[RASMB] Re: WinMatch

[Karen Fleming]

Here's my two cents...
For our sedimentation equilibrium experiments, we always, always, always 
collect a scan every hour. This way, we will always be able to run 
WinMatch to determine whether or not the experiment is at sedimentation 
equilibrium. And if weird things happen during the run we will have a 
time estimate for them. Once the protein is purified and loaded into the 
cells, collecting the data is essentially free, and so I collect as much 
as possible.

Normally, our samples are stable, and so we do not need to reduce the 
time to equilibrium, so we worry less about predicting what that time 
will be - we just determine it. Whenever we are conducting experiments 
on a new system, we typically set it up and let the first speed go 
overnight and then check it with WinMatch in the morning. We then change 
the speed or let it go for a few more hours, depending on the shape of 
the curve from WinMatch.

Also, whenever there's any trouble fitting any of the sedimentation 
equilibrium data, I always insist that my students demonstrate to me 
that the data are at equilibrium using WinMatch. There's no point to 
analyzing non-equilibrium data with equilibrium equations.

Another advantage of WinMatch is that the rmsd resulting from the 
comparison of several equilibrium scans gives us a feel for how high the 
noise in the data is going to be, and whether or not we need to think 
about cleaning our lamp.

Regards,

Karen F.



-- 
* * * * * * * * * * * * * * * * * * * * * * * * * * * *
Karen G. Fleming, Ph.D.
Assistant Professor
T. C. Jenkins Department of Biophysics
Johns Hopkins University
3400 North Charles Street
Baltimore, MD 21218

Karen.Fleming at jhu.edu
Voice: 410-516-7256
Fax:  410-516-4118
http://www.jhu.edu/~biophys/