Hi Edward, I am a last-year grad student working at a Max Planck Institute in Potsdam, Germany. My thesis is concerned with a Ca2+ binding protein. I collected full set of backbone relaxation data of the apo and holo form at two fields (600 and 750) and saw a slight difference in R2 (about 10% decreased in holo form), some difference in R1 (slightly increased in holo form), and no change in NOE. However, after I run model free analysis (using the holo structure for both apo and holo form since no apo structure is available, all 9 local_tm models, and all diffusion models), I saw a global tm difference of more than twofold and tremendous changes in s2 values in both forms with up to 50% decrease for the holo form. Is this a likely outcome? I do not know if I should trust model selection especially since the oblate model that was chosen needed about 200 iterations to converge. I used the Newton minimizing method. Below, I copied the AIC output from the console and the corresponding global tm values.
I'd be happy for any advice! Thanks in advance, Jonas AIC model selection for apo form Global model - all diffusion tensor parameters and spin specific model-free parameters. # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion sphere - mf (Wed Dec 30 14:23:37 2015) 197 468 526.81736 920.81736 prolate - mf (Wed Dec 30 14:23:37 2015) 185 468 538.26716 908.26716 oblate - mf (Wed Dec 30 14:23:37 2015) 197 468 512.99733 906.99733 ellipsoid - mf (Wed Dec 30 14:23:37 2015) 197 468 518.69107 912.69107 The model from the data pipe 'oblate - mf (Wed Dec 30 14:23:37 2015)' has been selected. Global tm = 1.5247e-08 s AIC model selection for holo form Global model - all diffusion tensor parameters and spin specific model-free parameters. # Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion sphere - mf (Tue Jan 5 18:26:27 2016) 206 504 2305.05273 2717.05273 prolate - mf (Tue Jan 5 18:26:27 2016) 209 504 2299.94808 2717.94808 oblate - mf (Tue Jan 5 18:26:27 2016) 209 504 2281.81543 2699.81543 The model from the data pipe 'oblate - mf (Tue Jan 5 18:26:27 2016)' has been selected. Global tm = 6.8584e-09 s _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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-users