[RASMB] recommended max rmsd for achieved equilibrium

[Frank Niesen]

Dear all,

Thank you very much, to everyone who sent a reply to my question! Your
advice was much appreciated and helped me extend my understanding. Since
many replies were sent to me by-passing the mailing list, I want to give a
short summary, for the sake of others who might have or will have a similar
problem:
- The main advice was to not use such large volumes for the experiment and,
consequently, don't have to wait that long for the equilibrium. A 3-mm
column should be sufficient, and Allen even reported to me that 1-mm
columns would give usable data very fast so one could run a number of
experiments per day (also, in 6-sector cells) and get a sufficient number
of data points for the analysis of the association.
- Secondly, regarding the RMSD the common advice was to compare whatever
number is seen with the noise level, and not target any special number. And
to pay attention more to how than how far the deviations are distributed in
the comparison between successive scans.

Again, thank you very much. I was able, in the meantime, to figure out what
is happening in my sample. I used three different wavelengths and the
interference data for fitting and ended with a satisfying
quality/confidence. My luck was that the protein is very stable at the
experimental temperature, and made it fine through the length of time it
took to get the data.

Best wishes,
Frank


On Fri, Oct 11, 2013 at 10:23 AM, Frank Niesen <dr.frank.niesen at gmail.com>wrote:

> Hello everybody,
>
> I was hoping for advice on what rmsd between successive scans at one speed
> I should be aiming for to determine if equilibrium is achieved? Below 0.01?
> Below 0.005? Or dependent on how the residuals are distributed?
> To give an example, I am spinning samples of a protein that forms trimers
> in 2-sector cells (190 ul/cell). The highest concentrated sample is 200 uM
> and I waited for about 90 hours, seeing gradual improvement, to currently
> 0.019 rmsd (I use Sedfit to match, thanks Peter & Co. for the excellent
> tool!). The differences toward the meniscus and the bottom are about -0.03
> and 0.04, respectively. So, the distribution is still "developing"...
> But, how good is good enough, having in mind the demand for answers by my
> collaborators and my desire to proceed to the next speed for the weekend?
> ;o)
>
> Many thanks for any help you can give, and a great weekend for all!
>
> Frank
>
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