz, and rad.s^-1 units.
• Many improvements to the relaxation dispersion chapter of the user manual.
• The NS MMQ 3-site linear numeric model - the model for 3-site exchange using 3D magnetisation vectors linearised with k_AC = k_CA = 0 with the parameters {R₂⁰, ..., p_A, p_B, Δω_AB, Δω_BC, Δω^H_AB, Δω^H_BC, k_ex^AB, k_ex^BC}.
• The NS MMQ 3-site numeric model - the model for 3-site exchange using 3D magnetisation vectors with the parameters {R₂⁰, ..., p_A, p_B, Δω_AB, Δω_BC, Δω^H_AB, Δω^H_BC, k_ex^AB, k_ex^BC, k_ex^AC}.
• The NS R1rho 3-site linear numeric model - the model for 3-site exchange using 3D magnetisation vectors linearised with k_AC = k_CA = 0 with the parameters {R_1ρ', ..., p_A, p_B, Δω_AB, Δω_BC, k_ex^AB, k_ex^BC}.
• The NS R1rho 3-site numeric model - the model for 3-site exchange using 3D magnetisation vectors wit'h the parameters {R_1ρ', ..., p_A, p_B, Δω_AB, Δω_BC, k_ex^AB, k_ex^BC, k_ex^AC}.
• More model nesting in the relaxation dispersion auto-analysis (CR72 and MMQ CR72, LM63 and LM63 3-site).
• Large speed up of the TP02 and NS R1rho 2-site dispersion models by minimising repetitive calculations.
• Support for the loading of spins directly from peak lists.
• Support for the reading of peak intensities from NMRPipe seriesTab formatted files (*.ser).

Changes

• Small improvement for the devel_scripts/log_converter.py script for detecting commit boundaries.
• Added many small details to the release checklist document. This is for the formatting and editing of the CHANGES file, which is used for the release announcements. Some additional details about the API documentation at http://www.nmr-relax.com/api have been added too.
• Added sectioning printouts for the relaxation dispersion auto-analysis. This simply tells the user which part of the protocol is currently being performed.
• Setup for testing the sample_scripts/relax_disp/R1rho_analysis.py sample script. The script was copied into the test_suite/shared_data/dispersion/r1rho_off_res_tp02/ data directory where it will be tested on real data. The 'fake_sequence.in' and 'unresolved' files have been created to allow the script to run. And the script itself has been heavily debugged.
• All of the relaxation dispersion auto-analysis options are now exposed by the sample scripts. This included the pre_run_dir argument for specifying a directory of results from a non-clustered analysis and the flag for running MC simulations for all models.
• Added the DATA_PATH variable to the cpmg_analysis.py dispersion sample script. This allows the user to more easily specify a different directory for the files.
• Docstring improvement for the test_suite/shared_data/dispersion/r1rho_off_res_tp02/R1rho_analysis.py script.
• Synchronised the test_suite/shared_data/dispersion/Hansen/relax_disp.py with the sample script. This script now matches very closely with the sample_scripts/relax_disp/cpmg_analysis.py sample script. This is for sample script debugging purposes.
• Created a base data pipe for Flemming Hansen's truncated CPMG data for testing out missing data. The :4 spin is missing just a few data points, whereas the :71 spin is missing all 800 MHz data.
• Created the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. This is used to demonstrate a failure in the R2eff model when some data is missing.
• Expansion and fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. The parameters for spin :4 are now being checked, and all the checks updated for the changed data. The parameter values are slightly different as data is now missing and because only 3 spins are used for the error analysis whereas in all other Hansen CPMG data sets the more accurate errors are from all spins.
• The lib.dispersion.cr72.r2eff_CR72() function is now more robust. Values less than 1.0 are now caught to avoid passing it into the numpy.arccosh() function. This avoids many warning messages on Mac OS X.
• Added a Gaussian DFT optimisation log file to the shared data directories. This will be used to test the reading of structural data from Gaussian files.
• Modified the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test to catch another failure. This is the failure of all numeric models when all data from one magnetic field strength is missing for a spin.
• Created data for a NS MMQ 3-site (branched) model using cpmg_fit from Dmitry Korzhnev.
• The relax_disp.r2eff_read_spin user function now really strips comments and empty lines from the file.
• A big change to the usage of the relax_disp.r2eff_read_spin user function. Now the nu_CPMG frequency or the spin-lock field strength must be set prior to calling this user function. This allows for more flexibility as often the experiment IDs and frequency values in the files do not match to the same number of decimal places. The frequency is no longer read from the file but must be preset.
• Created a relax script for back calculating R_2eff values for the same parameters as cpmg_fit. This is for the NS MMQ 3-site (branched) CPMG dispersion model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite.
• Created the Relax_disp.test_ns_mmq_3site_branched system test. This is for the NS MMQ 3-site (branched) CPMG dispersion model. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite.
• Added the NS MMQ 3-site models to the dispersion variables. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.
• Added another Gaussian log file of strychnine, this time with DFT structure optimisation. The file is bzip2 compressed to save space.
• Created the Structure.test_read_gaussian_strychnine system test. This will be used for implementing and testing the structure.read_gaussian user function.
• Created the lib.periodic_table module for storing information about the periodic table. This is via the periodic_table object which will have different methods for obtaining different information about an element.
• Implemented the structure.read_gaussian user function. This will read the final structural data out of a Gaussian log file.
• Improved the checking of the Structure.test_read_gaussian_strychnine system test. This now checks all the atomic information loaded.
• Simple fix for the Relax_disp.test_korzhnev_2005_*_data system tests. The CPMG frequencies are now being set up in the setup_korzhnev_2005_data() method.
• Added support for the NS MMQ 3-site model parameters to the lib.text.gui module. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax.
• Added the NS MMQ 3-site models to the relax_disp.select_model user function frontend. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.
• Added support for the NS MMQ 3-site models to the relax_disp.select_model user function back end. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.
• Added support for the new 3-site exchange dispersion parameters. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_support_for_the_parameters.
• Removed the brackets from the NS MMQ 3-site (linear) dispersion model name.
• Renamed the Relax_disp.test_ns_mmq_3site_branched system test to Relax_disp.test_ns_mmq_3site.
• Fixes for the loop_parameters() dispersion function for the new NS MMQ 3-site model parameters. The new parameters were not being handled by this function.
• Created the target functions for the NS MMQ 3-site models. This is for the NS MMQ 3-site and NS MMQ 3-site (linear) CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.
• Added the R_2eff calculating functions for the NS MMQ 3-site models to the relax library. This is for the NS MMQ 3-site and NS MMQ 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
• Added the NS MMQ 3-site models to the dispersion auto-analysis. This is for the NS MMQ 3-site and NS MMQ 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.
• Added the NS MMQ 3-site models to the GUI model list. This is for the NS MMQ 3-site and NS MMQ 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.
• Updated the MMQ 2-site model description in the manual. The R2_DQ = R2_ZQ = R₂⁰ assumption is now explained.
• Added the NS MMQ 3-site models to the relax user manual. This is for the NS MMQ 3-site and NS MMQ 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
• Completed the MMQ 2-site documentation in the manual. The equations for the numeric evolution of SQ, ZQ and DQ data was missing.
• Huge speed ups of the relaxation dispersion analysis. This is due to the removal of huge inefficiencies in the loop_point(), return_cpmg_frqs() and return_spin_lock_nu1() functions of the specific_analysis.relax_disp.disp_data module. Two new functions return_cpmg_frqs_single() and return_spin_lock_nu1_single() have been introduces to pull out the nu_CPMG and spin-lock field strengths for a given experiment and spectrometer frequency. This avoids calling the loop_exp() and loop_frq() functions from within loop_point() which itself is often called inside a loop_exp() and loop_frq() sequence.
• Added the results of cpmg_fit minimisation of the cpmg_fit synthetic data for the NS MMQ 3-site model.
• Fixes for the NS MMQ 3-site dispersion models - the evolution matrix is now correctly constructed.
• Another fix for the NS MMQ 3-site dispersion models. The creation of the Z-matrix had a copy and paste error in that the heteronuclear chemical shift sign was negated when it should be positive. This was only in one of the two chemical shift numbers.
• Loosened the chi-squared check of the Relax_disp.test_ns_mmq_3site system test to allow it to pass.
• Speed up of the Relax_disp.test_ns_mmq_3site system test. The relax_disp.plot_disp_curves user function call is now skipped as it takes too long.
• Renamed the 'ns_mmq_3site_branched' dispersion test data directory to 'ns_mmq_3site'.
• Created the Relax_disp.test_ns_mmq_3site_linear system test and modified Relax_disp.test_ns_mmq_3site. The Relax_disp.test_ns_mmq_3site_linear system test uses the old data from the directory test_suite/shared_data/dispersion/ns_mmq_3site/, as this had k_AC = 0, now copied into the ns_mmq_3site_linear/ directory. This system test uses the NS MMQ 3-site linear model. The base data generated by cpmg_fit for the Relax_disp.test_ns_mmq_3site system test was modified so that k_AC is no longer 0, but set to 1000. This should properly test the NS MMQ 3-site model.
• Renamed the MMQ 2-site model to NS MMQ 2-site. This is so that the name matches those of the NS MMQ 3-site linear and NS MMQ 3-site models.
• Renamed all remaining instances of MMQ 2-site to NS MMQ 2-site. This is simply changing variable, method and module names.
• Removed the MMQ 3-site branched and MMQ 3-site linear models from the to do list in the manual. These two dispersion models are now implemented.
• Renamed the MQ CR72 dispersion model to MMQ CR72. The model is designed by Korzhnev et al., 2004 for proton-heteronuclear SQ, ZQ, DQ, and MQ data (or MMQ data), so the change is logical as the model is not just for MQ data.
• Clean up of the NS R1rho 3-site model names in the manual. The word 'branched' has been removed and the notation now matches the NS MMQ 3-site models.
• Clean up of the parameter lists in the dispersion model table of the manual.
• The p_C parameter constraints are now implemented for the 3-site dispersion models. The new constraints are 0 <= p_C <= p_B.
• Editing of the introduction section of the dispersion chapter of the manual.
• Added the NS MMQ 3-site parameters to the optimisation section of the dispersion chapter of the manual.
• Added some R_1ρ data from Dmitry Korzhnev's Fyn SH3 domain. This originates from the cpmg_fit software and is published data.
• Small fix for the documentation of the relax_disp.r2eff_read* user functions. This is for both relax_disp.r2eff_read and relax_disp.r2eff_read_spin.
• Created the new lib.nmr relax library module. This currently has a few simple functions for converting between ppm units and Hertz or rad/s units.
• The relax_disp.spin_lock_offset user function now uses the lib.nmr module. This is for converting between ppm and rad/s units.
• The relax_disp.r2eff_read_spin user function now can handle offset data in the file. If the new offset_col argument is set and disp_point_col is not, then the file being read can contain the spin-lock offset information rather than the spin-lock field strength values. This is only for R_1ρ-type data.
• Implemented GUI test which caches the bug #21076 - when loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur.
• Large redesign of the R_2eff/R_1ρ data structures. The five indices {Ei, Si, Mi, Oi, Di} for the experiment type, the spins of the cluster, the magnetic field strengths, the pulse offsets, and the dispersion points (nu_CPMG or nu1) respectively are now much better defined. The Oi dimension is new and allows for support of R_1ρ-type data whereby both different offsets and different spin-lock field strengths have been collected. Previously only one or the other was supported, but not both together. The offset information is now included as part of the spin R_2eff/R_1ρ key, even if not set. To support this, the specific_analyses.relax_disp.disp_data module now has the new functions loop_exp_frq_offset(), loop_exp_frq_offset_point(), loop_exp_frq_offset_point_time(), loop_frq_offset(), loop_frq_offset_point_key(), loop_offset(), and loop_offset_point(). All of the {Ei, Si, Mi, Oi, Di} dispersion indices throughout the source tree have been changed to ei, si, mi,oi, and di respectively. And the time index ti has also been introduced. These changes hugely simplify the code.
• The relax_disp.plot_disp_curves user function can now support 150 sets per Grace graph.
• The relax_disp.plot_disp_curves user function can now support 3000 sets per Grace graph.
• System test for sequence read expanded to include assertions of correct data. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added some more files for the Fyn SH3 R_1ρ test data. This includes the cpmg_fit input and output files, R₁ data files for relax as R₁ cannot optimised yet, and a relax script.
• Added system test for reading spins from a Sparky list. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added interpreter.spectrum.read_spins function. Work in progress for Support Request #3044 - load spins from Sparky list.
• Created the back end function for the read_spins function. Work in progress for Support Request #3044 - load spins from Sparky list.
• Fix for system test. Work in progress for Support Request #3044 - load spins from Sparky list.
• Extended reading of Sparky files to include residue names. Work in progress for Support Request #3044 - load spins from Sparky list.
• Expanded system test and made it pass for user function spectrum.read_spins. Work in progress for Support Request #3044 - load spins from Sparky list.
• Updated the GUI test to check for first ID in list. Fix for bug #21076 - When loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur.
• Added keyword dim to frontend function for spectrum.read_spins(). Work in progress for Support Request #3044 - load spins from Sparky list. This is associate data with the spins of up to two dimensions.
• Implemented system test for reading spins from NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Extended reading of spin residue names from NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Modified NMRPipe SeriesTab to read residue numbers and name for two-dimensional list. Work in progress for Support Request #3044 - load spins from Sparky list.
• Insert check if spin already exist before creating it. Work in progress for Support Request #3044 - load spins from Sparky list.
• Issuing a warning instead of error when loading spins from Sparky list where residue names are not present. Work in progress for Support Request #3044 - load spins from Sparky list.
• Issued a warning instead of error when loading spin residue names from a NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Changed to use return_spin for testing presence of spin. Work in progress for Support Request #3044 - load spins from Sparky list.
• Implemented another system test for reading NMRPipe SeriesTab files. Work in progress for Support Request #3044 - load spins from Sparky list.
• Fix for issuing a warning in reading spins from a NMRPipe SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Fix for issuing a warning when reading spins from a Sparky formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Implemented system test for reading spin IDs from NMRView formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Made reading of NMRView formatted file return the residue number as integer instead of string. Work in progress for Support Request #3044 - load spins from Sparky list.
• Fix for calling the warn() function. Work in progress for Support Request #3044 - load spins from Sparky list.
• Extended the error description for reading NMRView files. Work in progress for Support Request #3044 - load spins from Sparky list.
• Implemented system test for reading spins from a NMRPipe SeriesTab formatted file whereby the assignments for second dimension is missing. This will be a typically export from Sparky, converted to NMRPipe format, and processed with SeriesTab. Work in progress for Support Request #3044 - load spins from Sparky list.
• Fixed for reading spins from a NMRPipe SeriesTab formatted file whereby dimension 2 misses residue number and residue name. Work in progress for Support Request #3044 - load spins from Sparky list.
• Expanded the warning message for a system test. Work in progress for Support Request #3044 - load spins from Sparky list.
• Modified system test for reading an assignment whereby the second dimension is missing. Work in progress for Support Request #3044 - load spins from Sparky list.
• If dimension 2 in a SeriesTab formatted file does not contain residue number+name, it defaults to the dimension 1. Work in progress for Support Request #3044 - load spins from Sparky list.
• Implemented system test for reading spins from an XEasy file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Modified XEasy reading function to pass residue names back. Work in progress for Support Request #3044 - load spins from Sparky list.
• Copied a SeriesTab file for the implementation of double assignments in Sparky files.
• Redesign of the CPMG frequency and spin-lock field strength data structures. These now have an extra dimension for the offset so that the values are now experiment, magnetic field strength and offset dependent. If many offsets are present but are variable for each dispersion point, then this saves a lot of calculation time. This mainly affects R_1ρ-type data. To better handle this, all of the specific_analyses.relax_disp.disp_data.loop_*() functions have been modified to accept data values rather than indices.
• Improved the printout of the relax_disp.r2eff_read_spin user function for the R_2eff keys.
• Extended the system test for reading spins from Sparky files with empty residue name+number second dimension assignment. Work in progress for Support Request #3044 - load spins from Sparky list.
• Modified the Sparky peak list for two dimensional assignment example. This will typically be the export from CcpNmr Analysis. Work in progress for Support Request #3044 - load spins from Sparky list.
• Implemented a system test for using double assignments in Sparky formatted files. Work in progress for Support Request #3044 - load spins from Sparky list.
• Extended reading of spins from Sparky files for up to two dimensional assignments. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added example of CcpNmr analysis exported Sparky file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added system test for reading CcpNmr Analysis exported Sparky file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Modified the reading of Sparky files when exported from CcpNmr Analysis. The keyword 'Data' is not present here. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added a system test for using generic file for reading spins. Work in progress for Support Request #3044 - load spins from Sparky list.
• Modified the generic list to also return spin information when intensity is not present. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added another system test for returning spins from a generic file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added residue 4 to the R_2eff files for the truncated CPMG data from Flemming Hansen.
• Added cpmg_fit results to the software comparison table for Flemming Hansen's CPMG data. The cpmg_fit input and log files have been added as well.
• Shifted the software comparison down a directory so it can be used for all the different data.
• Added system test for reading chemical shift from NMRPipe SeriesTab file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Implemented reading of chemical shifts from NMRPipe SeriesTab formatted files. Work in progress for Support Request #3044 - load spins from Sparky list.
• Additional chemical shift reading test for SeriesTab formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Improvements for the find_intensity_keys() dispersion analysis function. This now handles the reference point None being converted to NaN in numpy arrays and the logic is now clearer.
• Changed some warnings in the dispersion analysis so they only show if R_1ρ data is loaded. This is for missing chemical shifts and R₁ data.
• Increased the size of the grid search in the Relax_disp.test_m61_exp_data_to_m61 system test. This should increase the stability of this test.
• Introduced the eliminate argument for the dispersion auto-analysis. This flag allows model and Monte Carlo simulation elimination to be deactivated.
• Updated two dispersion scripts in the test data directories to work with the current design.
• Updated more test suite scripts to call the relax_disp.cpmg_frq user function.
• The CR72 and MMQ CR72 models are now classified as nested in the dispersion auto-analysis. The grid search for the MMQ CR72 model will therefore be skipped and the parameters taken from the CR72 model. This will however rarely, if ever, be used.
• Fix for the relax_disp.plot_disp_curves user function. The interpolated curves now have all invalid points of 1e100 removed from the graph. This allows for reasonable graph scaling.
• The LM63 and LM63 3-site models are now classified as nested in the dispersion auto-analysis. The grid search for the LM63 3-site model is therefore skipped and the starting parameters for optimisation are set to those of the optimised LM63 model.
• Updated the relax results for the truncated CPMG data from Flemming Hansen. This includes the new results for the MMQ CR72 model. The analysis uses more model nesting. And the Grace plots now include the interpolation graphs (hence the plots are now bzip2 compressed).
• Updated the NESSY results for the truncated CPMG data from Flemming Hansen. This now uses the data from all residues to allow for a proper error analysis so the results are comparable to all the other software.
• Updated and reformatted the dispersion software comparison document.
• Made a system test test pass on Mac OS 10.9.
• Complete reworking of the NS R1rho 2-site dispersion model. The original code of Nikolai Skrynnikov and Martin Tollinger has been modified to match the behaviour of Dmitry Korzhnev's cpmg_fit software. The equations from Korzhnev et al., JACS 2005 (http://dx.doi.org/10.1021/ja0446855) have been used for the initial magnetisation and the R_1ρ' calculation. All equations have been added to the manual to clarify the model.
• Both relax and cpmg_fit input and output files for the Fyn SH3 R_1ρ data have been added. This is for the TP02 model and NS R1rho 2-site models. The cpmg_fit results include source code modifications to show the differences between the various 'corrections'. The dispersion software comparison file has been updated to include this data and to show the cpmg_fit verses relax differences.
• Updated the Relax_disp.test_tp02_data_to_ns_r1rho_2site system test. This is for the fixes of the NS R1rho 2-site dispersion model.
• Added the Korzhnev 2005 R_1ρ constant time correction to the 'To do' section of the dispersion chapter of the user manual.
• Removed the CR72 model for cpmg_fit from the dispersion software comparison table in the dispersion chapter of the user manual.
• Removed the CR72 model for GUARDD from the dispersion software comparison table in the dispersion chapter of the user manual. This software, like cpmg_fit, only supports the MMQ CR72 model which gives slightly different results to the original CR72 model when using only SQ CPMG-type data. Hence supporting MMQ CR72 does not automatically mean that the CR72 model can be optimised.
• Updated the ShereKhan error estimation technique in the dispersion software comparison table. This is for the dispersion chapter of the user manual. Adam Mazur communicated that errors are estimated using the covariance matrix in a private mail.
• Large rearrangements in the dispersion chapter of the user manual. The MMQ CPMG-type experiments now follow from the SQ CPMG-type experiments, hence the R_1ρ models are now listed last.
• Added a to do entry for the 3-site and N-site analytic R_1ρ models listed in Palmer and Massi 2006. This is for the 'To do' section of the dispersion chapter of the user manual.
• Updated the lib.dispersion.ns_r1rho_2site module docstring to explain the origin of the equations. This includes the Korzhnev 2005 reference where the modifications come from.
• Created some synthetic data for the NS R1rho 3-site linear dispersion model using cpmg_fit.
• Added cpmg_fit results for the Fyn SH3 R_1ρ test suite data using the 3-site numeric solution.
• Created the Relax_disp.test_ns_r1rho_3site_linear system test. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite.
• Added the NS R1rho 3-site models to the dispersion variables. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_the_model_to_the_list.
• Added the NS R1rho 3-site models to the relax_disp.select_model user function frontend. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end.
• Changed the order of the experiment types in the relax_disp.select_model user function frontend. The R_1ρ-type models have been shifted to the end so that the MMQ CPMG-type models are just after the SQ CPMG-type models.
• Changed the 'CPMG-type' to 'SQ CPMG-type' in the relax_disp.select_model user function frontend.
• Added support for the NS R1rho 3-site models to the relax_disp.select_model user function back end. This is for the NS R1rho 3-site and NS R1rho 3-site linear CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end.
• Decreased the amount of synthetic data in the ns_r1rho_3site_linear test suite shared data directory. The number of offsets for this NS R1rho 3-site linear model synthetic data has been decreased from 81 points to 21. This is because the large quantities of data slow the test suite down too much.
• Added a GUI test for reading spins from a spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added the GUI key 'new spectrum' to point to 'spectrum.read_spins'. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added the spectrum.read_spins GUI page for reading spins from a spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added radio button for reading spins from a spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Further added to the GUI test for reading spins from spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Speed up of the Relax_disp.test_ns_r1rho_3site_linear system test. Half of the data has been commented out, as too much data was being loaded for the test.
• Created the target functions for the NS R1rho 3-site models. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function.
• Added the R_2eff calculating functions for the NS R1rho 3-site models to the relax library. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library.
• Fix for GUI text string for the select radio button for reading spins from a spectrum formatted file. Work in progress for Support Request #3044 - load spins from Sparky list.
• Bug fix for the new NS R1rho 3-site dispersion models - the Y and Z initial magnetisations were switched. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging.
• Added cpmg_fit results for the program modified to turn off the PEAK_SHIFT flag. These are the results which should most closely match the relax results. This is for the simulated R_1ρ data for the NS R1rho 3-site linear model.
• Fix for the MODEL_NS_R1RHO_3SITE_LINEAR dispersion variable. The model name was not correct.
• Turned off the Δω dispersion parameter constraints for the NS R1rho 3-site models.
• Added the NS R1rho 3-site models to the dispersion auto-analysis. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis.
• Added the NS R1rho 3-site models to the GUI model list. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.
• Removed the p_C <= p_B constraint from the 3-site dispersion models. This is important for the linear models where a violation of this constraint is reasonable. This has been replaced by the p_C <= p_A constraint.
• Added the NS R1rho 3-site models to the relax user manual. This is for the NS R1rho 3-site and NS R1rho 3-site linear dispersion models. This follows the tutorial for adding relaxation dispersion models at http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual.
• Transposed some of the NS R1rho 3-site model evolution matrix elements. These now match the NS R1rho 2-site model.
• Last fixes for the NS R1rho 3-site dispersion models. These now behave identically to the cpmg_fit program with the PEAK_SHIFT flag disabled. The tilt angle for the initial magnetisation is no longer that for the average offset but that of state A.
• Fixes for swapped indices in the relaxation evolution matrix for the NS R1rho 3-site dispersion models.
• Docstring fix for the lib.dispersion.ns_r1rho_3site module.
• Added the Omega_A,B,C resonance offset parameter definitions to the dispersion chapter of the manual.
• Updated the relax results for the synthetic data of the NS R1rho 3-site linear dispersion model.
• Modified the NS R1rho 2-site dispersion model to match the NS R1rho 3-site models. The 6D evolution matrix indices have been rearranged to match the 9D matrix indices. The tilt angle for the initial magnetisation is no longer that for the average offset but that of state A, as was changed for the NS R1rho 3-site models earlier. The system test was therefore updated for the slightly different behaviour.
• Updated the relax results for the Fyn SH3 R_1ρ dispersion data. This is for the recent changes to the NS R1rho 2-site dispersion model.
• Updated the Relax_disp.test_ns_r1rho_3site_linear system test so it now passes. The chi-squared value is not exactly zero as there are numerical differences between relax and cpmg_fit due to different approaches being used.
• Added the RMSD determined via showApod for the 69 experiments. Work in progress for Support Request #3083 - Addition of Data-set for R_1ρ analysis.
• Added system test for the analysis of optimisation of the Kjaergaard et al., 2013 Off-resonance R_1ρ relaxation dispersion experiments using the DPL model. Work in progress for Support Request #3083 - Addition of Data-set for R_1ρ analysis.
• Modified analysis script for example data of R_1ρ. Work in progress for Support Request #3083 - Addition of Data-set for R_1ρ analysis.
• Created synthetic R_1ρ dispersion data for the NS R1rho 3-site model. This is a simple modification of the data for the NS R1rho 3-site linear model. The k_AC parameter was simply changed from 0 to 1000. The cpmg_fit software was used to create the data. Both cpmg_fit and relax results have been updated to the new model.
• Created the new Relax_disp.test_ns_r1rho_3site system test. This was copied from the Relax_disp.test_ns_r1rho_3site_linear test and modified to use the new NS R1rho 3-site model synthetic data.
• Fix for wrong use of relax_fit.relax_time instead of relax_disp.relax_time. Work in progress for Support Request #3044 - load spins from Sparky list.
• Added the ns_r1rho_3site module to the lib.dispersion package __all__ list. This allows the unit tests to pass.
• turned off a system test until the release of relax 3.1.1 is over. Work in progress for Support Request #3044 - load spins from Sparky list.
• Fix for the Relax_disp.test_bug_21076_multi_col_peak_list GUI test. The peak intensity wizard is now closed at the end of the test so that subsequent tests can cleanly operate. Without closing this wizard, launching it a second time in another test will always fail.
• Capitalised 'Python' in the IO redirection messages.
• Epydoc docstring fix for the lib.dispersion.ns_mmq_3site.r2eff_ns_mmq_3site_sq_dq_zq() function. This allows the API to be compiled correctly.
• Bug fix for the dispersion grid_search_setup() optimisation function. This function was not updated for the recent addition of the spin-lock or hard pulse offset dimension in the specific_analyses.relax_disp.disp_data module (and hence all structures used by the dispersion target functions). The loop_exp_frq_point() function call has been replaced by a loop_exp_frq_offset_point() function call to allow the R2eff model parameters to be looped over. For more details, see the thread http://thread.gmane.org/gmane.science.nmr.relax.scm/19685. This solution was mentioned at http://thread.gmane.org/gmane.science.nmr.relax.scm/19685/focus=4859.
• Removed a printout from the Relax_disp.test_r1rho_kjaergaard GUI test as this is fatal for Python 3.
• Python 3 fixes for the relax_disp.r2eff_read_spin user function. The check for the dispersion point column now only runs if that argument is set. In addition, the offset column is now also being checked.

Bugfixes

• Fix for the sample_scripts/relax_disp/R1rho_analysis.py sample script. This was identified by Justin Lecher <jlec att gentoo doot org> in the post http://article.gmane.org/gmane.science.nmr.relax.devel/4748 (Message-ID:<52984043.3030808@gentoo.org>), or the threaded view http://thread.gmane.org/gmane.science.nmr.relax.announce/46/focus=4748. The problem was some extra commas which should not have been there.
• Bug fixes for the non-functional R1rho_analysis.py relaxation dispersion sample script. This script was horribly broken, but it should now work. It can even be executed from the base relax directory or from within the sample_scripts/relax_disp/ directory and perform the full analysis (assuming write access to the relax source directory).
• Fix for a number of PNG files for NESSY and Bruker icons for broken IDAT entries. This problem was identified by Justin Lecher <jlec att gentoo doot org> in the post http://article.gmane.org/gmane.science.nmr.relax.devel/4750 (Message-ID:<5298572C.5010409@gentoo.org>), or in the threaded view http://thread.gmane.org/gmane.science.nmr.relax.announce/46/focus=4750. As a result those icons are missing in the GUI. This was fixed using the pngcrush tool.
• Fix for a typo in a model name in the cpmg_analysis.py relaxation dispersion sample script.
• Fix for bug #21309, the R2eff dispersion model failure when peak intensity data is missing. The problem was that the check for missing data in the _calculate_r2eff() private API method was accidentally deleted in the relax_disp branch. See the commit at http://article.gmane.org/gmane.science.nmr.relax.scm/19261 and the accidental deletion at http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?view=diff&r1=21504&r2=21505&pathrev=21505.
• Another fix for bug #21309, the R2eff dispersion model failure when peak intensity data is missing. This second problem is only for the numeric CPMG models for when all data at one magnetic field strength is missing. When the relaxation dispersion target function is being set up, the creation of the self.power data structure holding the number of CPMG blocks fails. The problem is that the relaxation time for the missing field strength is set to NaN. This is now caught using lib.float.isNaN().
• Loosened a check in the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test. This is to allow this test to pass on certain Mac OS X machines. It was reported by Troels in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/4773/focus=4774.
• Basic fix for the Relax_disp.test_r2eff_read_spin system test - the CPMG frequencies are now set. This was identified in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/4773/focus=4774.
• Fixes for the parameters in the Relax_disp.test_ns_mmq_3site system test script.
• Fix for optimisation of Dr. Flemming Hansen's CPMG data to the NS CPMG 2-site star dispersion model. Fix for bug #21322 - 5x Test suite fail for version 3.1.0, reported for system CentOS 2.6.32-358.18.1.el6.x86_64. Adjusted p_A, Δω, k_ex, χ².
• Fix for optimisation of the Korzhnev et al., 2005 ¹⁵N DQ CPMG data using the MMQ 2-site model. Fix for bug #21322 - 5x Test suite fail for version 3.1.0, reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
• Fix for optimisation of the Korzhnev et al., 2005 ¹⁵N MQ CPMG data using the MMQ 2-site model. Fix for bug #21322 - 5x Test suite fail for version 3.1.0, Reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
• Fix for optimisation of the Korzhnev et al., 2005 ¹⁵N ZQ CPMG data using the MMQ 2-site model. Fix for bug #21322 - 5x Test suite fail for version 3.1.0, Reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
• Fix for optimisation of all the Korzhnev et al., 2005 CPMG data using the MMQ 2-site model. Fix for bug #21322 - 5x Test suite fail for version 3.1.0, Reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
• Fix for optimisation of Dr. Flemming Hansen's CPMG data to the NS CPMG 2-site star dispersion model. Changed so assertAlmostEqual matches 2 digits. Fix for bug #21322 - 5x Test suite fail for version 3.1.0, reported for system CentOS 2.6.32-358.18.1.el6.x86_64.
• Bug fixes for the dispersion analysis when certain data sets are completely missing.
• Fix for loading a seriesTab formatted intensity, and getting the ID for the following GUI elements. Fix for bug #21076 - when loading a multi-spectra NMRPipe seriesTab file through the GUI, several Error messages occur.
• Fix for the relax_disp.r2eff_read_spin user function. The offsets are now converted to ppm prior to finding the R_2eff/R_1ρ key.