Don't bother - that'll just waste time. As long as the values are similar to the previous ones and not completely different, it'll be ok.
Regards, Edward On 17 June 2014 11:13, Troels Emtekær Linnet <[email protected]> wrote: > Should I then make a grid search for all values, and do a new > analysis? > > > > 2014-06-17 11:08 GMT+02:00 Edward d'Auvergne <[email protected]>: >> >> Ah, that is probably because of a bug you fixed >> (https://gna.org/bugs/?21954). The results were generated before this >> bug was fixed, so now they will be slightly different as the >> test_suite/shared_data/dispersion/Hansen/base_pipe.bz2 and >> test_suite/shared_data/dispersion/Hansen/r2eff_pipe.bz2 files have >> been updated. From the log file >> test_suite/shared_data/dispersion/Hansen/relax_results/relax_disp.log, >> you can see that the results are not too different. So just change >> the values at the start of the test to the final optimised values, and >> then change the values in the assertAlmostEqual() checks to the final >> values. I'll update the precision of these checks after running this >> on different OSes and 32-bit vs. 64-bit systems. >> >> You can probably see that this is not ideal, but the only 2 other >> programs that support this 3-site model are Art Palmer's CPMGFit, and >> Michael Bieri's NESSY. But CPMGFit has the same R20 values for all >> fields, so we cannot compare. And the NESSY model number 4, which is >> this model, is not fully implemented and functional. So we have >> nothing to compare to. I have created synthetic data in >> test_suite/shared_data/dispersion/lm63_3site which was to be used for >> a system test, but I don't know why that is not in a test :S There is >> even a relax script at >> test_suite/shared_data/dispersion/lm63_3site/relax_results/relax_disp.py >> which can be converted into a single model optimisation. I must have >> been so busy with the paper drafting that I simply forgot to convert >> this to a system test. >> >> Regards, >> >> Edward >> >> On 17 June 2014 09:18, <[email protected]> wrote: >> > Author: tlinnet >> > Date: Tue Jun 17 09:18:24 2014 >> > New Revision: 24009 >> > >> > URL: http://svn.gna.org/viewcvs/relax?rev=24009&view=rev >> > Log: >> > Added systemtest for model LM63 3 site. >> > >> > According to results folder in: >> > test_suite/shared_data/dispersion/Hansen/relax_results/LM63 3-site >> > >> > This should pass. >> > >> > But i doesnt? >> > >> > Modified: >> > trunk/test_suite/system_tests/relax_disp.py >> > >> > Modified: trunk/test_suite/system_tests/relax_disp.py >> > URL: >> > http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=24009&r1=24008&r2=24009&view=diff >> > >> > ============================================================================== >> > --- trunk/test_suite/system_tests/relax_disp.py (original) >> > +++ trunk/test_suite/system_tests/relax_disp.py Tue Jun 17 09:18:24 2014 >> > @@ -2492,6 +2492,70 @@ >> > self.assertAlmostEqual(spin71.phi_ex, 0.0553787828347638) >> > self.assertAlmostEqual(spin71.kex/1000, 2781.72293906248/1000) >> > self.assertAlmostEqual(spin71.chi2, 17.0776399916287) >> > + >> > + >> > + def test_hansen_cpmg_data_to_lm63_3site(self): >> > + """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. >> > + """ >> > + >> > + # Base data setup. >> > + self.setup_hansen_cpmg_data(model='LM63 3-site') >> > + >> > + # Alias the spins. >> > + spin70 = return_spin(":70") >> > + spin71 = return_spin(":71") >> > + >> > + # The R20 keys. >> > + r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, >> > frq=500e6) >> > + r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, >> > frq=800e6) >> > + >> > + ## Set the initial parameter values. >> > + spin70.r2 = {r20_key1: 7.570370921220954, r20_key2: >> > 8.694446951909107} >> > + spin70.phi_ex_B = 0.14872003058250227 >> > + spin70.phi_ex_C = 0.1319419923472704 >> > + spin70.kB = 4103.672910444741 >> > + spin70.kC = 7029.001690726248 >> > + spin71.r2 = {r20_key1: 5.1347793381636, r20_key2: >> > 7.156573986051575} >> > + spin71.phi_ex_B = 0.04013553485505605 >> > + spin71.phi_ex_C = 0.020050748406928887 >> > + spin71.kB = 4045.3007136121364 >> > + spin71.kC = 3586.38798270774 >> > + >> > + #self.interpreter.relax_disp.r20_from_min_r2eff(force=False) >> > + #self.interpreter.grid_search(lower=None, upper=None, inc=41, >> > constraints=True, verbosity=1) >> > + >> > + # Low precision optimisation. >> > + self.interpreter.minimise(min_algor='simplex', >> > line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-25, >> > grad_tol=None, max_iter=10000000, constraints=True, scaling=True, >> > verbosity=1) >> > + >> > + # Printout. >> > + print("\n\nOptimised parameters:\n") >> > + print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value >> > (:71)")) >> > + print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", >> > spin70.r2[r20_key1], spin71.r2[r20_key1])) >> > + print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", >> > spin70.r2[r20_key2], spin71.r2[r20_key2])) >> > + print("%-20s %20.15g %20.15g" % ("phi_ex_B", spin70.phi_ex_B, >> > spin71.phi_ex_B)) >> > + print("%-20s %20.15g %20.15g" % ("phi_ex_C", spin70.phi_ex_C, >> > spin71.phi_ex_C)) >> > + print("%-20s %20.15g %20.15g" % ("kB", spin70.kB, spin71.kB)) >> > + print("%-20s %20.15g %20.15g" % ("kC", spin70.kC, spin71.kC)) >> > + print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, >> > spin71.chi2)) >> > + >> > + # Checks for residue :70. >> > + #self.assertAlmostEqual(spin70.r2[r20_key1], 6.74362294539099) >> > + #self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406797067481, >> > 6) >> > + self.assertAlmostEqual(spin70.phi_ex_B, 0.148720030582502) >> > + self.assertAlmostEqual(spin70.phi_ex_C, 0.13194199234727) >> > + self.assertAlmostEqual(spin70.kB/1000, 4103.67291044474/1000, >> > 6) >> > + self.assertAlmostEqual(spin70.kC/1000, 7029.00169072625/1000, >> > 6) >> > + #self.assertAlmostEqual(spin70.chi2, 363.534044873483) >> > + >> > + # Checks for residue :71. >> > + #self.assertAlmostEqual(spin71.r2[r20_key1], 5.00776657712558) >> > + self.assertAlmostEqual(spin71.phi_ex_B, 0.040135534855056) >> > + self.assertAlmostEqual(spin71.phi_ex_C, 0.0200507484069289) >> > + self.assertAlmostEqual(spin71.kB/1000, 4045.30071361214/1000) >> > + self.assertAlmostEqual(spin71.kC/1000, 3586.38798270774/1000) >> > + #self.assertAlmostEqual(spin71.chi2, 17.0776399916287) >> > >> > >> > def test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self): >> > >> > >> > _______________________________________________ >> > relax (http://www.nmr-relax.com) >> > >> > This is the relax-commits mailing list >> > [email protected] >> > >> > To unsubscribe from this list, get a password >> > reminder, or change your subscription options, >> > visit the list information page at >> > https://mail.gna.org/listinfo/relax-commits >> >> _______________________________________________ >> relax (http://www.nmr-relax.com) >> >> This is the relax-devel mailing list >> [email protected] >> >> >> To unsubscribe from this list, get a password >> reminder, or change your subscription options, >> visit the list information page at >> https://mail.gna.org/listinfo/relax-devel > > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
