Hi,
This model selection technique is called Akaike's Information Criteria
(AIC). See http://www.nmr-relax.com/refs.html#dAuvergneGooley03 for
details on this. How would you produce a plot in Grace of the models
selected? I don't know how this would work for the dispersion models.
In a model-free analysis I have deliberately taken the decision to
not create such a plot. In model-free, relax supports models m0 to
m9, so these could be plotted as 0 to 9 on the Y-axis. But this is
not done and will never be implemented. The reason is because the
information about which model is selected is worthless. What is
important is the dynamics extracted. This is especially the case of
nested models. Just because a parameter is missing from a model, this
does not mean that it is not present. For example there are
model-free models without the Rex parameter. If these are selected,
this does not mean that Rex is not present. It means that Rex is
statistically insignificant in the current data set. Model
differences are an academic question and is not interesting in
practice. Sometimes the AIC value for two nested models is very
similar and that means that the parameter different between the two is
sitting directly on the boarder of statistical
significance/insignificant. You could pick either model and it should
not make a statistical difference in the dynamics picture. It does
not relate to the dynamics, just the judgement of statistically
significance for parameters. Therefore for practical reasons, for
model-free at least, the interesting plots, text files, and
PyMOL/MOLMOL macros are of the parameter values themselves. I think
is would be much more of interest to implement PyMOL/MOLMOL macros for
the dispersion parameters so you can see the dynamics directly on the
3D structure. This is performed in NESSY and needs to be added to
relax.
Also note that when you are analysing data, you would probably limit
the number of models to 2-3. For example if you know that all
residues are experiencing slow exchange, the LM63 fast exchange model
does not need to be used. It is interesting to see that sometimes the
analytic models are selected and sometimes the numeric models. But
this is an academic curiosity, it is probably not a practical question
anyone analysing real dispersion data is interested in. The way an
analysis would normally be performed is to first decide if the
analytic or numeric approach is to be used. For the analytic approach
with slow exchange, you only need the 'No Rex' and 'CR72' models. You
could add the 'IT99' model if you can see that pA >> pB in the
spectra, i.e. the pB peak is tiny. If you take the numeric approach,
then the 'No Rex' and 'NS 2-site expanded' models can be used. Once
you perform an initial analysis of all residues separately, you can
then look at the dynamics parameter values and judge which spins to
cluster together to have the same model of dynamics, then re-perform
the analysis.
Regards,
Edward
On 28 August 2013 12:02, Troels Emtekær Linnet <tlinnet@xxxxxxxxx> wrote:
Hi.
After a AIK selection between models
CR72/
IT99/
LM63/
NS 2-site expanded/
I get this selected list of models.
Would it be possible to add to the grace images in the final directory,
the selected model and the residue number?
3 LM63
4 CR72
5 NS 2-site expanded
6 CR72
7 LM63
8 No Rex
9 NS 2-site expanded
10 CR72
11 LM63
12 CR72
13 IT99
14 NS 2-site expanded
15 NS 2-site expanded
16 LM63
17 CR72
18 CR72
20 NS 2-site expanded
21 NS 2-site expanded
22 CR72
23 LM63
24 LM63
25 CR72
26 IT99
27 NS 2-site expanded
28 NS 2-site expanded
29 CR72
30 NS 2-site expanded
31 CR72
32 CR72
33 IT99
34 IT99
35 IT99
36 IT99
37 IT99
38 NS 2-site expanded
39 LM63
40 No Rex
41 CR72
42 No Rex
43 NS 2-site expanded
45 IT99
46 CR72
47 CR72
48 IT99
49 NS 2-site expanded
50 LM63
51 NS 2-site expanded
52 CR72
53 NS 2-site expanded
54 NS 2-site expanded
55 No Rex
56 IT99
57 LM63
58 LM63
59 NS 2-site expanded
60 CR72
61 IT99
62 NS 2-site expanded
63 NS 2-site expanded
64 CR72
65 IT99
66 No Rex
67 CR72
68 No Rex
69 NS 2-site expanded
70 NS 2-site expanded
71 NS 2-site expanded
72 NS 2-site expanded
73 LM63
74 LM63
75 NS 2-site expanded
76 NS 2-site expanded
77 IT99
78 CR72
79 No Rex
80 LM63
81 NS 2-site expanded
82 IT99
83 IT99
84 NS 2-site expanded
85 LM63
86 IT99
Troels Emtekær Linnet
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Re: Should the AIK selected model and residue number be shown in the grace files?