On 11/14/2013 10:36 AM, santhu kumar wrote:
Hi Gabriel and Chales,
Thanks for the response.
@Gabriel : The percent deviation seems like a good indicator for most
of the RDC values except those very small RDC values. I am not sure if
thats the right metric over-all. In almost all the RDC's I am using,
there seems to be 1-2 RDC's of this small magnitude.
it depends on the molecule and alignment tensor, some proteins have
dozens very small RDCs (e.g. if a helix is oriented at magic angle
relative to the longest alignment tesnor axis)
@Charles : Can you please elaborate a bit more about semi-quantitative
errors, |err| .. Is that the experimental observation errors ? or the
RMS between Experimental and calculated RDC's.
[err] must be experimental errors, they are generally inversely
proportional to the S/N
And also I have questions about modelling errors in RDC's. In the work
you have did, you used 0.26 HZ as the standard deviation for NH for
synthetic data, but when you have experimental data of magnitude 0.03
[less than the standard deviation used in error modelling], is this
approach still valid?
Thanks
santhosh
On Thu, Nov 14, 2013 at 10:00 AM, Charles Schwieters
<char...@schwieters.org <mailto:char...@schwieters.org>> wrote:
Hello Santhosh--
>
> To find how good a refinement is, R-factors or Q-factor is used
as a general
> broad indicator.
>
> R-factor defined as : sqrt{Sum[(Exp-obs)^2])/Sum[Exp^2]/2}
>
> This R-factor is a good indicator of the over-all data fit but
is there any such
> indicator for residue wise improvement. I tried residue wise
R-factor as :
>
> Residue R-factor : |Exp - Obs| / |Exp|
> [basically percent deviation].
>
Gabriel is correct that R-factor does take into account the magnitude
of RDCs, but for a per-residue metric, if you have semi-quantitative
errors, how about this residual:
|Exp - Calcd| / |err|
??
Charles
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