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Class for testing various aspects specific to relaxation dispersion curve-fitting.
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Skip certain tests if the C modules are non-functional.
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Set up for all the functional tests.
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Setup data for the catch of bug #22146, the failure of unpacking R2A and R2B, when performing a clustered full dispersion models.
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Set up the data for the test_hansen_cpmg_data_*() system tests.
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Set up the data for the test_kteilum_fmpoulsen_makke_cpmg_data_*() system tests.
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Set up the data for the test_korzhnev_2005_data_*() system tests using the 'NS MMQ 2-site' model. This loads the proton-heteronuclear SQ, ZQ, DQ, and MQ (MMQ) data from:
It consists of the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant.
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Setup of data SOD1-WT CPMG. From paper at http://dx.doi.org/10.1073/pnas.0907387106. Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius. |
Test synthetic data of Andrew J. Baldwin B14 model whereby the simplification R20A = R20B is assumed. Support requst sr #3154 https://web.archive.org/web/https://gna.org/support/index.php?3154. This uses the synthetic data from paper DOI: 10.1016/j.jmr.2014.02.023 with R20A, R20B = 2. rad/s. |
Test synthetic data of Andrew J. Baldwin B14 model. Support requst sr #3154 https://web.archive.org/web/https://gna.org/support/index.php?3154. This uses the synthetic data from paper DOI: 10.1016/j.jmr.2014.02.023. |
Test synthetic cpmg data. This script will produce synthetic CPMG R2eff values according to the NS CPMG 2-site 3D model, and the fit the data with CR72. |
Test synthetic cpmg data. This script will produce synthetic CPMG R2eff values according to the NS CPMG 2-site 3D model, and the fit the data with B14. Try to catch bug #22021 https://web.archive.org/web/https://gna.org/bugs/index.php?22021: Model B14 shows bad fitting to data. |
Test synthetic cpmg data. For CR72 with small noise and cluster. This script will produce synthetic CPMG R2eff values according to the selected model, and the fit the selected model. |
Test synthetic cpmg data, calling the dx.map function with one or two points. This script will produce synthetic CPMG R2eff values according to the selected model, and the fit the selected model. |
Test the curve type detection using the Dr. Flemming Hansen's CPMG fixed time test data. |
Conversion of Dr. Flemming Hansen's CPMG R2eff values into input files for CATIA. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Test of the numeric model only dispersion auto-analysis using Dr. Flemming Hansen's CPMG data. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data (using the R2eff data directly instead of peak intensities). This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Test of the dispersion auto-analysis using Dr. Flemming Hansen's CPMG data with parts missing. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the CR72 dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the CR72 full dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the IT99 dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the LM63 dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site 3D' dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site 3D full' dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site expanded' dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star' dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star full' dispersion model. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Conversion of Dr. Flemming Hansen's CPMG R2eff values into input files for CPMGFit. This uses the data from Dr. Flemming Hansen's paper at http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed relaxation time period. |
Optimisation of the Korzhnev et al., 2005 15N DQ CPMG data using the 'NS MMQ 2-site' model. This uses the data from Dmitry Korzhnev's paper at DOI: 10.1021/ja054550e. This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. Here only the 15N DQ data will be optimised. The values found by cpmg_fit using just this data are:
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Optimisation of the Korzhnev et al., 2005 15N MQ CPMG data using the 'NS MMQ 2-site' model. This uses the data from Dmitry Korzhnev's paper at DOI: 10.1021/ja054550e. This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. Here only the 15N MQ data will be optimised. The values found by cpmg_fit using just this data are:
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Optimisation of the Korzhnev et al., 2005 15N SQ CPMG data using the 'NS MMQ 2-site' model. This uses the data from Dmitry Korzhnev's paper at DOI: 10.1021/ja054550e. This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. Here only the 15N SQ data will be optimised. The values found by cpmg_fit using just this data are:
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Optimisation of the Korzhnev et al., 2005 15N ZQ CPMG data using the 'NS MMQ 2-site' model. This uses the data from Dmitry Korzhnev's paper at DOI: 10.1021/ja054550e. This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. Here only the 15N ZQ data will be optimised. The values found by cpmg_fit using just this data are:
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Optimisation of the Korzhnev et al., 2005 1H MQ CPMG data using the 'NS MMQ 2-site' model. This uses the data from Dmitry Korzhnev's paper at DOI: 10.1021/ja054550e. This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. Here only the 1H MQ data will be optimised. The values found by cpmg_fit using just this data are:
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Optimisation of the Korzhnev et al., 2005 1H SQ CPMG data using the 'NS MMQ 2-site' model. This uses the data from Dmitry Korzhnev's paper at DOI: 10.1021/ja054550e. This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. Here only the 1H SQ data will be optimised. The values found by cpmg_fit using just this data are:
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Optimisation of all the Korzhnev et al., 2005 CPMG data using the 'NS MMQ 2-site' model. This uses the data from Dmitry Korzhnev's paper at DOI: 10.1021/ja054550e. This is the 1H SQ, 15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain mutant. Here all data will be optimised. The values found by cpmg_fit using just this data are:
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Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0509100103. This is CPMG data with a fixed relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride). |
Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0509100103. This is CPMG data with a fixed relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride). |
Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0509100103. This is CPMG data with a fixed relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride). Figure 3 shows the ln( k_a [s^-1]) for different concentrations of GuHCl. The precise values are:
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Optimisation of Kaare Teilum, Flemming M Poulsen, Mikael Akke 2006 "acyl-CoA binding protein" CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0509100103. This is CPMG data with a fixed relaxation time period. Experiment in 1.01 M GuHCl (guanidine hydrochloride). The comparison is to Figure 2, which is for dataset with 1 M GuHCl. The reported results are expected to be in rad.s^-1. Conversion into relax stored values is preferably. Representative 15N CPMG relaxation dispersion curve measured on the cross peaks from residue L61 in folded ACBP at pH 5.3, 1 M GuHCl, and 40C:
Conversion of paper results to relax results is performed by:
Figure 3 shows the ln( k_a [s^-1]) for different concentrations of GuHCl. The precise values are:
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Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho relaxation dispersion experiments using the 'DPL' model. This uses the data from Kjaergaard's paper at DOI: 10.1021/bi4001062. |
Test speeding up grid search. Support requst sr #3151 https://web.archive.org/web/https://gna.org/support/index.php?3151. User function to set the R20 parameters in the default grid search using the minimum R2eff value. Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius. |
Error analysis of SOD1-WT CPMG. From paper at http://dx.doi.org/10.1073/pnas.0907387106. Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius. bug #21954 https://web.archive.org/web/https://gna.org/bugs/index.php?21954: Order of spectrum.error_analysis is important. |
Optimisation of SOD1-WT CPMG. From paper at http://dx.doi.org/10.1073/pnas.0907387106. Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius. |
Conversion of SOD1-WT CPMG R2eff values into input files for sherekhan. Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009 'SOD1-WT' CPMG data to the CR72 dispersion model. This uses the data from paper at http://dx.doi.org/10.1073/pnas.0907387106. This is CPMG data with a fixed relaxation time period recorded at fields of 500 and 600MHz. Data is for experiment at 25 degree Celcius. |
Test the 'MMQ CR72' model fitting against Remco Sprangers' ClpP data. This uses the data from Remco Sprangers' paper at http://dx.doi.org/10.1073/pnas.0507370102. This is MMQ CPMG data with a fixed relaxation time period. |
Test the 'NS MMQ 2-site' model fitting against Remco Sprangers' ClpP data. This uses the data from Remco Sprangers' paper at http://dx.doi.org/10.1073/pnas.0507370102. This is MQ CPMG data with a fixed relaxation time period. |
System test of the value.write function to write intensities for an R1rho setup. This system test is to make sure, that modifying the API for special parameters theta and w_eff does not alter the functionality value.write. This uses the data of the saved state attached to bug #21344. |
System test of the value.write function to write return values of theta from calc_rotating_frame_params() function for an R1rho setup. This uses the data of the saved state attached to bug #21344. |
System test of the value.write function to write return values of w_eff from calc_rotating_frame_params() function for an R1rho setup. This uses the data of the saved state attached to bug #21344. |
System test of the auto_analysis value.write function to write theta and w_eff values for an R1rho setup. This uses the data of the saved state attached to bug #21344. |
Trees | Indices | Help |
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