Hi Jonas,
Welcome to the relax mailing lists! From the output, I guess you are
using the automated model-free analysis protocol (the one I developed
and published). Or are you running a custom analysis protocol? Such
results are not uncommon and are usually an indication of a bigger
problem. Often this comes back to inadequate temperature calibration
and/or control - have a close look at this text I wrote on the
subject:
http://www.nmr-relax.com/manual/Temperature_control_and_calibration.html
Other times it can be due to a bias in the fitting of relaxation
curves. Which software did you use to calculate the relaxation rates
from the base data? Another reason could be the failure of the
diffusion tensor optimisation due to the specific tensor not being an
adequate description of reality. This happens if you have large scale
internal motions, partial dimerisation (even with 5-10%), long
flexible tails, etc. A good test is to use the local_tm global model,
which is strangely absent from the above list of global models. The
local_tm global model will always be too noisy and give some terrible
outlier values, but in general it is a good test for the diffusion
tensor approximation. As there is no global diffusion assumed, the
local tm values can adapt to the local diffusion contribution. The
single value may be a good enough approximate average value for the
spread of 3, 5, 10 or more global diffusion coefficients. Therefore
if you see the same trend in S2 values in the local_tm models as you
do in the oblate spheroid, then you know that the trend is real.
Whether that real trend is due to the protein system or due to bad
input data is another question. Hopefully this helps.
Regards,
Edward
On 6 January 2016 at 10:14, Jonas Hanske <Jonas.Hanske@xxxxxxxxxxxx> wrote:
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
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Re: Confidence in Model-free output