[RASMB] Am I missing something?

[Peter Schuck]

Hi Dror,

If it were possible to scan all cells sequentially at a single radial 
point, and cover the radial range from 6 to 7.2 cm by stepping through 
the cell in this fashion from radial point to radial point, and finally 
all the radial scans would be assembled, there would be a considerable 
error with the time at which the different radial points within one scan 
are measured.  In the current approach to finish scanning each cell 
before moving to the next cell, the time-difference between reading the 
different radii within one scan is small enough not to cause significant 
artificial broadening of the absorbance boundaries. 

It may depend what you have in mind in terms of data analysis, but we 
have had no problem with the timing of absorbance scans so far.  We've 
been doing a lot of sedimentation velocity runs scanning 7 cells, even 
at 2 or 3 wavelengths simultaneously.  We use a radial incrmement of 
0.003, and no averages, in the continuous mode.  Yes, if you are running 
at 50,000 rpm, and have 7 cells and 2 absorbance wavelenghts (+ 1 set if 
IF scans in between), you get time intervals of scans of about 15 min.  
For one absorbance wavelength it would be about half.  For a 10 mm 
column, if your material is about 5 S, at 50,000 rpm, that will give you 
about 15 scans per wavelength for a dual-wavelength experiment, or 30-40 
for a single absorbance wavelength.  In the data analysis, there's no 
problem with that at all.  15 scans covering the sedimentation process 
can be sufficient to get a good c(s) or ls-g*(s) distribution, or define 
any other model reasonably well.  I would only expect difficulties if 
you were using dc/dt, since the time-intervals get too large.
 
Regards,
Peter






Dror Noy wrote:

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> Dear all,
> I'm running sedimentation velocity experiments on our XLA where a 
> typical scan (no replicates, r=6.0 to 7.2) takes about 1 min. If I try 
> to scan two cells or more, the time interval between scans increases 
> proportionally because the XLA software scans the cells one at a time 
> (i.e. scans the whole radial range for cell 1 then cell 2 etc.). This 
> makes scanning several cells unreasonably slow. Does anybody know if 
> it's possible to scan multiple cells simultaneously a radial step at a 
> time (i.e. measure at r=x for all the cells then for r = x+dx for all 
> cells etc.)?
> Thanks,
> Dror
> =========================
> Dror Noy, Ph.D.
> Structural Biology Dept.
> Weizmann Institute of Science
> Rehovot 76100
> Israel
>
> e-mail: dror.noy at weizmann.ac.il
> Tel: (972)-8-934 2525
> Fax: (972)-8-934 4154
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