[RASMB] recommended max rmsd for achieved equilibrium

Lake Paul lpaul at purdue.edu
Fri Oct 11 08:33:04 PDT 2013


Frank,
The max RMSD is sample dependent. A well behaving, low absorbing
sample (< 1 OD at bottom) will have a low RMSD. High absorbing samples
(> 1.5 OD) might give you a higher RMSD. But again that is sample
dependent. It does not really matter about the RMSD, what really
counts is that you are in equilibrium e.g. the difference of your
scans analyzed is not changing. This can be assessed in SEDFIT,
Winnonlin, Ultrascan etc etc.
Hope this helps,
Lake


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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-- 
Lake Paul, PhD
Facility Director

Biophysical Analysis Lab
Purdue Proteomics Facility

Bindley Bioscience Center
Purdue University
1203 West State Street,
West Lafayette, Indiana, 47095
765.494.4960



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