Author: bugman Date: Fri May 23 10:06:32 2014 New Revision: 23368 URL: http://svn.gna.org/viewcvs/relax?rev=23368&view=rev Log: Changed most default dispersion parameter values to avoid edge cases where there is no exchange.
The dw parameters were all 0.0 and kex 1e5, both of which result in no exchange. If this is ever used for an optimisation starting point - which it never should, apart from development, test suite, and debugging purposes - then the optimisation algorithm will have a very hard time recovering. The pA parameter has been changed to 0.90 to set it to a reasonable value while still staying far away from the no exchange condition of pA = 1.0. This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5917. Modified: trunk/specific_analyses/relax_disp/parameter_object.py Modified: trunk/specific_analyses/relax_disp/parameter_object.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameter_object.py?rev=23368&r1=23367&r2=23368&view=diff ============================================================================== --- trunk/specific_analyses/relax_disp/parameter_object.py (original) +++ trunk/specific_analyses/relax_disp/parameter_object.py Fri May 23 10:06:32 2014 @@ -61,32 +61,32 @@ self._add('r2', scope='spin', default=10.0, desc='The transversal relaxation rate', set='params', py_type=dict, grace_string='\\qR\\s2\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) self._add('r2a', scope='spin', default=10.0, desc='The transversal relaxation rate for state A in the absence of exchange', set='params', py_type=dict, grace_string='\\qR\\s2,A\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) self._add('r2b', scope='spin', default=10.0, desc='The transversal relaxation rate for state B in the absence of exchange', set='params', py_type=dict, grace_string='\\qR\\s2,B\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) - self._add('pA', scope='spin', default=0.5, desc='The population for state A', set='params', py_type=float, grace_string='\\qp\\sA\\N\\Q', err=True, sim=True) + self._add('pA', scope='spin', default=0.90, desc='The population for state A', set='params', py_type=float, grace_string='\\qp\\sA\\N\\Q', err=True, sim=True) self._add('pB', scope='spin', default=0.5, desc='The population for state B', set='params', py_type=float, grace_string='\\qp\\sB\\N\\Q', err=True, sim=True) self._add('pC', scope='spin', default=0.5, desc='The population for state C', set='params', py_type=float, grace_string='\\qp\\sC\\N\\Q', err=True, sim=True) self._add('phi_ex', scope='spin', default=5.0, desc='The phi_ex = pA.pB.dw**2 value (ppm^2)', set='params', py_type=float, grace_string='\\xF\\B\\sex\\N = \\q p\\sA\\N.p\\sB\\N.\\xDw\\B\\S2\\N\\Q (ppm\\S2\\N)', err=True, sim=True) self._add('phi_ex_B', scope='spin', default=5.0, desc='The fast exchange factor between sites A and B (ppm^2)', set='params', py_type=float, grace_string='\\xF\\B\\sex,B\\N (ppm\\S2\\N)', err=True, sim=True) self._add('phi_ex_C', scope='spin', default=5.0, desc='The fast exchange factor between sites A and C (ppm^2)', set='params', py_type=float, grace_string='\\xF\\B\\sex,C\\N (ppm\\S2\\N)', err=True, sim=True) self._add('padw2', scope='spin', default=1.0, desc='The pA.dw**2 value (ppm^2)', set='params', py_type=float, grace_string='\\qp\\sA\\N.\\xDw\\B\\S2\\N\\Q (ppm\\S2\\N)', err=True, sim=True) - self._add('dw', scope='spin', default=0.0, desc='The chemical shift difference between states A and B (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q (ppm)', err=True, sim=True) - self._add('dw_AB', scope='spin', default=0.0, desc='The chemical shift difference between states A and B for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAB\\N (ppm)', err=True, sim=True) - self._add('dw_AC', scope='spin', default=0.0, desc='The chemical shift difference between states A and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAC\\N (ppm)', err=True, sim=True) - self._add('dw_BC', scope='spin', default=0.0, desc='The chemical shift difference between states B and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SBC\\N (ppm)', err=True, sim=True) - self._add('dwH', scope='spin', default=0.0, desc='The proton chemical shift difference between states A and B (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q (ppm)', err=True, sim=True) - self._add('dwH_AB', scope='spin', default=0.0, desc='The proton chemical shift difference between states A and B for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAB\\N (ppm)', err=True, sim=True) - self._add('dwH_AC', scope='spin', default=0.0, desc='The proton chemical shift difference between states A and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAC\\N (ppm)', err=True, sim=True) - self._add('dwH_BC', scope='spin', default=0.0, desc='The proton chemical shift difference between states B and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SBC\\N (ppm)', err=True, sim=True) - self._add('kex', scope='spin', default=10000.0, desc='The exchange rate', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) - self._add('kex_AB', scope='spin', default=10000.0, desc='The exchange rate between sites A and B for 3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SAB\\N (rad.s\\S-1\\N)', err=True, sim=True) - self._add('kex_AC', scope='spin', default=10000.0, desc='The exchange rate between sites A and C for 3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SAC\\N (rad.s\\S-1\\N)', err=True, sim=True) - self._add('kex_BC', scope='spin', default=10000.0, desc='The exchange rate between sites B and C for 3-site exchange with kex_BC = k_BC + k_CB (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SBC\\N (rad.s\\S-1\\N)', err=True, sim=True) - self._add('kB', scope='spin', default=10000.0, desc='Approximate chemical exchange rate constant between sites A and B (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sB\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) - self._add('kC', scope='spin', default=10000.0, desc='Approximate chemical exchange rate constant between sites A and C (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sC\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) - self._add('tex', scope='spin', default=1.0/10000.0, desc='The time of exchange (tex = 1/kex)', set='params', py_type=float, grace_string='\\q\\xt\\B\\sex\\N\\Q (s.rad\\S-1\\N)', err=True, sim=True) + self._add('dw', scope='spin', default=1.0, desc='The chemical shift difference between states A and B (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q (ppm)', err=True, sim=True) + self._add('dw_AB', scope='spin', default=1.0, desc='The chemical shift difference between states A and B for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAB\\N (ppm)', err=True, sim=True) + self._add('dw_AC', scope='spin', default=1.0, desc='The chemical shift difference between states A and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SAC\\N (ppm)', err=True, sim=True) + self._add('dw_BC', scope='spin', default=1.0, desc='The chemical shift difference between states B and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\Q\\SBC\\N (ppm)', err=True, sim=True) + self._add('dwH', scope='spin', default=1.0, desc='The proton chemical shift difference between states A and B (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q (ppm)', err=True, sim=True) + self._add('dwH_AB', scope='spin', default=1.0, desc='The proton chemical shift difference between states A and B for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAB\\N (ppm)', err=True, sim=True) + self._add('dwH_AC', scope='spin', default=1.0, desc='The proton chemical shift difference between states A and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SAC\\N (ppm)', err=True, sim=True) + self._add('dwH_BC', scope='spin', default=1.0, desc='The proton chemical shift difference between states B and C for 3-site exchange (in ppm)', set='params', py_type=float, grace_string='\\q\\xDw\\B\\sH\\N\\Q\\SBC\\N (ppm)', err=True, sim=True) + self._add('kex', scope='spin', default=1000.0, desc='The exchange rate', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) + self._add('kex_AB', scope='spin', default=1000.0, desc='The exchange rate between sites A and B for 3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SAB\\N (rad.s\\S-1\\N)', err=True, sim=True) + self._add('kex_AC', scope='spin', default=1000.0, desc='The exchange rate between sites A and C for 3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SAC\\N (rad.s\\S-1\\N)', err=True, sim=True) + self._add('kex_BC', scope='spin', default=1000.0, desc='The exchange rate between sites B and C for 3-site exchange with kex_BC = k_BC + k_CB (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sex\\N\\Q\\SBC\\N (rad.s\\S-1\\N)', err=True, sim=True) + self._add('kB', scope='spin', default=1000.0, desc='Approximate chemical exchange rate constant between sites A and B (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sB\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) + self._add('kC', scope='spin', default=1000.0, desc='Approximate chemical exchange rate constant between sites A and C (rad.s^-1)', set='params', py_type=float, grace_string='\\qk\\sC\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) + self._add('tex', scope='spin', default=1.0/1000.0, desc='The time of exchange (tex = 1/kex)', set='params', py_type=float, grace_string='\\q\\xt\\B\\sex\\N\\Q (s.rad\\S-1\\N)', err=True, sim=True) self._add('theta', scope='spin', desc='Rotating frame tilt angle : ( theta = arctan(w_1 / Omega) ) (rad)', grace_string='Rotating frame tilt angle (rad)', py_type=dict, set='all', err=False, sim=False) self._add('w_eff', scope='spin', desc='Effective field in rotating frame : ( w_eff = sqrt(Omega^2 + w_1^2) ) (rad.s^-1)', grace_string='Effective field in rotating frame (rad.s\\S-1\\N)', py_type=dict, set='all', err=False, sim=False) - self._add('k_AB', scope='spin', default=10000.0, desc='The exchange rate from state A to state B', set='params', py_type=float, grace_string='\\qk\\sAB\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) - self._add('k_BA', scope='spin', default=10000.0, desc='The exchange rate from state B to state A', set='params', py_type=float, grace_string='\\qk\\sBA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) + self._add('k_AB', scope='spin', default=1000.0, desc='The exchange rate from state A to state B', set='params', py_type=float, grace_string='\\qk\\sAB\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) + self._add('k_BA', scope='spin', default=1000.0, desc='The exchange rate from state B to state A', set='params', py_type=float, grace_string='\\qk\\sBA\\N\\Q (rad.s\\S-1\\N)', err=True, sim=True) # Add the minimisation data. self._add_min_data(min_stats_global=False, min_stats_spin=True) _______________________________________________ relax (http://www.nmr-relax.com) This is the 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