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
