[RASMB] sedfit vs SOMO vs structure

[Borries Demeler]

> 
> Hi, Andrew,
> 
> I agree that Borries' number seems a bit low.  0.004 to 0.005 seems to be a good number on our machine.
> 
> I suspect that Borries keeps his lamps and slits very clean.  I also suspect that the number he is quoting is from pseduoabsorbance measurements, but I could be wrong.  Care to comment, Borries?
> 
> Cheers,
> Chad

Yes, Chad, you are absolutely correct! Pseudo-absorbance will give you
a factor of ~ 1.4 improvement in stochastic noise. And yes, our Beckman
service does a phantastic job to keep our 15 year old XLAs operating
optimally. The rest is achieved by regular cleaning of the lamp.

I want to emphasize that reducing noise is just as important as fitting
with the correct model in order to derive meaningful information from
any data. If you have non-random residuals all bets are off.

I also want to mention that the appearance of "two minima" is nothing
unusual at all, it really is a reflection of a fundamental principle:

When you fit noisy data there is no guarantee of a UNIQUE solution,
in fact there may be an infinite number of solutions that will all give
the same RMSD. The principle also suggests that a reduction in random
noise also diminishes this problem.  The best way around this problem is
a Monte Carlo analysis of your model to map out the confidence regions
of the solution, which tells you what you really want to know: what is
the chance that my model is correct?

RMSD values from absorbance data around 0.009 when fitted with a finite
element solution suggests there is something wrong with the model or
the instrument, or both.

Best wishes, -Borries