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* The [[R2eff]] model - used to determine the R<sub>2eff</sub> or R<sub>1ρ</sub> values and errors required as the base data for all other models.
* The [[No Rex]] model - the model for no chemical exchange being present.
* The [[LM63]] SQ CPMG-type analytic model - the original Luz and Meiboom 1963 2-site fast exchange equation with parameters {R<sub>2</sub><sup>0</sup>, ...…, φ<sub>ex</sub>, k<sub>ex</sub>} [Luz and Meiboom 1963].* The [[LM63 3-site]] SQ CPMG-type analytic model - the original Luz and Meiboom 1963 3-site fast exchange equation with parameters {R<sub>2</sub><sup>0</sup>, ...…, φ<sub>ex,B</sub>, k<sub>B</sub>, φ<sub>ex,C</sub>, k<sub>C</sub>} [Luz and Meiboom 1963].* The [[CR72]] SQ CPMG-type analytic model - the reduced Carver and Richards 1972 2-site equation for most time scales whereby the simplification R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed with the parameters {R<sub>2</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, k<sub>ex</sub>} [Carver and Richards 1972].* The [[CR72 full]] SQ CPMG-type analytic model - the full Carver and Richards 1972 2-site equation for most time scales with parameters {R<sub>2A</sub><sup>0</sup>, R<sub>2B</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, k<sub>ex</sub>} [Carver and Richards 1972].* The [[IT99]] SQ CPMG-type analytic model - the Ishima and Torchia 1999 2-site model for all time scales with p<sub>A</sub> ≫ p<sub>B</sub> and with parameters {R<sub>2</sub><sup>0</sup>, ...…, φ<sub>ex</sub>, p<sub>A</sub>.δω<sup>2</sup>, k<sub>ex</sub>} [Ishima and Torchia 1999].* The [[TSMFK01]] SQ CPMG-type analytic model - the Tollinger et al., 2001 2-site very-slow exchange model for time scales within range of microsecond to second time scale with parameters are {R<sub>2A</sub><sup>0</sup>, ...…, δω, k<sub>AB</sub>} [Tollinger et al., 2001].* The [[NS CPMG 2-site expanded]] SQ CPMG-type numeric model - A model for 2-site exchange expanded using Maple by Nikolai Skrynnikov (Tollinger et al., 2001) with the parameters {R<sub>2</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, k<sub>ex</sub>}.* The [[NS CPMG 2-site 3D]] SQ CPMG-type numeric model - the reduced model for 2-site exchange using 3D magnetisation vectors whereby the simplification R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed with the parameters {R<sub>2</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, k<sub>ex</sub>}.* The [[NS CPMG 2-site 3D full]] SQ CPMG-type numeric model - the full model for 2-site exchange using 3D magnetisation vectors with parameters {R<sub>2A</sub><sup>0</sup>, R<sub>2B</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, k<sub>ex</sub>}.* The [[NS CPMG 2-site star]] SQ CPMG-type numeric model - the reduced model for 2-site exchange using complex conjugate matrices whereby the simplification R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed with the parameters {R<sub>2</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, k<sub>ex</sub>}.* The [[NS CPMG 2-site star full]] SQ CPMG-type numeric model - the full model for 2-site exchange using complex conjugate matrices with parameters {R<sub>2A</sub><sup>0</sup>, R<sub>2B</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, k<sub>ex</sub>}.* The [[M61]] R<sub>1ρ</sub>-type analytic model - the Meiboom 1961 2-site fast exchange equation for on-resonance data with parameters {R<sub>1ρ</sub>', ...…, φ<sub>ex</sub>, k<sub>ex</sub>} [Meiboom 1961].* The [[M61 skew]] R<sub>1ρ</sub>-type analytic model - the Meiboom 1961 2-site equation for all time scales with p<sub>A</sub> ≫ p<sub>B</sub> and with parameters {R<sub>1ρ</sub>', ...…, p<sub>A</sub>, δω, k<sub>ex</sub>} [Meiboom 1961].* The [[DPL94]] R<sub>1ρ</sub>-type analytic model - the Davis et al., 1994 2-site fast exchange equation extending the [[M61]] model for off-resonance data with parameters {R<sub>1ρ</sub>', ...…, φ<sub>ex</sub>, k<sub>ex</sub>} [Davis et al., 1994].* The [[TP02]] R<sub>1ρ</sub>-type analytic model - the Trott and Palmer 2002 2-site equation for all time scales with p<sub>A</sub> ≫ p<sub>B</sub> and with parameters {R<sub>1ρ</sub>', ...…, p<sub>A</sub>, δω, k<sub>ex</sub>} [Trott and Palmer 2002].* The [[TAP03]] R<sub>1ρ</sub>-type analytic model - the Trott et al., 2003 off-resonance 2-site equation for all time scales with the weak condition p<sub>A</sub> ≫ p<sub>B</sub> and with parameters {R<sub>1ρ</sub>', ...…, p<sub>A</sub>, δω, k<sub>ex</sub>} [Trott et al., 2003].* The [[MP05]] R<sub>1ρ</sub>-type analytic model - the Miloushev and Palmer 2005 off-resonance 2-site equation for all time scales with parameters {R<sub>1ρ</sub>', ...…, p<sub>A</sub>, δω, k<sub>ex</sub>} [Miloushev and Palmer 2005].* The [[NS R1rho 2-site]] R<sub>1ρ</sub> numeric model - the model for 2-site exchange using 3D magnetisation vectors with the parameters {R<sub>1ρ</sub>', ...…, p<sub>A</sub>, δω, k<sub>ex</sub>}.* The [[MQ CR72]] MMQ-type analytic model - the Carver and Richards 1972 2-site model for most time scales expanded for MMQ CPMG data by Korzhnev et al., 2004 with the parameters {R<sub>2</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, δω<sub>H</sub>, k<sub>ex</sub>}.* The [[MMQ 2-site]] MMQ-type numeric model - the model for 2-site exchange whereby the simplification R<sub>2A</sub><sup>0</sup> = R<sub>2B</sub><sup>0</sup> is assumed with the parameters {R<sub>2</sub><sup>0</sup>, ...…, p<sub>A</sub>, δω, δω<sub>H</sub>, k<sub>ex</sub>}.
* An automated protocol for relaxation dispersion which includes sequential optimisation of the models, fixed model elimination rules to remove failed models and failed MC simulations increasing both parameter reliability and accuracy [d'Auvergne and Gooley 2006], and a final run whereby AIC model selection is used to judge statistical significance.
* Additional methods to speed up the auto-analysis by skipping the grid search: Model nesting, the more complex model starts with the optimised parameters of the simpler; Model equivalence, when two models have the same parameters; And spin clustering, the analysis starts with the averaged parameter values from a completed non-clustered analysis.
* Changed all instances of 'relax_times' to 'cpmg_frqs' and made other small changes.
* Changed 'relax_time' instances to 'cpmg_frq'.
* Changed the index name and description. The description might change later to be more appropriate when the code is more mature...…* Included the setting of the spectrometer frequency and uncommented a few lines of code. Of course, this won't work until the sample data has been introduced and the right names for the different files be input in the system test script...…
* Fixed many formatting errors and made the 'relax_disp' code accessible (pipes, interpreter, etc.). These changes also include a coming back to using the C code 'math_fns/relax_fit.py' since there is still no such code associated to relaxation dispersion. This will allow working in the code without relax crashing and complaining about the lack of a C module name 'relax_disp.py'.
* Added the user function cpmg_delayT() which allows setting the CPMG constant time delay T used for the analysed dataset. This follows a post at https://mail.gna.org/public/relax-devel/2009-01/msg00027.html.
* Created a directory for the data recorded at 800 MHz and put a readme file explaining its origin.
* Added the relaxation dispersion dataset recorded at 800 MHz in the system-test. This was kindly provided by Dr Flemming Hansen (flemming AT pound DOT med DOT utoronto DOT ca) and was previously published in Hansen, Vallurupalli & Kay (2008) J. Phys. Chem. B, 112, 5898-5904. The original format was different and two formats were made ('generic' and 'sparky'), as for the dataset recorded at 500 MHz.
* Renamed the directories containing the sample datasets provided by Flemming Hansen. The names are now more obvious as to their content... … This was proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00056.html.
* Added an 'unresolved' file to the 800 MHz data and moved (and modified) some files (sequence and readme) so there is only one copy for the 500 and 800 MHz data. This prevents duplicated files.
* Changed the object names so they are lower case as they should be, based on the rest of the code. Made the equivalent change in the function assemble_param_vector() to allow the system-test to go further.. This was spotted by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00058.html.
* One more unit test.
* One more unit test for the relaxation dispersion code.
* Added more unit tests and tried to debug what was uncovered by these tests. Still more work is needed for debugging...…
* A few fixes based on the unit tests problems.
* Changed the default value for 'int_cpmg' to avoid an impossible mathematical situation: ln(0).
* Fixed a bug where the 'id' argument was not set. This was proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00127.html.
* Started to make changes for multiple field relaxation dispersion analysis. This seems necessary, so maybe we should not support single field analysis of relaxation dispersion at all. -> Kovrigin et al. (2006) JMagRes, 180: 93-104. The changes made here are only a first draft and may not work. In particular, maybe the spectrum.read_intensities(), relax_disp.cpmg_frq(), spectrum.replicated(), spectrum.error_analysis(), and deselect.read() functions will need to know the magnetic field to which the particular dataset is associated... … In fact, the different datasets should be input first and their R<sub>2eff</sub> calculated independently. In a second step, the actual relaxation dispersion curve fitting should be made with all data.
* Fixed a bug which prevented the manual pdf to be compiled. The problem was caused by a ':' character in the references (after the volume number, as usual). This was changed for a '.' character. Equations were fine.. Moreover, a better formatting was done by adding ':' characters after the word 'are' before enumerations.
* Fixed the unit tests. This is as proposed by Ed in a post at https://mail.gna.org/public/relax-devel/2009-01/msg00132.html.
* Reordered a few functions for alphabetical reasons.
* A small fix to the system test. However, is this fix the solution or is there something wrong with the reading of data (such as 'R<sub>2eff</sub>') by relax_data.read()? Shouldn't the data, for example 'R<sub>2eff</sub>', be available in 'cdp.mol[0].res[0].spin[0].R2eff_val[0]' or 'cdp.mol[0].res[0].spin[0].R2eff[0]' for the 1st spin of the 1st residue in the 1st molecule?
* Fixed an import (as well as a few comments). This however introduces an error concerning the 'chi2' being undefined in the C module for relaxation dispersion...…
* Solved an issue created during the merge process concerning the 'return_data_name_doc' call. The solution is based on the code in 'specific_fns/relax_fit.py'.
* Brought the relaxation dispersion branch into sync with the 1.3 line. There were many design changes within the 1.3 line that required that the old relaxation dispersion code be updated.
