[RASMB] " SEGAL"

[Chin, Christopher]

Dear Ariel,

Your SEGAL program arouses my curiosity.  I find that it is very user
friendly. Beckman's software is OK to use, but editing data to achieve a
good variance is a pain in the neck. I assume your correlation value is
related to the variance. The idea of simulating a good correlation value
simultaneously with a dynamic graph before your eyes is very cool and heaven
sent, I like it.  I hope that you can expand your program to include
analyzing six-channel equilibrium cell, which is often used for denaturation
studies, all in one single page of data. I can analyze two cells now, print
out data and then do another cell to print another page data. I think you
can create part 3 for the third cell, even though this will make all graphs
smaller but the trade off is great, you can include all three-cell (or
so-call six-channel) data in one single page. It will save space and time
and make life simple. Using Beckman's software, in this case, is much more
tedious.  You need to select and save three subsets.  You then have to go to
equilibrium program to analyze each saved subset, which may or may not get
the best variance value.

I was wondering if SEGAL program could do multiple fitting (global fitting).
Also can one go head and calculate association constant with this more
accurate apparent molecular weight obtained by SEGAL.  If not, do you have
any plan to add that capability in the future?

Thank you for your contribution to create a much needed user-friendly
program.



--------------------------------------------------------------------------
Christopher Chin
Manager, XLA-Analytical Ultracentrifugation facility
Sealy Center for Structural Biology
HBC&G, 5.134 MRB.UTMB, Galveston, TX 77555-1055
cchin at utmb.edu, 409-772-1693, efax 708-585-1920
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-----Original Message-----
From: Lustig [mailto:ariel.lustig at unibas.ch]
Sent: Wednesday, June 26, 2002 7:49 AM
To: rasmb at rasmb.bbri.org
Subject: [RASMB] 2 subjects, overspeed, " SEGAL"


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Dear  RASMB colleagues ,
Dear  Andrew,

Subject 1

in the "Manual of  Methodes" (C H Chervenka) for the AUC  Spinco -Beckman 
Division-Palo Alto
(for the  model "E") is the Overspeed -technic discussed, page 44 and
ref.75:

Hexner P E, Radford L E ,Beams J W "Achievement  of  SE "
Proc. Natl. Acad. Sci. 47, 1848  (1961)

As you ask for a practical procedure=rule of thumb, I like first of all to 
emphasize
that the time to reach equilibrium depence on  three  parameters, 1)The 
filling  height
of the  cell, 2) the diffusion  constant  of the solute=substance . 3) the 
viscosity of the solution.
The optimal over-speeded  rotor speed and time is,  that still at least   a 
1/3 to 2/3  of the plato,
(the region that in case of  absorption shows  approximately  the 
C(0)=initial concentration
you filled and tested it  at very low speed , just at the run -start or 
compaire it with the wavelength
scan at the same nM value.(Be a bit carefully  about the  WL baseline.)

What are  the dangerous points on have to be careful : at a too relative 
high speed the sample
  may be dragged too  far to the cell bottom , so you loose  the  time 
-spare   advantage,
but worth is if the particles
or molecules du not reversibly back-diffuse (means insoluble aggregates) 
due to high
concentration near the  bottom.
On principle we have to look several times  during the overspeed - 
procedure on the partly
depleted part near  the  meniscus and the unreached  bottom cell part.

Subject 2.
I would like to remind you  that at the 23 of may 2002 I sent to all of 
you  our =(Biozentrum)
SEGAL computer that can be loaded  down  from the  net

http://www.biozentrum.unibas.ch/personal/jseelig/AUC/index.html

I  would like to hear from you  if there are some difficulties  loading it 
down or to use it.
please inform me .
WE can do a play:
You send me  a single SE(at equilibrium ) scan by E-mail of one of your 
scans with
the information  of  V = the part.spec. volume  and the solution density. 
BUT PLEASE
DON'T give me  the  Mw. Later we will compaire  with your  result  from the 
same scan.

Thanks to  all of  you ....ariel


Lustig Ariel
Dept. of Biophysical Chemistry  / Analytical Ultracentrifuge Lab.TEL....+61 
2672187
Biozentrum der Universität 
Basel                                             Fax    +61 2672189
email 
lustig at ubaclu.unibas.ch
Klingelbergstr. 70
CH 4056 Basel
Switzerland 




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