Author: bugman
Date: Fri Sep 6 13:56:59 2013
New Revision: 20892
URL: http://svn.gna.org/viewcvs/relax?rev=20892&view=rev
Log:
Started a system test for model TSMFK01.
Progress sr #3071: https://gna.org/support/index.php?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
Troels E. Linnet provided this patch. Commit by: tlinnet _aaattt_
gmail_dot_com
Signed-off-by: Edward d'Auvergne <edward@xxxxxxxxxxxxx>
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=20892&r1=20891&r2=20892&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Fri Sep 6
13:56:59 2013
@@ -1056,6 +1056,60 @@
self.assertAlmostEqual(res61L.chi2, 65.99987828890289, 5)
+ def test_kteilum_fmpoulsen_makke_cpmg_data_to_tsmfk01(self):
+ """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
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period.
+
+ The comparison is to Figure 2. This dataset is the 0.48 M GuHCl,
but similar results are expected. 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.}
+ 1. The dotted line represents a residue-specific fit of all
parameters in Eq. 1.
+ - ka = 11.3 +/- 0.7 s^{-1}
+ - dw = (2.45 +/- 0.09) * 10^3 s^{-1}
+ - R2 = 8.0 +/- 0.5 s^{-1}.
+ 2. The solid line represents a global fit of ka to all protein
residues and a residue-specific fit of dw and R2.}
+ -.ka = 10.55 +/- 0.08 s^{-1}
+ - dw = (2.44 +/- 0.08) * 10^3 s^{-1}
+ - R2 = 8.4 +/- 0.3 s^{-1}.
+
+ Conversion of paper results to relax results is performed by
+ - dw(ppm) = dw(rad.s^-1) * 10^6 * 1/(2*pi) *
(gyro1H/(gyro15N*spectrometer_freq)) = 2.45E3 * 1E6 / (2 * math.pi) *
(26.7522212E7/(-2.7126E7 * 599.8908622E6)) = -6.41 ppm.
+ """
+
+ # Base data setup.
+ self.setup_kteilum_fmpoulsen_makke_cpmg_data(model='TSMFK01')
+
+ # Alias the spins.
+ res61L = cdp.mol[0].res[0].spin[0]
+
+ print res61L.params
+
+ # Set the initial parameter values.
+ res61L.r2a = [8]
+ res61L.dw = 6.5
+ res61L.kA = 11.0
+
+ # Low precision optimisation.
+ self.interpreter.minimise(min_algor='simplex', line_search=None,
hessian_mod=None, hessian_type=None, func_tol=1e-05, grad_tol=None,
max_iter=1000, constraints=True, scaling=True, verbosity=1)
+
+ # Printout.
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s" % ("Parameter", "Value (:61)"))
+ print("%-20s %20.15g" % ("R2A (600 MHz)", res61L.r2a[0]))
+ print("%-20s %20.15g" % ("dw", res61L.dw))
+ print("%-20s %20.15g" % ("kA", res61L.kA))
+ print("%-20s %20.15g\n" % ("chi2", res61L.chi2))
+
+ # Checks for residue :61. Reference values from paper
+
+ self.assertAlmostEqual(res61L.r2a[0], 8.4, -1)
+ self.assertAlmostEqual(res61L.dw, 6.41, 2)
+ self.assertAlmostEqual(res61L.kA, 10.55, 0)
+ self.assertAlmostEqual(res61L.chi2, 60.0, 5)
+
+
def test_m61_data_to_m61(self):
"""Test the relaxation dispersion 'M61' model curve fitting to fixed
time synthetic data."""
r20892 - /branches/relax_disp/test_suite/system_tests/relax_disp.py