[RASMB] Using SEDFIT with multispeed SV

[Walter Stafford]

SEDANAL's multi-speed (3000 to 60000 RPM or about a 400 fold range in centrifugal field strength in the same experiment), gravity sweep methods can handle a range of sedimentation coefficients more than about 10-20 times wider than a single speed run can in the same amount of time with other methods. The problem with a single speed run is that for some species the speed may be just fine to create a boundary but for the smaller species the speed would be more appropriate for an equilibrium run and for smallest species even to slow for a proper equilibrium run. Generally the smallest material must sediment at least half way (further is better) down the cell during the run



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Walter F. Stafford, Ph.D.
Senior Scientist
Boston Biomedical Research Institute
64 Grove Street
Watertown, MA 02472
617-658-7808
skype: w.stafford3
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"Be kind, for everyone you meet is fighting a hard battle."  -Plato
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On Oct 13, 2011, at 17:08, Schuck, Peter (NIH/NIBIB) [E] wrote:

> Randy,
> 
> I have not implemented any such capability in SEDFIT because I doubt that it is really necessary to do gravitational sweep. With ls-g*(s) or c(s) you can observe s-values over a 1000-fold range at one single speed.  For various reasons, this is not possible with dc/dt-based g(s*), from where I think the motivation for gravitational sweep arises.  For example, in SEDFIT you don't need to see all the boundaries at once - they can just pass through sequentially, and they also can have very large displacements between subsequent scans without distortions.  In a case like this, I often suggest just to do an experiment at a fairly low speed and let it go a long time to see the smaller material coming behind, and do a conventional c(s) analysis.
> 
> Peter
> 
> 
> 
> 
> -----Original Message-----
> From: Randy Burton [mailto:randall.burton at ABBOTT.COM] 
> Sent: Thursday, October 13, 2011 4:35 PM
> To: List SEDFIT-L
> Subject: Using SEDFIT with multispeed SV
> 
> Hi,
> 
> I have run several "gravity sweep" experiments to look for very large aggregates in my samples.  These runs comprise 50 IF scans at speeds ranging from 3k to 42k rpm.  I was able to analyze this data pretty efficiently with the wide-distribution analysis feature in SEDANAL, but I was hoping to see what SEDFIT (or SEDPHAT) could do with it.  Can these programs deal with data collected at multiple speeds like this?  I've tried a couple of basic things in SEDFIT without much success.  Any comments would be greatly appreciated!
> 
> Randy